[This webpage contains all the 127 messages posted during the FAO Biotechnology Forum e-mail conference on biotechnology and genetic resources that took place in June/July 2005.
For further information on the Biotechnology Forum see the Forum website.
Note, participants are assumed to be speaking on their own behalf, unless they state otherwise.]

-----Original Message-----
From: Biotech-Mod1
Sent: 03 June 2005 17:47
To: 'biotech-room1@mailserv.fao.org'
Subject: Opening of FAO e-mail conference on biotechnology and genetic resources

Dear Colleagues,

Welcome to the FAO e-mail conference entitled "The role of biotechnology for the characterisation and conservation of crop, forest, animal and fishery genetic resources in developing countries" !!!!

You can send messages now (send them to biotech-room1@mailserv.fao.org). Messages will be posted from Monday 6 June onwards while the last day for receiving messages for posting will be Sunday 3 July.

We hope that the conference will be interesting, constructive and beneficial and we encourage you to participate actively. We would like to briefly remind you of some of the main points about the running of the conference:

i) Participants should introduce themselves briefly in their first posting to the conference. They should also provide their full address at the end of the message (when posted, we will replace @ with (at) because of spamming).

ii) Messages should not exceed 600 words

iii) People posting messages are assumed to be speaking on their own behalf and not on behalf of their employers (unless they indicate otherwise)

iv) The Background Document to the conference, sent by e-mail to the Forum members on 27 May, sets the scene for the conference and so we strongly encourage you to read it, especially Section 5 which describes some of the potential factors that should be considered and provides a selection of the kinds of specific questions that participants might wish to address in the e-mail conference. The document is available at http://www.fao.org/biotech/C13doc.htm and can also be retrieved by Forum members sending an e-mail to mailserv@mailserv.fao.org, leaving the subject blank and entering the one-line text message:
send listlog/biotech-l.may2005

v) Messages posted in the conference will later (usually within a day or two) be placed on the Forum website - at http://www.fao.org/biotech/logs/c13logs.htm

vi) No messages will be posted with attachments. If you receive a message during the conference with an e-mail attachment, just delete it without opening the attachment.

vii) The conference covers the crop, forestry, livestock and fishery sectors and brings together people who may have knowledge/experience from one or more but not all of these sectors. As terminology is occasionally sector-specific, we ask participants to try and give a brief explanation of any sector-specific terms when they are first used.

viii) As for all other conferences hosted by this Forum, when it is finished a document will be prepared to provide a summary of the main arguments and concerns discussed during the e-mail conference, based on the messages posted by the participants. The summary document will be put on the Forum website and disseminated as widely as possible.

Finally, we encourage you to tell any potentially interested colleagues or contacts about this conference. A short notice is included below for this purpose.

With our sincere best wishes for a successful conference,

John

John Ruane, PhD
Moderator, Conference 13
e-mail: mailto:biotech-mod1@fao.org
FAO website http://www.fao.org
Forum website http://www.fao.org/biotech/forum.asp
FAO Biotechnology website http://www.fao.org/biotech/index.asp

FAO e-mail conference - Biotechnology and characterisation/conservation of genetic resources

The FAO Biotechnology Forum is devoting its next e-mail conference to the role that biotechnology (with tools such as molecular markers or cryopreservation and reproductive technologies) can play in the characterisation and conservation of crop, animal, forest and fishery genetic resources in developing countries. To discuss and exchange experiences on this theme, we invite you to join the conference. This will be the 13th conference hosted by the Forum since it was launched in 2000. The conference, as usual, is open to everyone, is free and will be moderated. It begins on 6 June and runs for four weeks, finishing on 3 July 2005. All e-mail messages posted during the conference will also be placed on the Forum website (http://www.fao.org/biotech/forum.asp). A 16-page background document to the conference has been prepared and is available from the same website. To join the Forum (and also register for the conference), send an e-mail to mailserv@mailserv.fao.org leaving the subject blank and entering the following text on two lines:
subscribe BIOTECH-L
subscribe biotech-room1

Those who are already Forum members should leave out the first line of the above message, to register for the conference. For more information, contact biotech-mod1@fao.org.

-----Original Message-----
From: Biotech-Mod1
Sent: 06 June 2005 17:03
To: 'biotech-room1@mailserv.fao.org'
Subject: 1: Plant genetic resources - SADC countries

[Welcome everybody to this FAO e-mail conference on biotechnology and genetic resources for food and agriculture in developing countries !!! The four weeks available for this conference will go very fast, so we encourage you to participate actively right from the beginning to get the maximum benefit from it. Participants are also reminded to briefly introduce themselves in their first message to the conference. Note, some messages about GMOs have been received, so to avoid any confusion we will repeat what was written in the Introduction section of the Background Dcoument to the conference i.e. "The focus in this conference will be on biotechnology tools, such as molecular markers or cryopreservation and reproductive technologies, that can be used directly for the characterisation and/or conservation of genetic resources for food and agriculture. Genetic modification and GMOs will not be considered here" (http://www.fao.org/biotech/C13doc.htm) ...Moderator].

My name is Charles Nkhoma and I am currently acting Director of SADC Plant Genetic Resources Centre (SPGRC) based in Zambia but with a mandate to cover the 13 member countries of SADC (Southern African Development Community). [SADC is a community of 13 Member States (Angola, Botswana, the Democratic Republic of Congo, Lesotho, Malawi, Mauritius, Mozambique, Namibia, South Africa, Swaziland, United Republic of Tanzania, Zambia and Zimbabwe), with headquarters in Botswana (http://www.sadc.int/) ...Moderator].

SPGRC maintains the base collection on behalf of SADC countries while the active collections are maintained by each country at the National Plant Genetic Resources Centre (NPGRC). While the programme has succeeded fairly well with common cereals, legumes etc, we are completely incapacitated to work with our own indigenous materials when they happen to be difficult to cultivate for example. Ironically, we are forced to work on those crops which others with more resources than ourselves are already working on and we are unable to work on our plants which no one else is working on just because we lack the biotechnology facilities that would help us to tackle specific problems in these plants.

In the Democratic Republic of Congo, Malawi, Tanzania and Zambia there is a ground orchid that occurs in some habitats in these countries. The tubers of these orchids are edible and their popularity has increased steadly in recent years from being rural foods and are now found on the buffet table of Intercontinental Hotel! Yet they are still harvested only from the wild. There is not much knowledge about these orchids but we know that they belong to various species of Disa, Habenaria and Satyrium. Molecular marker techniques would be useful in studying the diversity in these orchids in order for us to determine the actual range of these species which are utilised, their diversity and thereby understand the extent to which the current methods of destructive harvesting is threatening these resources. Furthermore, studies that may lead to eventual domestication of these species require use of tissue culture facilities. In terms of the kinds of useful plant species that occur in the tropics and subtropics, its quite clear that developing countries need biotechnology to develop appropriate conservation methods and to promote species utilization maybe even more than developed countries.

Much of the genetic resources conserved in the genebanks of our network are landraces. Currently, we only record agronomic and morphological data in order to characterise our collections. This is, of course, very useful and will continue to be done. However, there are also many instances when use of molecular markers become inevitable in helping to remove unnecessary duplicates and also in those species that are agronomically difficult to propagate. I believe the issue at hand should be more on how to access use of biotechnology to support plant genetic resources work. I look forward to the day that we will manage to acquire facilities to be able to utilise molecular markers.

Charles Nkhoma, M Sc.,
SADC Plant Genetic Resources Centre
Private Bag Ch6
Lusaka
Zambia
Fax: 260 1 233746
Phone: 260 1 233391/2
Email: spgrc (at) zamnet.zm

-----Original Message-----
From: Biotech-Mod1
Sent: 06 June 2005 17:06
To: 'biotech-room1@mailserv.fao.org'
Subject: 2: Low cost options for tissue culture

My name is Edo Lin, independent consultant.

One of the issues raised in the Background Document to the conference are the high costs and high investments needed for the use of biotechnology.

Tissue culture and other forms of micropropagation are useful tools not only to provide disease-free planting material to farmers (for instance banana, sugarcane etc.) but are also used for the conservation and multiplication of plant species. These techniques are especially useful in species that do not normally produce seeds or, in the case of (fruit) trees, where seeds are only produced several years after planting. Facilities for micropropagation are expensive to build (need for sterile work environment, air conditioning, artificial lighting etc.) and expensive to operate (labour intensive and high cost of consumables like media, containers, hormones). These high costs are a problem in developing countries where, in addition, the cost of energy is high and the reliability of electricity supplies is low.

Fortunately there have been several initiatives to study low cost options for micropropagation using locally available materials (media, polybags) and the use of natural light and ventilation. For people interested to know more about low cost options, the Joint FAO/IAEA Division for nuclear techniques in Food and Agriculture has a document available on the internet: "Low cost options for tissue culture technology in developing countries" http://www-pub.iaea.org/MTCD/publications/PDF/te_1384_web.pdf

Edo Lin
Ceres Consulting International
309, rue de Bombon
77720 Breau
France
tel and fax: +33 164387844
e-mail: ceres.consult (at) free.fr

[The publication referred to here, provided free on the web about a year ago, was prepared on the basis of contributions made at a meeting on "Low cost tissue culture technology for developing countries", held on 26-30 August 2002 in Vienna, Austria. It describes options for reducing costs in the establishment and operation of plant tissue culture facilities and focuses primarily on plant micropropagation. It includes the basics of tissue culture technology, bioreactors, low-cost options in the design of laboratories, use of media and containers, energy and labour saving, integration and adoption of low cost options, increasing plant survival after propagation, and outreach of material to growers and farmers in developing countries...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 06 June 2005 17:08
To: 'biotech-room1@mailserv.fao.org'
Subject: 3: Livestock - biotechnology - Pakistan

In developing countries (for example, Pakistan), the livestock production system is mostly of subsistence nature. Farmers have poor access to financial, technical and marketing resources. Their immediate need is income enhancement and poverty reduction. So they choose breeds which can give them quick financial return.

Selective breeding of animals is a time consuming and expensive process. So the farmers go for crossbreeding. On one hand, the state has failed to provide support for conservation of genetic resources and, on the other, genetic conservation is not a priority area for farmers. So it remains a neglected activity and someone else should take the task.

Through biotchnology, germplasm can be preserved in the form of gametes or embryos. This again needs sufficient resources in the form of highly trained manpower, equipment and supplies, and which is neither the priority of the states of the developing countries nor the farmers.

At university level, this dream can become true as the environment there is suitable for such type of jobs. The teachers and students possess sufficient enthusiasm and the task can be completed in a better way. Our group is working on genetic studies and preservation of some sheep breeds and would be pleased to collaborate with other fellow groups for this purpose.

Prof. Dr. Muhammad Subhan Qureshi,
In-Charge Animal Health Department
NWFP Agricultural University
Peshawar-25000,
Pakistan.
Tel.Office 9291-9216573-3087, Home 5842354
Mobile 92-300-5877933,
E.mail: drmsqureshi (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 06 June 2005 17:10
To: 'biotech-room1@mailserv.fao.org'
Subject: 4: Apomixis and crop genetic resources

My name is Nagib Nassar, Professor with the University of Brasilia, geneticist and plant breeder, dealing principally with the maipulation of cassava genetic resources for improvement of the crop with emphasis on apomixis and interspecific hybridization (see my site: www.geneconserve.pro.br).

A question I have is: How much may apomixis contribute to conservation of a certain crop genetic resources?
Since it preserves genetic constitution, including clearly heterozygosity, it logically avoids any segregation that may lead to production of unfavoured and inferior genotypes. These inferior genotypes may be discarded by breeders and lost forever, consequently losing the genes from the gene pool of the crop.

I shall be happy to hear the comments of my colleage participants of this conference, certainly it will enrich our knowledge on the subject. We, at Brasilia, have produced for the first time apomictic cassava clones by transferring the gene from the wild followed by backcrosses. It was confirmed by molecular markers (satellite technique) - details can be seen in our site on the web www.geneconserve.pro.br

Nagib Nassar
Departamento de Genetica e Morfologia,
Instituto de Ciencias Biologicas,
Universidade de Brasilia,
Campus Universitario Darcy Ribeiro, Asa Norte.
CEP: 70910–900, Brasilia – DF,
Brazil.
Phone: (+55.61) 349.3253
Fax: (+55.61) 349.3562
nagnassa (at) rudah.com.br

[Regarding apomixis, Jefferson (1994) gives a nice definition, writing "Plant reproduction occurs by complex and diverse mechanisms. Sexual reproduction is most common in flowering plants of agricultural importance. Male and female gametes (the pollen and the egg cells respectively) are separately produced with half the normal chromosome number. These combine during fertilization and further develop to give rise to a seed. This seed contains genes derived from both parents in a form that is distinct from both parents so that once that seed germinates a plant of unique genetic constitution is generated. By contrast, apomixis produces seeds through asexual processes. The genetic make­up of the seeds is identical to that of the mother plant. If the mother plant is well adapted to a particular environment or purpose, so will be the offspring. Although many wild plants are naturally apomictic, for instance the common dandelion (Taraxacum sp.), very few crop species are apomictic" (http://www.biotech-monitor.nl/1906.htm) ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 06 June 2005 17:13
To: 'biotech-room1@mailserv.fao.org'
Subject: 5: Interspecific hybridization - Cassava

This is Nagib Nassar, Brazil, again.

I wish to ask a question to colleagues of this conference - probably somebody has a similar experience of mine in certain crop. The question is how much does interspecific hybridization contribute in preserving the gene pool of a wild species threatened by extinction or that has come to extinction?

An interesting case cames from Manihot oligantha, a wild cassava possessing the highest protein content ever known in this crop, 9%, while it is 1.5% in common cassava cultivars. This species has become extinct but, early in the 1970s, we hybridized it with cassava and obtained a root productive hybrid that has 5% protein. When we planted its progeny (second generation), some progenies could be detected which have protein as high as 7%. True protein yes !! judged from evaluating amino acids. Is this is a proof that interspecific hybrids can preserve wild gene pools, where other methods fail? Can somebody tell me a similar case?, or may may disaccord? Fo more details on what I said, see www.geneconserve.pro.br.

A second question: Can we preserve genetic resources of a crop by re-introducing both wild relatives and their interspecific hybrids, and let them grow in small farmers properties? i.e conserve them through a participatory project.

We have a project in Brasilia to begin this season. It aims to re-introduce some wild cassava which had become extinct in their natural habitats into some small farmers properties. They will be acompanied by their interspecific hybrids. We will teach small farmers how important the conservation is. Since the interspecific hybrids are more productive than common ones, more resistant to predominant diseases, we expect farmers will adopt them as new varieties.

These interspecific hybrids, being grown close to the wild species, may hybridize with them and, who knows in the future, probably evolve new species like that what happened in maize and wheat. Our role in this process is to introduce this material and teach small farmers.

It took a lot of time and effort to break barriers between the wild species and cassava in our living collection, we used different techniques and methods, finally we have about 12 different hybrids. Another aspect of our role in this process is to have preserved the wild species which have become extinct in their natural habitat.

I shall be grateful to have comments from conference participants, certainly these comments will more refine this project. Kindly see details of this program and reprints in our site on the web www.geneconserve.pro.br

Nagib Nassar
Departamento de Genetica e Morfologia,
Instituto de Ciencias Biologicas,
Universidade de Brasilia,
Campus Universitario Darcy Ribeiro, Asa Norte.
CEP: 70910–900, Brasilia – DF,
Brazil.
Phone: (+55.61) 349.3253
Fax: (+55.61) 349.3562
nagnassa (at) rudah.com.br

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:25
To: 'biotech-room1@mailserv.fao.org'
Subject: 6: Establishing a universal molecular marker data base

[As part of the build-up to this e-mail conference, an international workshop on the same theme was held at the beginning of March 2005 in Turin, Italy. We wish to inform you that, in addition to the 20 papers, the abstracts of 37 posters presented at the workshop are now also available on the web - at http://www.fao.org/biotech/torino05.htm ...Moderator].

This is from Theodore J. Kisha, United States.

Molecular markers have become an accepted and widely used tool for the measurement of genetic diversity. Molecular marker technology can be used to characterize the extent of diversity within a collection and for the development of collection management strategies, which may include establishment of core collections, identification of redundancies or contamination, guidance for future collection efforts, and identification of gaps of ancestral crop relatives. Additionally, analysis of world-wide genetic diversity can identify areas suited for the establishment of in situ conservation sites.

The amount of research dedicated to the analysis of genetic diversity using molecular markers has grown each year. A search of the AGRICOLA data base by year using search terms “diversity” and each respective molecular marker type returned over 1200 published studies on molecular marker diversity. [AGRICOLA is a bibliographic database of citations to the agricultural literature created by the United States National Agricultural Library (NAL) and its cooperators http://agricola.nal.usda.gov/ ...Moderator].

The one thing that studies in plant genetic diversity have in common is that few, if any, can be directly compared or compiled. Following publication, marker data can be lost or forgotten. Studies of genetic diversity are usually limited to a few accessions or accessions from a limited area of interest.

Through a concerted, international effort, over 32 billion DNA sequences are available in GenBank for use in studies limited only by the imagination of its users. At the same time, molecular marker data, fundamental to the study of world-wide genetic biodiversity, is lagging behind. Virtual cluster analyses based on the comparison of new accessions to a complete data base of accrued marker information would result in savings of both expense and time. Relationships queries can be adjusted to filter data based on geographical regions, environments, latitude, etc., if the data base is formatted to contain such information. [GenBank is the National Institutes of Health (NIH) genetic sequence database, an annotated collection of all publicly available DNA sequences. The most recent figures indicate it contains 44,575,745,176 base pairs of DNA and 40,604,319 sequence records - http://www.ncbi.nlm.nih.gov/Genbank/index.html. GenBank data can be searched on the National Center for Biotechnology Information (NCBI) website...Moderator].

The construction of a universal molecular marker data base may seem like a daunting task, but it can come to fruition by the construction of locally created data bases developed through collaborative efforts among members of germplasm conservation centers and other interested parties. The first step is to come to a consensus on the format of such locally generated data bases for eventual linking to a world-wide network. Genbank, and the organization of the NCBI web site is a model for international cooperation among agencies and institutions. A molecular marker data base would need to follow the example of that model. It would need to be a curated data base because of the somewhat imprecise nature of naming markers based on fragment size. A “center”, or collaborating “centers” within the network, should be responsible for a particular species and define a core set of primers for each marker type which randomly and uniformly cover the genome. A number of “control” accessions, with defined markers should be included around which to anchor a virtual analysis, and an image of the expected marker pattern with monomorphic and polymorphic bands defined to ease the construction of an input file with which to conduct a virtual cluster analysis and for submission to the data base. As with sequence submissions, the file will be linked to any publications resulting from the analysis.

I advocate the establishment of a universal molecular marker data base, and would like to establish a network of like-minded researchers to exchange ideas.

Theodore J. Kisha
USDA-ARS
Washington State University
Box 646402
Pullman, WA 99164-6402
United States
Phone:(509)335-6898
FAX: (509)335-6654
kisha (at) @mail.wsu.edu

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:27
To: 'biotech-room1@mailserv.fao.org'
Subject: 7: Applying biotechnology to livestock - Egypt

I am Mahmoud Abdel Aziz, Professor of Animal Breeding and Genetics, Department of Animal Production, Alexandria University, Egypt.

In developing countries, such as Egypt, the livestock sector is facing many problems that can be stated in the following points:

1. No recording systems operating on a nationwide scale. Thus, animals with good genetic make-up cannot be genetically identified or characterized.

2. As a result of point (1), no breeding programs are operated.

3. 90% of the livestock populations are owned by small farmers who have 4-5 animals at most. This makes the application of biotechnology very difficult.

4. Farmers are not aware of the importance of issues such as animal genetic resources conservation, biotechnology and the genetic improvement of animals' productivity.

5. The national policy is to replace our local breeds by exotic breeds through adaptation or crossbreeding. So, we lose our genetic resources that may have good characteristics such as heat tolerance and disease resistance, but low production.

6. Application of biotechnology needs financial support, well educated people, equipment and good infrastucture, which the developing countries cannot afford.

I think the first step that should be considered is to try to find concrete solutions for establishing good and gradual recording systems, taking into consideration the socio-economic and -cultural aspects prevailing in each country. We need, all of us, to cooperate in solving these problems through workshops, symposiums etc...

Mahmoud Mohamed Ahmed Abdel Aziz
Department of Animal Production
Faculty of Agriculture
Alexandria University
Alexandria,
Egypt
fassad9 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:28
To: 'biotech-room1@mailserv.fao.org'
Subject: 8: Genetic diversity in asexually propagated plants - Agave

My name is Diogenes Infante, from the Biotechnology Center, Institute for Advanced Studies (IDEA), Caracas, Venezuela. My fields are plant molecular biology, micropropagation, genetic improvement and transformation. Also the use of wild relatives for improvement of cultivated plants.

I want to talk about our work in asexual genetic variability and its use in genetic improvement of asexually propagated plants, which can be useful for the conservation of genetic resources.

It was assumed that genetic diversity was the product of sexual reproduction and that asexually propagated plants were clones all identical. This is the case of many important tropical crops like bananas or agaves. Agaves are tropical and subtropical plants forming a rosette of leaves. Toward the end of their life cycle they develop a long stem in the center, which is the flower, and usually the plant dies after the blossoming. Some agaves have three different reproductive mechanisms: rhizomes, with subterraneous shoots emerging as a new individual, and bulbils in the flower stem, both asexual reproduction, and at the top of the flower seeds, sexual reproduction.

We studied genetic diversity in henequen (Agave fourcroydes) a plant whose fiber is employed in the manufacture of agricultural twine, sacks, carpets and other products. It is only cultivated in Mexico and Cuba. This plant is asexually propagated by rhizomes, so it would be expected that henequen populations are genetically homogenous. However, an analysis with molecular markers, using Amplification Fragment Length Polymorphism (AFLP), demonstrates differences in the AFLP pattern in a natural population, while this pattern is conserved in samples from the same plant. An analysis of five different plantations showed differences at the population level, with each population clustering together. Comparison of the AFLP banding pattern between two mother plants with their derived suckers shows that, in this species, genetic variability is generated and transmitted to descendants through asexual reproduction. We published this result (Infante et al, 2003, Plant Science 164/2: 223–230).

The study of morphological characters in selected individuals of henequen shows that differences exist in a clonally propagated population. Therefore, the molecular marker variability is accompanied by differences in morphological characteristics. This fact indicates the possibility of selection among individuals in a clonally propagated population and its use for an improvement program via micropropagation through somatic embryogenesis. After micropropagation of three elite lines and three years under field conditions, we demonstrated using morphological analysis that plants originating from the same mother plant formed a group in Principal Component Analysis (PCA). AFLP and cluster analysis showed that each mother plant and its somatic embryogenesis derived daughter plants clustered, indicating the conservation of the molecular marker patterns in the micropropagated daughter plants. Both results indicate the conservation of the superior characteristic in the micropropagated daughter plants. We published this method of genetic improvement for asexually propagated plants (Gonzalez et al, 2003, Plant Science 165/3: 595-601).

We made a similar study in coffee, Coffea arabica, and we demonstrate that somatic embryogenesis per se introduces genetic variability (Sanchez-Teyer et al, 2003, Molecular Biotechnology 23/2: 107-116). Currently, we are finding the same asexual variability in Cocuy (Agave cocui) a plant used in western Venezuela to produce alcoholic beverages. In my opinion, the asexual genetic variability is present in many clonally propagated plants species.

These results are useful in the conservation of genetic resources, because it is possible to introduce and select variability through asexual propagation.

Dr. Diogenes Infante H.
Centro de Biotecnologia
Instituto de Estudios Avanzados
http://www.idea.org.ve
Tel: 58-0212-903-5104v Fax:58-0212-903-5092
Cel:58-0416-632-9805
dinfante (at) idea.gov.ve

Apdo. 17606 Parque Central
Caracas 1015-A, Venezuela
Carretera Hoyo de la Puerta
Sartenejas, Caracas 1080
Venezuela

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:29
To: 'biotech-room1@mailserv.fao.org'
Subject: 9: Re: Low cost options for tissue culture

This is Professor Joe Cummins, Professor Emeritus of Genetics University of Western Ontario, Ontario Canada. I have done research in molecular genetics since the early nineteen sixties. Since 1989 I have been a critic of genetic engineering.

Edo Lin (Message 2, June 6) promoted use of plant tissue culture for plant micropropagation to preserve local crop varieties. As everyone will probably know, such procedures are frequently beset by a high frequency of somaclonal variation associated with the activation of mobile genetic units that produce very high frequency somatic mutation and chromosome instability. For example, the high frequency genetic alterations associated with tissue culture in coffee has been patented as a means of producing selectable genetic variants (mutations). There are numerous other examples of the high level genetic variation initiated in tissue cultures of both angiosperms and gymnosperms. It seems to me that it may be that "preserving" local material using plant tissue culture may be an oxymoron. How can mutated materials be considered preserved?

Prof. Joe Cummins,
738 Wilkins Street,
London, Ontario N6C4Z9
Canada
jcummins (at) uwo.ca

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:29
To: 'biotech-room1@mailserv.fao.org'
Subject: 10: Re: Plant genetic resources - SADC countries

My name is Kazhila Croffat Chinsembu, a lecturer at the University of Namibia. I teach Molecular Biology, Immunology, Microbiology and Molecular Genetics. Fomerly, I taught at the University of Zambia from 1996 to 2002. I have an MSc degree in Tropical Molecular Biology from the Free University of Brussels. I am currently working on molecular markers of drought tolerance in food crop landraces of northern Namibia.

I have read Message 1 (June 6) of Charles Nkhoma, the acting Director of the SADC Plant Genetic Resources Centre based in Zambia. Incidentally, I know Charles from the early 1990s when we worked at Mt Makulu Research Station but because of job movements we have not been in touch for a few years now. But such is the beauty of the e-conference, we can now trace long lost friends!

Regarding the diversity of the ground orchids, it will be interesting if you provided us with some fresh materials on which we could do RAPD-PCR and sequencing of putative PCR fragments in order to unravel the molecular diversity among the landraces. Over the past three years we have been working on the molecular diversity of selected crops here in Namibia, and it will be interesting to do the same on the wild orchids.

Kazhila Croffat Chinsembu
Lecturer, University of Namibia
Private bag 13301
Windhoek,
Namibia
Tel: 264-61-206 3426
Fax: 264-61-206 3791
Email: kchinsembu (at) unam.na

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:30
To: 'biotech-room1@mailserv.fao.org'
Subject: 11: Molecular markers // Apomixis

I am Vijay, working as a scientific assistant in International Plant Genetic Resources Institute (IPGRI Office for South Asia) at New Delhi, India. I worked on molecular markers with respect to ageing in seeds during my PhD.

The different tools of biotechnology, particularly molecular markers, are very useful and necessary tools with the increased awareness and need for conservation and understanding the existing as well as exploitable diversity. The morphological and biochemical markers having their own limitations have paved way to more useful and robust molecular markers. With the use of advanced techniques like AFLP the reliability of molecular markers is increased and now there is a great need for their extensive use in the practical situations.

I agree with Nagib Nassar (Message 4, June 6) regarding the use of apomixis for the purpose of conservation. But the important thing to consider here is how many genotypes have their natural apomictic relatives and how many cultivated species have this kind of reproductive system? If we can find a way to identify and transfer this condition as you and your colleagues did in cassava it will bring a great change not only in the present conservation scenario but also in hybrid seed production on commercial scale.

Vijay. D, PhD
Scientific Assistant
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012, India
Mobile: 09868412855
E-mail: vijaydunna (at) gmail.com
URL: http:// www.geocities.com/vijaydunna

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:31
To: 'biotech-room1@mailserv.fao.org'
Subject: 12: The Southeast Asian swamp buffalo

I am S.G. Tan, Professor of Genetics at the Dept. of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia. My research interest over the past 30 years has been on the Molecular Population Genetics of Southeast Asian human, animal and plant populations. Currently, we are using DNA microsatellites to study the giant freshwater prawn, Macrobrachium rosenbergii, green lipped mussel, Perna viridis and the Asian river catfish, Mystus nemurus in our lab.

Here is an opinion that I would like to share on an important but now rather neglected animal genetics resource of Southeast Asia.

The Southeast Asian swamp buffalo (2n=48) is worthy of attention as it could be further developed to be a meat source. Our molecular genetic characterization studies of various geographical populations of Asian water buffaloes in the region in the 1990's, based on allozymes (Barker et al, 1997 Animal Genetics 28, 1-13)and DNA microsatellite markers (Barker et al, 1997, Animal Genetics 28, 103-115), showed that the swamp populations formed a separate cluster from the river buffalo populations (2n=50).

Interestingly, among the various swamp buffalo populations, the genetic distances between them were of the same order of magnitudes as those between recognized European cattle breeds. Hence, we would expect that crosses between selected animals from different swamp buffalo populations could have positive impacts on the breeding of this hardy indigenous animal. For instance in Malaysia, crosses could be made between animals from the Peninsula and Sabah or Sarawak state on Borneo Island.

Prof. Dr. S.G. Tan BSc.(Hons. Malaya), PhD. (Hawaii), J.S.M. (Malaysia).
Professor of Genetics.
Dept. of Biology,
Faculty of Science,
Universiti Putra Malaysia,
43400 UPM Serdang,
Malaysia.
email: sgtan (at) fsas.upm.edu.my
Fax: 603-86567454/89432508

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:32
To: 'biotech-room1@mailserv.fao.org'
Subject: 13: Re: Interspecific hybridization - Cassava

This is Professor Joe Cummins.

Commenting on the question of Nagib Nassar (Message 5, June 6) on recovering lost wild species from allopolyploids:

First, it is worth pointing out that species are made up of both nuclear and cytoplasmic genomes. In the allopolyploid, the maternal parent contributes both mitochondrial and chloroplast genes in most angiosperms so that the species "recovered" from an allopolyploid always has the cytoplasmic genes from maternal species. It is not likely, but possible, that the allopolypoid originated from a mother that was "lost". The cytoplasmic origin can be determined by looking at the surviving parent of the allopolyploid.

Next, it is very rare to find a long term allopolyploid which maintains the original genome of the parental species. One striking effect is activation of mobile genetic elements that effect gene activity, cause mutations and effect chromosome stability. Along with the genetic changes there are numerous epigenetic impacts.

Finally, it is certainly worth recovering useful genes from allopolyploids but, in the main, you cannot go "back again" and recover a pristine genome from an allopolyploid. Claims that such has been done will be questioned by many geneticists.

Prof. Joe Cummins,
738 Wilkins Street,
London, Ontario N6C4Z9
Canada
jcummins (at) uwo.ca

[The term alloploid refers to a polyploid organism with sets of chromosomes derived from different species...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:33
To: 'biotech-room1@mailserv.fao.org'
Subject: 14: Fisheries genetic resources

This is from Ron Jones. I am an environmental biologist specializing in fisheries and aquaculture livelihoods issues and I am currently employed with the International Development Research Centre (IDRC) in Ottawa, Canada. At present I am working on biotechnology and conservation issues related to aquatic genetic diversity and how these issues fit into the traditonal knowledge, access and benefit sharing and other aspects of the CBD.

I am glad I have the opportunity to participate in e-conference 13. There are some very important issues nested here pertaining to our future understanding, conservation and use of these genetic resources. My interest and history pertains to fisheries resources. Fisheries resources are undervalued and underrepresented in discussions on the conservation and sustainable use of germplasm. The importance of our topic to fisheries was brought home recently (June 2) when I attended a lecture by Dr. Harald Rosenthall on the conservation and management of sturgeons where he highlighted a number of key areas where biotechnology plays roles in conservation, management and rehabilitation. For example, DNA fingerprinting to ascertain stock make up, determining potential loss of genetic diversity in Russian broodstocks, caviar tracking, use of gene banking (cryo) etc. The sturgeons are important and charismatic species but many of the same arguments could apply to other species as well (Mekong catfish, taimen, ornamentals, South American river stocks etc.).

We all recognize the increasing importance of fish in diets and livelihoods around the world (see FAO stats). It might be prudent today to focus on areas/species of high importance. Whether for aquaculture or ecological/evolutionary importance. For example, tilapia genomics (aquaculture breeding) or to address stock and metapopulation questions relating to migratory patterns of important Mekong or other riverine stocks. It will be key to determine when, for example, conservation of indigenous species/habitats would be a more effective approach for increasing aquatic produce contributions to food or livelihood security than promoting indigenous/exotic aquaculture practices OR vise versa. [The FAOSTAT online database is available at http://faostat.fao.org ...Moderator].

My personal research interest lies in fisheries of rice-fields, flood plains or other ephemeral/marginal water bodies. I was a bit set back when years ago they found little or no genotype by environment (G X E) interactions in the GIFT Tilapia project, so there would be no specific "ricefield" breed/variety of T. nilotica!!. Nevertheless, the identification of "traits of relevance" for such systems may still be available in wild ecosystems, hence the enormous importance of the documentation and conservation of indigenous aquatic biodiversity for local consumption and future breeding purposes, especially if these lie in cryptic species or within intraspecific diversity whcich must be teased out via molecular methods. [This refers to the GIFT (Genetically Improved Farmed Tilapia) project - see e.g. http://www.cgiar.org/impact/research/fisheries.html ...Moderator].

Jared Diamond`s book "Guns, Germs and Steel" highlights the history of human movement of crops and amnimals worldwide. This will continue as aquatic organisms are hauled about for a myriad of reasons. Therefore we really must begin to operationalize our understanding of the multi-scale (and some will say complex systems) interactions between local risks and benefits of aquatic introductions AND the global/historical context of trade and human-induced dispersion of organisms. Let us look at the genetic/biodiversity implications of the proposed stocking of Nam Theun 2. A "classification of choices" relating to the necessary trade-offs between conservation and fisheries use is urgently needed. This, according to much of the literature will involve much broader public involvement, transdisciplinary approaches, and innovative and creative co-management arrangements, all of which we generally have very little experience with, or it appears, a real sincere willingness to learn (but there are a few examples globally where these approaches are beginning to be implemented). Time is running out for the sturgeons it seems, so we cannot afford to discredit any technology or institutional approach without a serious look at how it affects the resource AND the key users who are dependent on that aquatic resource. The documentary "Darwin`s Nightmare" is a confronting statement of human greed and institutional breakdown over fisheries resources. We must move beyond these scenarios with humility and the application of all the tools we have at our disposal.

Ron Jones
International Development Research Centre (IDRC)
Ottawa,
Canada
channastri (at) netscape.net

[Nam Theun 2 refers to a hydroelectric dam on the Nam Theun River in central Laos; "Darwin`s Nightmare" refers to a 2004 film documentary about fishing of Nile perch in Lake Victoria, Tanzania...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 07 June 2005 16:34
To: 'biotech-room1@mailserv.fao.org'
Subject: 15: Seduction of technology // Fish cryopreservation

This is Ron Jones, again.

I think one has to be careful not to be seduced by technology, especially within a developing country context where the capacities to understand, absorb and if necesary fix and upgrade may be limited or non-existent. Having said that, I am fully on the side on writers like Gordon Conway and these ideas of integration of technology and ecological principles in some form of "Doubly Green revolution". No country should be deprived of the knowledge of technologies available and its their choice if or how to apply them.

I think some of the work done, by World Fisheries Trust on low cost, portable crypreservation technology (genebanking) for fish gametes should have wider geographical applications, especially in areas where the conservation and breeding of important indigenous fishes is a growing necessity. In situ is best but our aquatic environments are being altered as we speak.

Ron Jones
International Development Research Centre (IDRC)
Ottawa,
Canadav
channastri (at) netscape.net

[The World Fisheries Trust is a non profit organisation, based in Victoria, British Columbia, Canada, established in 1994 "to promote sustainable use of global fisheries resources" - http://www.worldfish.org/index.html ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 13:59
To: 'biotech-room1@mailserv.fao.org'
Subject: 16: Introducing biotechnology in rural areas = sausages to a new born baby

I’m DOULDE DARMAN Roger (PhD. Food science and Nutrition), from the Institute of Agricultural Research for Development (IRAD), Cameroon.

I’m still inquiring about the issue and applications of biotechnology tools, such as molecular markers or cryopreservation and reproductive technologies, in the rural areas. Do they need such technology? If yes, is it useful for them? And can they use these "high technologies"? I trust the target group of these new biotechnologies may be those people from rural areas (if urban, we then do not contribute (or little) to alleviate poverty in developing countries, as 75-80% of the poor in developing countries live in the rural areas!). My point is wishing to introduce these new (high???) biotechnological methods in rural areas seems to be “trying to give a big sausage to a new born baby” (i.e. sausage is good for adults but don’t give it to your little baby because it’s good for you!!! Then he can get in trouble and can pass away because of indigestion).

Let me give a practical example with recent work on cassava process. We know cassava (Manihot esculenta Crantz) roots serve as food for more than 800 million people in the tropics. Despite this useful application, two drawbacks limit the utilisation of these roots as human food. These are its low protein content and potential cyanide toxicity. Traditional processing methods used by people in the rural areas to reduce these bottlenecks, always include a typical step of fermentation which occurs spontaneously. We notice that this natural fermentation is plagued with many problems related to its dependence on the chance of inoculation from the environment. These problems include high levels of residual cyanide (100 to 170 ppm), long softening time (4 to 5 days), non-reproducible quality and unhygienic products.

To solve these problems we use some applications of biotechnological methods, as we isolate from dried fermented cassava tubers some microorganisms on the basis of their ability to produce enzymes involved in biochemical and physiochemical phenomena, which occur in cassava natural fermentation and are responsible for the degradation of cyanide compounds and tuber softening (beta-glucosidase, alpha-amylase, pectin hydrolase and polygalacturonase). With the aim of large-scale utilization of this starter culture, selected microorganisms (a lactic acid bacteria identified as Lactobacillus plantarum and a mould identified as Rhizopus oryzae) were dried and used as starter culture for cassava fermentation. The use of these strains as a mix starter culture rapidly softened the roots permitting the reduction of the total cyanide content by about 95±4%. These results, apart from the fact that we published several articles, were not so interesting as they still remain in the laboratory and were never accepted by populations. And, believe me, all effort was made to transmit these findings to the target group (rural peoples) but NO WAY. So, sorry about this, but seems like we waste our time!!!! And my question remains do rural population need such technology? What’s the usefulness of biotechnological methods for rural population?

Dr. DJOULDE DARMAN Roger
Researcher
IRAD/CRRAD
B.P 33 Maroua
Cameroon
Tel: 0032477236041
Email: djoulde (at) gmail.com

[More details on biotechnology for processing of foods, including cassava, can be found from Conference 11 of this Forum (held 14 June to 15 July 2004), entitled "Biotechnology applications in food processing: Can developing countries benefit?" http://www.fao.org/biotech/C11doc.htm ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 14:01
To: 'biotech-room1@mailserv.fao.org'
Subject: 17: Re: Interspecific hybridization - Cassava

This is Nagib Nassar, Brazil, once again.

I wish to explain some topics related to conservation of crop wild relatives by interspecific hybridization: The case of cassava.

1. Interspecific hybridizations were made using the wild species as a maternal parent. This means that the hybrids maintained the cytoplasm of wild species. Reciprocal crosses in many cases (not in all cases of wild species) are not successful. In the case of Manihot glaziovii, M. pseudoglaziovii, M. dichotoma, M. brachyandra and M. leptophylla, using the wild species as female parent is far more successful than using it as a male.

2. Obtaining interspecific hybrids has been followed by doubling of their chromosome number to restore lost fertility due to chromosome pairing. This stage is as difficult as breaking interspecific barriers because chimera formation is predominant, its instability too.

3. Re-introducing the wild species accompanied by their polyploidized interspecific hybrids probably is the most interesting part of our work. By artificially polyploidizing the interspecific hybrids we imitated what had been done in nature and took millions of years to occur. This part is on what I adressed my participants colleages, and asked their opinion. Details on confirmation of interspecific hybridization using morphological gene markers are found at www.geneconserve.pro.br

Nagib Nassar
Departamento de Genetica e Morfologia,
Instituto de Ciencias Biologicas,
Universidade de Brasilia,
Campus Universitario Darcy Ribeiro, Asa Norte.
CEP: 70910–900, Brasilia – DF,
Brazil.
Phone: (+55.61) 349.3253
Fax: (+55.61) 349.3562
nagnassa (at) rudah.com.br

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 14:02
To: 'biotech-room1@mailserv.fao.org'
Subject: 18: Re: Establishing a universal molecular marker data base

This is from Vijay D., India.

The establishment of a universal molecular marker data base as advocated by Theodore J. Kisha (message 6, June 7) is really a remarkable idea. But before venturing into such development one has to look after certain issues like,

* Selection of a set of universally reliable and reproducible markers
* Consensus on the outcome from different markers
* Standardisation of methodologies including the mode of analysis etc.

Even though a lot of research articles have been published regarding the use of various molecular markers in identifying a biological unit (DNA fingerprinting) and in understanding the diversity through similarity indices, there has been no consensus and no acceptance from international bodies. Thus, the foremost and fundamental issue is to draw a conclusion in the usage of molecular markers rather than continuing the work with different markers in different cultivars by different persons.

D. Vijay, PhD
Scientific Assistant
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012, India
Mobile: 09868412855
E-mail: vijaydunna (at) gmail.com
URL: http://www.geocities.com/vijaydunna

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 14:05
To: 'biotech-room1@mailserv.fao.org'
Subject: 19: Re: Establishing a universal molecular marker data base

I am Emma Sales of the University of Southern Mindanao, Kabacan, Cotabato, Philipines.

I am glad to learn of this effort. There are already some data base for SSR markers especially in Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD) website. I have visited this website in search of the SSR markers for rubber and cocoa. It seems that, in rubber, no SSR marker is yet available. However in cocoa, markers are published but I cannot access the full sequences of the published markers. Can anyone from this conference tell me how to access the full sequence of those markers? I need them to order from PROLIGO or other companies.

Emma Sales
Department of Plant Breeding and Genetics,
University of Southern Mindanao,
Kabacan, 9407
Cotabato,
Philippines
ekalaw (at) yahoo.com

[Participants wishing to respond to this specific question about cocoa or rubber simple sequence repeat (SSR) markers should send a message directly to Emma. An SSR marker, also known as a microsatellite, is defined by the FAO biotechnology glossary (http://www.fao.org/biotech/index_glossary.asp?lang=en) as a segment of DNA characterized by a variable number of copies (typically 5-50) of a sequence of around 5 or fewer bases (called a repeat unit). At any one locus (genomic site), there are usually several different "alleles" in a population, each allele identifiable according to the number of repeat units. This existence of multiple alleles (high level of polymorphism) has enabled microsatellites to be developed as powerful markers in many different species. They are detected by the polymerase chain reaction (PCR)...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 14:11
To: 'biotech-room1@mailserv.fao.org'
Subject: 20: Re: Applying biotechnology to livestock - Egypt

I am Pradeepa Silva. A senior lecturer in animal genetics and breeding attached to the Department of Animal Science, University of Peradeniya, Sri Lanka.

I am in total agreement with Mahamoud Abdel Aziz (Message 7, June 7) in his description of the status of animal husbandry in developing countries. With the lapses in the field level, as described in his email, it is difficult to get benefits from applications of biotechnology.

In Sri Lanka, the limited applications of biotechnology we could see in the area of livestock is genetic characterization of indigenous animals other than commonly practiced artificial insemination (AI). The characterization is also not done as a national need but as individual attempts. However, when the animal conservation is considered again it too is not in the national agenda.

In this context, I guess the regional or global level involvement is very much appropriate to make the role of biotechnology more efficient and useful in the conservation of animal and fishery genetic resources in developing countries.

Pradeepa Silva
Senior Lecturer
Department of Animal Science
Faculty of Agriculture
University of Peradeniya
Sri Lanka
pradeepas (at) pdn.ac.lk

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 15:26
To: 'biotech-room1@mailserv.fao.org'
Subject: 21: Re: Low cost options for tissue culture

This is Edo Lin, independent consultant.

I would like to reply to the message posted by Joe Cummins (message 9, June 7) regarding low cost options for tissue culture.

In vitro conservation and regeneration as tools for the conservation of genetic resources has been widely studied and the general consensus seems to be that it provides an appropriate tool. It is especially useful in cases where plants do not produce seeds or seeds which lose their viability when dried down to safe storage moisture levels.

Such plants may be conserved in situ or in field collections but this is not always easy and they are prone to diseases/pests or climatological damages. Ex situ conservation in the form of low-growth tissue culture or cryopreservation may therefore be preferable.

Joe Cummins rightly points out that, due to inherent genetic instability of some plant species, in vitro collections may give rise to somaclonal variation which, in turn, may give rise to increased genetic variation. However, improved protocols as reported by Drew and others overcome these potential problems. Improved protocols are reported for passion fruit, coffee, neem, lychee and papaya.

Engelmann, F. 1998. In vitro conservation of horticultural genetic resources. Review of the state of the art. http://www.agrsci.unibo.it/wchr/wc2/engelman.html

Withers, L.A. and Engels, J.M.M. 1990. The test tube genebank - A safe alternative to field conservation. IPGRI-APO newsletter 3, 1990. http://www.ipgri.cgiar.org/regions/apo/newsletters/news03/index.htm

Drew, R.A. 1997. The application of biotechnology to the conservation and improvement of tropical and subtropical fruit species. http://www.fao.org/ag/agp/agps/pgr/drew1.htm

Edo Lin
309, rue de Bombon
77720 Bréau
France
tel and fax: +33 164387844
e-mail: lin.edo (at) free.fr

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 15:49
To: 'biotech-room1@mailserv.fao.org'
Subject: 22: Low cost options for tissue culture // Storing DNA

This is E.M. Muralidharan from India. I work for a public funded forestry research organization on tissue culture, genetic transformation and use of molecular markers for forestry crops.

I tend to agree with Joe Cummins (Message 9, June 7) regarding the unsuitability of tissue cultures as a means of conservation. While the use of slow growing shoot cultures may not carry a great risk of variability (consider the fact that the floriculture and horticulture industry depends a lot on micropropagation), other techniques are suspect. Except for purposes of bulking and international exchange of germplasm, tissue culture should not, in my opinion, be used as the major means of conservation of any species. However, it would be useful to undertake studies with molecular markers to understand the extent of the somaclonal variation in slow-growing or cryopreserved cultures to enable decisions to be taken on using the technology as a supplement to traditional methods of preserving germplasm.

While on the subject of supplementing technologies, I wish to get the opinion of participants on the potential for use of DNA (purified and properly stored) as a means of conservation of genetic material for the long-term. Will it be a viable option when we consider that it may serve only as a means of gene prospecting or as a means of resurrecting the plant (à la Jurassic Park !) at some future date?

Dr. E.M. Muralidharan
Biotechnology Division
Kerala Forest Research Institute
Peechi, Thrissur, Kerala 680653
India
emmurali (at) kfri.org

-----Original Message-----
From: Biotech-Mod1
Sent: 08 June 2005 16:44
To: 'biotech-room1@mailserv.fao.org'
Subject: 23: DNA barcodes for identification of plant species

I am PK Gupta, Meerut, India.

During the last few months I have read several articles on DNA barcoding for identification of plants. There are several sequences which are suitable for this purpose. A recent paper in PNAS (June 7) describes some of the work in this area. The conference should have a dialogue in this area for the benefit of those who are unaware of this important area of research.

P.K. Gupta
Honorary Emeritus Professor and INSA Senior Scientist
Molecular Biology Laboratory
Department of Genetics and Plant Breeding
Ch. Charan Singh University
MEERUT-250 004
India
Tel (Lab): 91-121-2768195
(Resi): 91-121-2762505
TeleFax : 91-121-2768195
e-mail : pkgupta36 (at) vsnl.com, pkgupta36 (at) hotmail.com

[The article referred to in the 7 June 2005 edition of the Proceedings of the National Academy of Sciences of the United States of America (PNAS) is by W.J. Kress et al., entitled "Use of DNA barcodes to identify flowering plants". They propose 2 specific DNA regions that could be used to discriminate between species of flowering plants, concluding that "the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes". They note that DNA barcodes "show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, and forensic analysis". The paper is freely available on-line at http://www.pnas.org/cgi/reprint/102/23/8369 (the e-mail address for correspondence is kressj (at) si.edu) ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 11:46
To: 'biotech-room1@mailserv.fao.org'
Subject: 24: Re: Establishing a universal molecular marker data base

My name is Dr Guy Barker (Director of Genomics, Warwick HRI, UK) and I work on plant genomics and in particular on Brassicas.

I agree that a large number of markers are available in the public domain and others in private consortium. The accessibility depends on what species you work on. Some species are making a concerted effort to make data available, not simply on primer sequences but also their reliability as markers and their use in different mapping populations. An example can be found on http://www.brassica.info. Trying to assemble a universal marker database would take a considerable amount of effort as each marker would need to be verified and entered accordingly. There would also need to be a great deal of curation to maintain this and it would also depend on scientists being willing to return data in a suitable format once they have used any marker on a different population. It is hard to see any country willing to put in the investment into such a database. Per species it is much easier to see this coming about. However, I would emphasise the requirement for international collaboration and for the data to be maintained in the public domain.

Dr Guy Barker
Director of Genomics,
Warwick HRI,
United Kingdom
Guy.Barker (at) warwick.ac.uk

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 11:47
To: 'biotech-room1@mailserv.fao.org'
Subject: 25: Re: Plant genetic resources - SADC countries

My name is M Carmen de Vicente. I'm the plant molecular geneticist of IPGRI (the International Plant Genetic Resources Institute) and Subprogramme Leader of Capacity Building and Enabling Delivery in the Generation Challenge Programme (www.generationcp.org).

Regarding Message 1 (June 6) from Charles Nkhoma:

The situation in the SADC region is common to many other regions worldwide. I don't think it is realistic that all countries have facilities to carry out their own work. It is not only about facilities, but about human capacity and sustainability in the long run. An important obstacle for the option of all countries with their own facilities is that technologies change very rapidly, or let's say new and more efficient ones are developed constantly. This often means different equipment, consumables, even expertise, etc. Then both facilities and expertise become obsolete quite fast. This situation does not affect only developing countries but developed ones too. The fact is that in many developed labs they tend to outsource some of the experiments and concentrate on data analysis, interpretation and application of results. I wonder whether institutions in SADC (Southern African Development Community) and similar regions would consider the possibility of having a hub center in the region where they can either send their samples for analysis or go there to do the work. This would certainly reduce the cost of providing up to date facilities to all institutions in all countries and would promote the use of this research in much wider areas of science.

M Carmen de Vicente
International Plant Genetic Resources Institute (IPGRI),
Office for the Americas,
c/o CIAT, A.A. 6713, Cali,
Colombia
c.devicente (at) cgiar.org

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 11:48
To: 'biotech-room1@mailserv.fao.org'
Subject: 26: Re: Establishing a universal molecular marker data base

This is from M Carmen de Vicente, again.

Just two comments:

1) There was an initiative to develop descriptors for genetic/molecular marker technologies, so that everyone can use the same type of information for comparability of results depending on the technology, etc. This was the result of a consultation among a large number of experts working with different species. This is not a finished product (and perhaps it will never be!), and comments/additions to improve it are very welcome. You can find this in the IPGRI web site through this link [No link was included in the message provided, but I can add that a November 2004 news item in FAO-BiotechNews ((http://www.fao.org/biotech/news_list.asp?Cat=131) provides more information on this initiative i.e. "The International Plant Genetic Resources Institute (IPGRI) has recently published "Descriptors for genetic markers technologies" by M.C. De Vicente, T. Metz and A. Alercia. This list of descriptors is an effort to define community standards for documenting information about genetic markers and is targeted to researchers using genetic marker technologies to generate and exchange genetic marker data that are standardized and replicable. See http://www.ipgri.cgiar.org/publications/pdf/913.pdf or contact ipgri-publications@cgiar.org for more information"...Moderator].

2) I encourage you to go the Generation Challenge Program website (www.generationcp.org) and see the information particularly in Sub-programme 1: genetic diversity of global genetic resources. The sub-programme agenda includes genotyping of quite large collections of important food security crops. The molecular marker technology chosen was microsatellites, as comparability is one of the most important issues for the reasons you pointed out. As a result, microsatellite "kits" are now being put together and hopefully will be available some time in the near future. The goal is to provide the tools and all necessary information (primer sequences, protocols, interpretation of results, reference accessions, etc...) to use them in these crops. I hope this can become a model to use for other crops as well. And, in terms of documentation, you can also take a look at Sub-programme 4 on informatics tools, etc...which takes care of compiling all information generated, not only in terms of molecular markers and their standards but also other more 'traditional' characterization data such as morphological descriptors, performance, etc...

M Carmen de Vicente
International Plant Genetic Resources Institute (IPGRI),
Office for the Americas,
c/o CIAT, A.A. 6713, Cali,
Colombia
c.devicente (at) cgiar.org

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 11:49
To: 'biotech-room1@mailserv.fao.org'
Subject: 27: Re: Introducing biotechnology in rural areas = sausages to a new born baby

This is M Carmen de Vicente, again.

Regarding Message 16 (June 8) from Roger Djoulde Darman:

I appreciate very much your example of application of biotech methods for the fermentation of cassava and the point made about adoption. But have you pondered why the findings were never adopted? Was it a cultural barrier? Or do rural people have to buy the mix starter culture and they cannot afford it? Were they shown the advantages in a way that they could tell the differences by themselves? In general, is the conclusion that we should stop working to solve these problems because rural people in the end do not 'care' about the solutions? Or should we concentrate our efforts on how to ensure the findings reach the rural people?

M Carmen de Vicente
International Plant Genetic Resources Institute (IPGRI),
Office for the Americas,
c/o CIAT, A.A. 6713, Cali,
Colombia
c.devicente (at) cgiar.org

[Note, apart from an eventual response from Roger to the above questions, please keep any further discussion on this thread in the context of biotechnology for the characterisation and/or conservation of genetic resources for food and agriculture and not biotechnology in general. Roger's message began with his questioning whether people in rural areas in developing countries, who make up the great majority of the world's hungry, need or will find use for biotechnology tools, such as molecular markers or cryopreservation and reproductive technologies. He then provided an example where biotechnology tools had been applied to cassava processing but the research outputs were not adopted by the rural people...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 11:50
To: 'biotech-room1@mailserv.fao.org'
Subject: 28: Core collection // Markers and morphology // Tissue culture

This is from Kioumars Ghmakhar, Australia. I'm a plant molecular biologist and systematist at CLIMA (Centre for Legumes in Mediterranean Agriculture), University of Western Australia: http://www.clima.uwa.edu.au

I am glad to see (almost) an initial movement towards establishing a universal molecular marker data base. I had this idea from 2 years ago when I started my current project on "developing a core collection for Trifolium spumosum L. using molecular (FAFLP and ISSR) and ecogeographical data" at the Centre for Legumes in Mediterranean Agriculture (CLIMA), University of Western Australia.

My project is a joint one with the Department of Agriculture Western Australia and I am using the Trifolium germplasm collection at the Annual Trifolium Genetic Resource Centre (ATGRC) at the Department. I have already developed a first subset based on passport/ecogeographical data and am screening the first subset using molecular data in order to introduce the final core collection.

I am planning to store my final data at the ATGRC and some day in future revealing it to anyone around the world and on the web. There are also some web-based databases for cereal SSR, RAPD, and AFLP data but it is highly limited to cereals and a few other plants. For legumes, for example, the dataset is available only for a couple of species (I think they are Glycine max and Medicago truncatula). [Simple sequence repeats (SSRs), Random amplified polymorphic DNAs (RAPDs) and Amplified fragment length polymorphisms (AFLPs) are 3 different kinds of molecular markers. Inter-simple sequence repeat (ISSR) techniques, referred to elsewhere in this message, are nearly identical to RAPD techniques, except that ISSR primer sequences are designed from microsatellite regions and the annealing temperatures used are higher than those used for RAPD markers...Moderator].

Regarding the use of molecular data, they are definitely one of the best among the whole collectable and variable traits. Morphology is the most classic and accepted method particularly in the developing countries but it can only give you a limited number of options knowing that we can only score a few characters and the possibility of homoplasy (similarity in appearance but dissimilarity in function, origin, etc.). Although the problem of homoplasy can still exist in molecular (particularly gel based) techniques, there is a much lower risk and also the number of characters obtained from molecular techniques such as ISSR and AFLP are tremendous compared to, say, morphology. However, I would always remind people that they should never forget what we (and our ancestors) have been looking at over thousands of years, that is, morphology. Therefore, my suggestion is that molecular markers must be definitely employed as the best technique for screening of genetic diversity but they must also be double checked by morphological data to make certain there is no major loss in our breeding and/or core collection development programs.

Generally, I think we must develop core collections first, find the gaps within our current collections by networking with other genetic resource centres (GRCs) around the world, suggest new more targeted seed collection missions, and at the very last stage use the molecular markers for molecular assisted selection but for now the use of molecular markers for developing core collections is a must for, particularly larger, collections and surveys on the smaller collections.

At the end, may I ask Joe Cummins (Message 9, June 7) why (in more detail) tissue culture techniques are not reliable for the purposes that he has discussed? I am just curious, as I have done almost everything in plant experimental techniques but have not done much of tissue culture technique. What about embryo rescue? Do Joe Cummins' comments apply to that technique, too?

P.S. The cheapest and most reliable molecular technique for developing countries is probably ISSR at present.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 15:52
To: 'biotech-room1@mailserv.fao.org'
Subject: 29: Re: Introducing biotechnology in rural areas = sausages to a new born baby

Here is Roger DJOULDE DARMAN, Cameroon, again.

First of all, I want to bring some clarifications to Carmen de Vicente’s message (nr. 27, June 9). In fact the project was based on the fact that, in order to improve artisanal cassava fermentations, rural populations usually re-use cassava chips coming from a previous fermentation as starter cultures for a new one. This means that there’s not a cultural barrier as they already use "artisanal" starters. But the real problem is that these new techniques found in laboratories by researchers are too complicated for rural illiterate population as they don’t have the technical background to use a starter.

Coming back to the topic, I want to point out again the difficulties of making rural populations adopt new methods related to biotechnology for the characterisation and/or conservation of genetic resources for food and agriculture. And again my point is that these methods will better serve us in developing countries if we find easier methods to adapt these complicated methods in rural areas. As Carmen says we have to concentrate our efforts on how to ensure the findings reach the rural people. Is it utopia to dream in future of typical rural groups of women from rural Africa using PCR, NMR...etc to control the safety of their village food, our mothers using cool dry technologies or spray dryer granulator methods etc. to produce dried and safe milk, meat, vegetables or preserve their seed?

In fact I want to end by this: There’s a huge gap between biotechnology tools, such as molecular markers or cryopreservation and reproductive technologies, and people in rural areas in developing countries, who make up the great majority of the world's hungry. If it’s clear that breeders and other specialists produce crop seed and other genetic material useful for illiterate population, it’s not the case for food safety and food preservation. Let me point out that we can produce as much food as we need, but if there’s not adequate easy to use methods, in order to preserve these foods, seeds and our local genetic materials, then it will be difficult to ensure food security in Africa.

Dr. DJOULDE DARMAN Roger
Researcher
IRAD/CRRAD
B.P 33 Maroua
Cameroon
Tel: 0032477236041
Email: djoulde (at) gmail.com

[Further messages on this topic will only be posted if dealing specifically with biotechnologies for the conservation and characterisation of genetic resources...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 16:38
To: 'biotech-room1@mailserv.fao.org'
Subject: 30: In vitro conservation supporting genetic conservation

I am Brian Ford-Lloyd, Reader in a School that has a longstanding involvement in Plant Genetic Resources and Applied Genetics, and Director of the MSc course in Plant Genetic Resources.

I wish to comment on the various submissions that have been made in relation to in vitro conservation. The problem with an e-mail conference is the tendency to try and fit into a few e-mails the knowledge generated from many years of research. The pros and cons of in vitro conservation have been well studied for maybe 25 years. Without going into detail, it is clear that in vitro conservation is being used in various ways to support the genetic conservation process, and notwithstanding genetic instability the technique does provide a means of conserving some plant material and is better than the alternatives. For example, some plantain genotypes are about as unstable as you can get in culture, but in vitro slow growth and cryopreservation is still used because the alternatives are largely inadequate. So, it is horses for courses!

On a different point, I have found the discussion about the need to develop databases for molecular markers interesting - but has anyone seen the work that has been done by IPGRI? I think that the publication 'Descriptors for Genetic Markers Technologies' edited by Carmen De Vicente et al in 2004 may be a useful step in the right direction. [This weblink and e-mail address for this publication was given in Message 26, June 9...Moderator].

Brian Ford-Lloyd
School of Biosciences,
University of Birmingham,
UK.
B.FORD-LLOYD (at) bham.ac.uk

-----Original Message-----
From: Biotech-Mod1
Sent: 09 June 2005 16:54
To: 'biotech-room1@mailserv.fao.org'
Subject: 31: Molecular characterisation of animal genetic resources

I'm Ilse Köhler-Rollefson, project coordinator of the League for Pastoral Peoples, and have done some research on indigenous/traditional/local management of animal genetic resources or "IK-AB" (Indigenous Knowledge about Animal Breeding) among pastoralist communities, mostly in India. Before that I worked for about 10 years as an archaeozoologist, identifying animal bones from archaeological sites and using the results to reconstruct ancient subsistence strategies and tracing the process of domestication. I've worked both on camel and on goat domestication.

Molecular characterisation of livestock breeds and genetic distancing is often justified by the need to identify those breeds that are genetically most unique, since there are too few resources to conserve ALL the many breeds that are threatened. Molecular characterisation has also been used to draw conclusions about the dispersal of domesticated animals and the relationships between different populations - for instance with respect to cattle domestication and dispersal in Africa.

Just to play the devil's advocate, I would like to pose the following questions:

1. Has molecular characterisation of livestock breeds actually produced data about domestication and dispersal superior to those that could be produced by a mixture of archaeology and ethnohistory, or do they not only just confirm what archaeologists and archaeozoologists already know?

2. Secondly, should genetic uniqueness really be the key criterion for deciding which breeds we should save? What about the role of the people who are associated with the animal genetic resources, might they not also be asked? When they allow their livestock to be sampled, are they aware that the results of the investigations may decide whether the animals are considered worthy of conservation or not?

I do not doubt that biotechnological methods for characterising animal genetic resources produce scientifically very interesting and fascinating results, but I feel that the relevance of these methods for livestock keepers themselves, and especially for poverty alleviation, still need to be proven.

Dr. med. vet. havil. Ilse Köhler-Rollefson
Consultant for Livestock and Pastoral Development
Pragelatostr. 20
64372 Ober-Ramstadt
Germany
Tel/Fax +49-6154-53642
Email: gorikr (at) t-online.de, ilsekr (at) rediffmail.com
www.pastoralpeoples.org

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 09:06
To: 'biotech-room1@mailserv.fao.org'
Subject: 32: DNA genebank

This is Richard Wang, Research Geneticist, USDA-ARS (United States Department of Agriculture - Agricultural Research Service). I work on germplasm improvement of forage crops.

In early 1980's, I suggested that pure DNA samples should be stored in genebanks to preserve genes in anticipation that someday scientists can utilize desirable genes directly from the DNA molecules. This form of germplasm preservation is already a reality in Australia and U.K. I hope it will become a common practice in all genebanks.

Richard Wang
Research Geneticist
USDA-ARS Forage and Range Res Lab
Utah State University
695 N 1100 E
Logan, UT 84322-6300
United States
(Office) 435-797-3222
(FAX) 435-797-3075
rrcwang (at) cc.usu.edu

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 10:23
To: 'biotech-room1@mailserv.fao.org'
Subject: 33: Re: Introducing biotechnology in rural areas = sausages to a new born baby

This is Kioumars Ghamkhar from Australia, again. I am sorry I did not properly introduce myself in my first email. I'm a plant molecular biologist and systematist at CLIMA (Centre for Legumes in Mediterranean Agriculture), University of Western Australia: http://www.clima.uwa.edu.au.

Regarding message 29 (June 9) from Roger DJOULDE DARMAN:

I think we have lost the point here. No rural farmer is supposed to use polymerase chain reaction (PCR) or any molecular technique in the lab. This is apparently the molecular diversity scientists' responsibility to undertake these tests and satisfy the farmers to use the outcomes and end products of these screening and/or breeding programs. Farmers in developing countries are and will be more than happy to use the accessions and/or varieties that we suggest if we prove that the suggested accessions are improved ones within a huge, or at least relatively large, collection. They do not really care what methods we have used as long as we provide them with the right thing and do not say "sorry, I was wrong" in a couple of years after their field trials. That is exactly why we need a global effort and coordination to establish a standard dataset and methodology for our molecular research.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 10:29
To: 'biotech-room1@mailserv.fao.org'
Subject: 34: Re: DNA genebank

This is Kioumars Ghamkhar from Australia, again.

Regarding message 32 (June 10) from Richard Wang:

There is already a DNA bank in the United States at the Missouri Botanic Gardens although it is not a "real DNA bank" as we know it but it is one step forward, having the leaves stored in silica gel. The best DNA bank, though, is at Kew Botanic Gardens in the UK as you said, but I am not aware of any well-established DNA bank in Australia.

Although I agree that DNA banks are good sources of conserving genetic resources, I draw your attention to the fact that there are advantages and disadvantages for both DNA banks and seed banks forcing people to prefer seed banks at this stage, particularly in the countries with less funding support for these purposes:

This information is from a talk by A.H.D. (Tony) Brown (CSIRO plant industry, Canberra, Australia) at the Centre for Legumes in Mediterranean Agriculture (CLIMA) last year, comparing these two storage systems, which has been a bit modified by myself:

Disadvantages of DNA banks:
1. Contamination diagnosis is difficult in DNA banks while it is much more obvious in seed banks.
2. Morphological screening is not possible at any stage to double check any wrong going practice in DNA banks.
3. DNA banks need highly skilled technicians for maintenance while seed banks do not really.

Advantages of DNA banks:
1. No quarantine issues for countries such as Australia with strict quarantine rules for seeds and any other parts of plants.
2. Quick availability for research.
3. Almost immortal for storage purposes.

Of course, there are even more advantages and disadvantages, with the latter decreasing over time and in future, but certainly for now we are better off sticking to seed banks.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 11:10
To: 'biotech-room1@mailserv.fao.org'
Subject: 35: Re: Molecular characterisation of animal genetic resources

I am Hans Lenstra, Faculty of Veterinary Medicine, Utrecht University, Netherlands. I am a molecular biologist and have coordinated a large-scale European project on cattle genetic diversity (GenRes CT98-118, 1999-2002) and have participated in a sheep-goat diversity project Econogene (2001-2005, coordinated by Prof. P. Ajmone-Marsan, Piacenza).

Ilse Köhler-Rollefson (Message 31, June 9) is asking the right questions about livestock conservation. Of course there is more in our world than DNA.

However, there are now several examples of DNA telling us something we did not know before:

Many papers are focused on a few local breeds with often a modest number of DNA markers. Now we have the large datasets generated by the above-mentioned projects and these contain a wealth of information. With the forthcoming papers of the European Cattle Genetic Diversity Consortium and the Econogene Consortium we hope to prove our point!

About the use of genetic data for conservation: this is quite a thorny subject. My view may appear provocative, but is based on the analysis of datasets of a size that for livestock were not available before. Genetic distances appear not at all to be reliable criteria for the value of a breed, since it tells more about the degree of genetic isolation than about unique properties. A Holstein population derived from one fibroblast would show up as more valuable than an old landrace with a lot of unique alleles! This is now leading (at least for livestock) to criticism of the popular Weitzman approach for estimating conservation priorities. We find that newer methods (marker-estimated kinship analysis, developed by Herwin Eding) make more sense.

However, like it or not, with the current state of art I would not dare to condemn any breed on the basis of DNA markers alone! Indeed, the perceived value of a breed is often linked to regional tradition and this is not in the DNA. On the other hand, DNA data give most relevant data about the history of a breed, e.g. by revealing ancient alleles or by detection of outcrossing, and this may very well contribute to decisions about conservation. Eventually, DNA has the future! Mutations coding for breed-specific phenotypes are being found. A new trend will be the male Y-chromosome, more vulnerable to extinction than autosomal DNA and potentially relevant for masculine traits.

Dr. J.A. Lenstra
Faculty of Veterinary Medicine
Yalelaan 8
3584 CL Utrecht
Netherlands
+31-30-2534992, fax 2518126
at home +31-30-6375622
J.A.Lenstra (at) vet.uu.nl

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 11:11
To: 'biotech-room1@mailserv.fao.org'
Subject: 36: Re: Molecular characterisation of animal genetic resources

This is Olivier Hanotte. I am a molecular geneticist working at the International Livestock Research Institute (ILRI-Nairobi) where I am leading the ILRI project on Animal Genetic resources which has a strong biotechnology component.

I am particularly welcoming Ilse Köhler-Rollefson's comments (Message 31, June 9) and would like to take this opportunity to comment on a couple of issues raised by her message.

I think we can all recognize the importance of characterizing our livestock breeds/species/population to better utilize it for the short and long term benefit of the farmers and for the long term benefit of the global community.

Importantly, we have to understand that the word characterization engulfed a lot of areas, of which biotechnology (molecular characterization) is only one of them.

Rightly we should ask ourselves the question, what has been then the deliverable of molecular characterization.

One area, as pointed out by Ilse Köhler-Rollefson, has been the unraveling of center of domestication and in some case dispersal routes etc. I would like to broaden this and say that molecular characterization has helped us to understand the origin and also the today genetic make-up of our livestock.

Have we learned anything through genetic methods that we did not know before? Broadly speaking, I think it is not the way we should be stating the question. Molecular characterization, archeology, linguistic, indigenous knowledge etc. are providing information which allows us to complete a puzzle about origin and history of agriculture. One kind of evidence pointing in a specific direction is good, several distinct sources of evidence is much better, much more convincing and exchanges of information between these fields can only better guide future research, initiative etc.

This understanding of the genetic make-up is also opening new doors for conservation and utilisation. One of which is to provide putative criteria for priority decision for conservation, these could be genetic uniqueness, level of diversity etc. Should the molecular criteria be the main criteria? If we think about ex-situ conservation, I think it should be a very important criteria (selection of animals representative of the diversity of the breeds conserved etc.).

But if we think about in situ conservation at the farmer community level we should be extremely careful here and realize that in-situ conservation and genetic improvement/utilization (through which we will have an impact at the farmers level and therefore on poverty) are not the same thing.

Undoubtedly, we should be targeting poverty alleviation and improvement of indigenous breeds is one possible avenue. Such an approach will result only on a subset of the indigenous livestock diversity conserved but in a likely sustainable way. A subset, but an important subset for the future

Biotechnology tools and information can help breeding improvement (pedigree reconstruction, marker-assisted selection etc.). Let's not forget that the raw genetic material for selection and therefore genetic improvement is diversity.

Olivier Hanotte, PhD
Project Leader
Animal Genetic Resources
International Livestock Research Institute (ILRI)
P.O. Box 30709
Nairobi 00100
Kenya
PLEASE NOTE NEW PHONE NUMBERS
Tel + 254 20 4223466 (office) + 254 20 4223140 (home)
Fax +254 20 4223001
Mobile + 254 (0)734 333071
E-mail o.hanotte (at) cgiar.org
http://www.ilri.cgiar.org/
ILRI via USA-Direct Tel + 1 650 8336660, Fax 1 650 833 6661

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 14:06
To: 'biotech-room1@mailserv.fao.org'
Subject: 37: Characterization of fish biodiversity

My name is Kazhila Croffat Chinsembu from the University of Namibia in Windhoek, again.

This time I am onto the subject of ecology and evolution of cichlid fishes of Southern Africa. So far, the only fisheries contribution has been from Ron Jones (Messages 14 and 15, June 7).

Let me draw your attention to the recent work by Joyce et al. reported in Nature volume 435 of 2005. It has revealed that the situation is different in Southern African rivers. Haplochromine cichlids in five Southern African rivers (Upper Congo, middle/upper Zambezi, Okavango, Cunene and Limpompo) show species richness and ecomorphological diversity similar to that in Lake Victoria and Lake Malawi. They found numerous sympatric haplochromines different in shape and size. Within this Southern African radiation, mitochondrial (mt) DNA haplotypes comprised six clades within which a large number of closely related haplotypes have arisen from a small number of more divergent haplotypes. On the other hand, several morphologically different and geographically distant species have very similar haplotypes. These phylogenetic relationships suggest a species flock that emerged rapidly and simultaneously in many geographically distant rivers, in which very similar haplotypes are found several thousand kilometers apart, yet for which strongly differentiated haplotypes are found within single populations. [African cichlids are extremely species-rich, making up an estimated 5% of all vertebrate species, and are much studied for evolutionary reasons. Haplochromine refers to one of the major lineages of African cichlids. Sympatric species are those which occupy the same area at the same time. A clade is a group of species with a common evolutionary ancestry. The paper referred to is Joyce, D.A. et al., 2005. "An extant cichlid fish radiation emerged in an extinct Pleistocene lake", Nature, 435, 90-94 - address for correspondence regarding the paper is ole.seehausen (at) aqua.unibe.ch ...Moderator].

Through the use of geological evidence, Joyce et al contend that the high diversity among Southern African river cichlids arose from palaeolake Makgadikgadi, a lake that disappeared about 2000 years Before Present. The centre of this extinct lake is now a saltpan north of the Kalahari Desert. They showed that the lake paleo-Makgadikgadi hosted a rapidly evolving cichlid species radiation (comparable in morphological diversity to that in the extant African Great lakes) that later seeded all major river systems of Southern Africa with ecologically diverse cichlids.

Now as a follow up to the above study, we propose to conduct the following research here in Namibia. Here is a short description of the proposed research:

Despite the huge biodiversity of cichlids in Southern African rivers, few known species have been documented in northern Namibian rivers (11 Serranochromine species were found in the Okavango river; 7 Serranochromine and 2 Thoracochromis species were found in the Cunene river - Joyce et al). Targeted biogeographical, ecological and phylogenetical studies to map out the species richness, ecomorphological diversity and phylogenetical relationships of known cichlids in Namibian rivers have not yet been conducted. Although the paleolake Makgadikgadi hypothesis is plausible (Joyce et al 2005), data to demonstrate the dispersal of species from a single centre of diversification and the subsequent coexistence of multiple species are not yet available.

While unidentified species are being discovered (2 Sargochromis species were discovered at the Kalembeza/Zambezi junction - Joyce et al), the scope to discover new species of cichlids still remains unfulfilled and selection pressures that lead to adaptive evolution and explosive speciation are not yet fully understood. Forces that limit coexistence such as ecological competition versus mating competition and introgression in cichlid fishes of Namibia have also not been elucidated.

Further, important genes and genetic variations responsible for phenotypic differences among cichlid species in rivers of northern Namibia are still to be identified.

Given that cichlids are commercially important food fishes in northern Namibia, inadequate information about their biodiversity and underlying mechanisms hampers correct decision-making in fisheries management, conservation, utilization, breeding and aquaculture.

What do I seek? I seek the collaboration and help of any organisation that may help us to conduct the field work as well as laboratory experiments. Information about sources of financial support is also welcome.

Kazhila Croffat Chinsembu, MSc
Lecturer, University of Namibia
Private bag 13301
Windhoek,
Namibia
Tel: 264-61-206 3426
Fax: 264-61-206 3791
Email: kchinsembu (at) unam.na

[People interested in collaboration should contact Kazhila directly...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 14:24
To: 'biotech-room1@mailserv.fao.org'
Subject: 38: Re: Core collection // Markers and morphology // Tissue culture

This is from Dr. Zosimo Huaman, PROBIOANDES, Lima, Peru. I was the curator of large potato and sweetpotato collections conserved at the International Potato Center. We selected core collection for those crops. At present I am a consultant on Biodiversity issues to promote public awareness in Peru to conserve in situ the diversity of 182 crop species domesticated by our ancestors and several thousands of other plant species with known uses.

On the issue of core collections, molecular markers are the most valuable source to get data on genetic diversity of a given crop or plant species. However, at the time of selecting a core collection, one has to take into account other characters such as ecogeographical data, disease and pest reaction, morphological diversity, etc. One has also to make sure to include rare alleles.

From a cluster of accessions with similar genetic constitution, it would be better to select an accession representing the group that has some desirable character such as disease or pest resistance, higher nutritive value, etc. Therefore, the collection should be evaluated for some of the most important biotic or abiotic factors that limit productivity of that crop.

Researchers in developing countries many times do not have the equipment nor the supplies needed to get molecular data. Therefore, the recipes that we get from researchers from industrialized countries are many times difficult to implement. However, the selection of core collections are extremely important to make sure that at least the most genetically diverse accessions in the collection are maintained. This is a better choice instead of losing accessions in the collections at random due to natural or man made causes.

Dr. Zosimo Huaman
PROBIOANDES
Calle El Herraje # 120
Urb. Rinconada Baja, La Molina
Lima 12,
Peru
email: z.huaman (at) probioandes.com
http://www.probioandes.com/

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 14:45
To: 'biotech-room1@mailserv.fao.org'
Subject: 39: Re: DNA genebank

This is Glaucia S.C. Buso, from Embrapa Genetic Resources and Biotechnology, Brazil.

Responding to Kioumars Ghamkhar (Message 34, June 10):

Is there any well-established DNA bank in any country? What should be the criteria to keep DNA samples for long time conservation? Is there any publication that establishes these criteria or requirements?

Glaucia Salles Cortopassi Buso, Ph.D.
Laboratorio de Genetica
Embrapa - Recursos Geneticos e Biotecnologia
Parque Estacao Biologica 70770-900
Caixa Postal 02372
Brasilia - DF
fone: 61- 448-4647
448-4645
fax: 61-340-3624
buso (at) cenargen.embrapa.br

[Responding also to Message 34, Rajeev Varshney from IPK-Gatersleben, Germany, rajeev (at) ipk-gatersleben.de, writes to say that he thinks that Robert Henry from Southern Cross University has also established a DNA Bank in Australia (http://www.scu.edu.au/research/cpcg/sxn3/staff.php?id=1) ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 16:20
To: 'biotech-room1@mailserv.fao.org'
Subject: 40: Re: DNA genebank

This is Elizabeth A. Widjaja from Botany Division, Research Centre for Biology, Indonesian Institute of Sciences, Bogor, Indonesia.

I am not a geneticist, but only a plant taxonomist. I would like to join in this e-conference to know what people talk in biotech e-conference to give me an idea because I am just a new person in the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) Focal Point from the developing countries so I need to learn everything regarding to the Convention on Biological Diversity (CBD).

Responding to Glaucia S.C. Buso (Message 39, June 10): In our research centre we have a collection of DNA bank although it is not a real one, because we keep the leaves and stored in silica gel or as dried extracts. Most of our DNA plant collection is kept in silica gel and comes from the threatened species. On the other hand, we also have DNA fauna collection such as bird, mammals and others - mostly kept as blood, hairs and extract collection.

Dr. Elizabeth Anita Widjaya
Research Center for Biology - Botany Division
Indonesia Institute of Science
c/o the Herbarium Bogoriense, botany Division
Jalan Ir. H. Juanda 22 - P.O. Box 110
Indonesia
+62 251 322 035
Fax: +62 251 325 854; 251 336 538
ewidjaja (at) indo.net.id

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 17:12
To: 'biotech-room1@mailserv.fao.org'
Subject: 41: Developing a core collection - Importance of choice of marker

I am Marie Noelle Ndjiondjop working as a rice molecular geneticist at WARDA - The Africa Rice Center (Cotonou, Benin). In African rice ecosystem, two cultivated rice are found: O. sativa L and O. glaberrima Steud. The objectives of our work is: To exploit the genetic diversity hidden in the rice germplasm found in diverse Africa ecosystems; to identify alleles that control the traits of interest; To identify superior alleles for breeding purposes; To identify and map genes/QTLs associated to traits such as drought, disease and pest and increase the stress adaptiveness of Asian rice with high yield potential; To apply target marker to select gene of interest at the early stage of plant growth in particular when the phenotyping becomes difficult and then enhance efficiency of breeding programs.

I would like to contribute to this important forum discussion by pointing out the importance of the choice of informative molecular marker to develop a core collection.

We have used molecular markers to assess the genetic diversity present in a collection of Oryza glaberrima accessions representative of the cultivated forms. Former studies using isozymes and RFLP markers had generally revealed little allelic diversity among Oryza glaberrima lines (Second 1982; Ishii et al. 1993), while a higher level of variability was revealed in other species of the genus Oryza, particularly Oryza sativa. Second (1982) postulated that lack of diversity of Oryza glaberrima is due to a bottleneck effect during the domestication process. Meanwhile, though less diverse than its Asian counterpart, Oryza glaberrima displays a large range of variation for many morphological and agronomic traits important for breeders (WARDA 1993; Jones et al. 1997).

Recent studies using repetitive sequences derived-molecular markers like minisatellites or retrotransposon probes have detected DNA polymorphism among a few Oryza glaberrima accessions (Dallas 1988; Fukuchi et al. 1993). The polymorphism detected among these varieties of Oryza glaberrima, later confirmed in the diversity analysis of the collection of 200 accessions, reinforces the usefulness of microsatellites in assessing the variability present in the African rice (Semon et al. 2005), while the utilization of marker systems such as isozymes or RFLP had generally failed in the past because of lack of polymorphism. This informative molecular marker will now be used to develop the core collection of O. glaberrima accessions store in our genebank.

Marie Noelle Ndjiondjop
Molecular Geneticist
WARDA The Africa Rice Center
Cotonou
Benin
m.ndjiondjop (at) cgiar.org

-----Original Message-----
From: Biotech-Mod1
Sent: 10 June 2005 17:31
To: 'biotech-room1@mailserv.fao.org'
Subject: 42: Re: Establishing a universal molecular marker data base

My name is Marilyn Warburton, and I work in the Genetic Resources Program of the International Maize and Wheat Improvement Center (CIMMYT). I work on the molecular characterization of maize and wheat using molecular markers.

Currently, we use SSR markers to study diversity, and we have had considerable experience working in conjunction with partner laboratories in other countries. In conjunction with the Asian Maize Biotechnology Network (AMBIONET), we did many studies on the feasibility of combining molecular marker studies in maize from different laboratories. Some relevant results have been published in George et al., 2004 (Molecular characterization of Asian maize inbred lines by multiple laboratories. Theor. Appl. Genet. (109:80-91). The main conclusion of these studies was that if different laboratories use the exact same protocols and platforms for genotyping, with multiple internal controls (same genotypes run in all labs), SOME of the markers (perhaps up to half) can be compared between laboratories. If any of the techniques vary between labs, the number of comparable markers goes down, although using a technique such as the allele kits referred to by Carmen de Vicente in Message 26 (June 9) does help somewhat. However, if different laboratories use different techniques, which is always the case in non-cooperating laboratories, the possibility of combining data sets afterwards is virtually non-existent. We have concluded, both in AMBIONET and the Generation Challenge Program, where large scale genotyping projects are coordinated between several labs, that each lab should run a subset of the markers on all genotypes for the project, rather than each lab running a subset of the genotypes with all the markers. Any other way cannot guarantee no introduction of bias into the study.

We have tried other marker types in the past (AFLP, RFLP, arbitrarily primed markers) and the repeatability between labs goes down for all but RFLPs, but these are simply too much work! We hope to try SNPs in the near future, where repeatability should be much higher.

Marilyn Warburton
Molecular Geneticist, Genetic Resources Program
CIMMYT, Int.
Apdo Postal 6-641
06600 Mexico, D.F.,
Mexico
Tel.:(52)555-804-2004 ext. 1381
Fax: (52-555-804-7567/7558
m.warburton (at) cgiar.org

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:14
To: 'biotech-room1@mailserv.fao.org'
Subject: 43: Re: Establishing a universal molecular marker data base

I am Rajeev Varshney, from the Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.

I enjoyed reading several messages on 'Establishing a universal molecular marker data base'. In particular, I agree with the recent message of Marilyn Warburton (nr. 42, June 10) who mentioned that ALL MARKERS tested did not produce ESSENTIALLY SIMILAR results across the lab in their studies. In fact, we also had similar kind of experiences. However, I think that in comparison to genomic simple sequence repeat (SSR) markers, EST-derived SSR markers shower higher reproducibility as we get very strong band or distinct peak in genotypes of interest (see a recent review: R.K. Varshney, A. Graner and M.E. Sorrells. 2005. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology 23:48-55 - copy on request from rajeev (at) ipk-gatersleben.de). [EST-SSRs are SSRs (also known as microsatellites) that have been identified from DNA sequences arising from expressed sequence tag (EST) sequencing projects. An advantage they have over traditional microsatellites is that they are present in expressed regions of the genome (i.e. the sequences are from the small fraction of the genome that contains genes, that result in proteins)...Moderator].

Furthermore, we argue that for molecular characterization of germplasm material (that needs to be verified or used across the labs)- single nucleotide polymorphism (SNP) markers are the best class of molecular markers. In the case of SNP markers, we expect (generally) one of two alleles and there should not be ambiguity in interpreting the results obtained by using SNP markers on any platform like Pyrosequencing etc. I am aware, though, of the fact that at present we are having a limited number of SNP markers in only a few crop plant species and that SNP genotyping (and genotyping platform) is very expensive. At the same time, accumulation of sequence data through genome/EST-sequencing projects in many plant species is providing us with the sequence data for more than one genotype for a given gene. Many bioinformatic tools are publicly available that can be used to identify the SNP (between two or more than two genotypes) and development of SNP markers. Furthermore, some bioinformatic tools like SNP2CAPS developed at IPK, are capable of identifying the restriction enzyme to assay a particular SNP. Thus cleaved amplified polymorphic sequence (CAPS) -based assays using agarose gel and restriction enzymes can be exploited for genotyping the SNP (in the form of 'cut' or 'uncut' fragment) in the germplasm collection.

Thus, it seems that probably SNP markers would prove to be the markers of choice for genotyping the genebank/breeding materials (and storing them in database) across the lab and we should expect many more markers with the possibility of high throughput genotyping in cost-effective manner.

Rajeev Kumar VARSHNEY, Ph.D.
Institute of Plant Genetics and Crop Plant Research (IPK)
Correnstrasse 3,
D 06466 GATERSLEBEN
Germany
Tel: ++ 49 39482 5594(off.),5231 (lab) Fax: ++ 49 39482 5595
E-mail: rajeev (at) ipk-gatersleben.de / rajeevkvarshney (at) hotmail.com
Web : http://www.ipk-gatersleben.de/en/ ; http://pgrc.ipk-gatersleben.de/

[Firstly, as a refresher, Marilyn (Message 42) wrote that from their use of SSR markers in maize with partner labs in different countries "The main conclusion of these studies was that if different laboratories use the exact same protocols and platforms for genotyping, with multiple internal controls (same genotypes run in all labs), SOME of the markers (perhaps up to half) can be compared between laboratories".

Secondly, the abstract of the Varshney et al. 2005 paper referred to above is "Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed"...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:14
To: 'biotech-room1@mailserv.fao.org'
Subject: 44: Markers vs. morphology for diversity analysis

This is PK Gupta, again, from the CCS University, Meerut, India. We have been involved in molecular marker work in bread wheat for almost a decade. In particular, we developed and used simple sequence repeat (SSR) markers (both genomic SSRs and EST-SSRs) for a variety of studies including gene tagging, QTL analysis, diversity studies, transferability of SSRs, etc.. We are also surveying the repetitive and unique sequences of the genome for the organization of SSRs within the genome using methyl filtered and Cot fractionated sequences of wheat genome.

Regarding the use of molecular markers for diversity analysis, we felt discouraged when, after first using SSRs (published in Theoretical and Applied Genetics (TAG), 1999), we tried SAMPL (published in TAG, 2002) and AFLP on the same set of genotypes (published in Biochemical Genetics 2004). The three marker systems gave different results, suggesting that perhaps data on large number of morphological traits will still give the best estimate of diversity. This may look like a retrograde step, but when we pooled the data from all the three marker systems and used it for diversity analysis, the results were comparable with those obtained using about a dozen morphological traits. [Selective amplification of microsatellite polymorphic loci (SAMPL) analysis is an extension of Amplification Fragment Length Polymorphism (AFLP) technology to include amplification of microsatellite loci...Moderator].

We also argued that a set of SSR markers (about 20-50), if used for diversity analysis, samples a very small fraction of the genome, and cannot be representative of the whole genome, which should be scanned for diversity analysis. Consequently, even if several labs combine together, they need to understand the limitations of using molecular markers for diversity analysis. Perhaps, for characterization and identification or for DNA barcoding of the germplasm, DNA-based markers are OK. But, for diversity analysis, unless large number of markers from different marker systems and representing whole genome are used, one would not get a correct estimate of diversity. After having worked for a decade on a variety of molecular markers, I believe that maximum information from morphology will still give the best measure of diversity.

One should also recognize that many of the markers that we use belong to repetitive and non-coding regions of the genome, so that a selection should be made and functional markers should be used for analysis. This has been done in some studies, and we have published a review on functional markers and their utility (Functional and Integrative Genomics, 2004). Therefore, as an afterthought, we feel that even if markers need to be used, functional markers should be preferred over random genomic markers for diversity analysis.

P.K. Gupta
Honorary Emeritus Professor and INSA Senior Scientist
Molecular Biology Laboratory
Department of Genetics and Plant Breeding
Ch. Charan Singh University
MEERUT-250 004
India
Tel (Lab): 91-121-2768195
(Resi): 91-121-2762505
TeleFax : 91-121-2768195
e-mail : pkgupta36 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:15
To: 'biotech-room1@mailserv.fao.org'
Subject: 45: Re: Molecular characterisation of animal genetic resources

I am Chanda Nimbkar from the Nimbkar Agricultural Research Institute, a small non-governmental organisation (NGO) in Maharashtra State of India. I am currently finishing a PhD in animal breeding at the University of New England in NSW, Australia. At our institute in India, we have an ongoing sheep breeding program which uses DNA testing to detect animals' genotypes within a month after birth so that this information can be used for early selection decisions. We work closely with local sheep owners and are testing improved genotypes in their flocks.

I have read with great interest, the important issues raised by Ilse Köhler-Rollefson (Message 31, June 9), Olivier Hanotte (Message 36, June 10) and Hans Lenstra (Message 35, June 10).

I would like to make a few comments in support of some of the pertinent issues Olivier Hanotte has brought into the debate. I see a worrying trend in developing countries such as India where it appears that a vast amount of effort and money are being put into molecular characterization while other areas more directly linked to poverty alleviation such as performance characterization of indigenous breeds leading to genetic improvement programs based on simple principles and methods of animal breeding have been ignored consistently. We need to ask ourselves whether the research funding in developing countries going into some areas of animal biotechnology is because of their 'glamour' and whether the scientists always keep in sight the final application of their research findings. e.g. tremendous efforts and money are invested in perfecting the techniques of embryo transfer (and even cloning) when hardly any attention is paid to producing highly genetically superior animals, for the multiplication of which these techniques were invented.

Ms. Chanda Nimbkar
Ph.D. student
Animal Science (Room 35, Postgrad Annexe)
School of Rural Science and Agriculture
University of New England
Armidale, NSW 2351
Australia
Phone: Work +61-2-6773-3008
Home +61-2-6772-0809
Fax +61-2-6773-3922
cnimbka2 (at) une.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:16
To: 'biotech-room1@mailserv.fao.org'
Subject: 46: DNA genebank - survey of institutions worldwide

This is Carmen de Vicente, again, and this message related to the DNA genebank issue.

About 2 and a half years ago, IPGRI organized a consultation among germplasm experts to talk about the future role of genebanks in the modern era of molecular genetics and genomics (http://www.ipgri.cgiar.org//publications/pubfile.asp?ID_PUB=986). One of the points discussed was DNA banking. As a result, in 2004 a questionnaire was circulated among 816 institutions worldwide (134 countries) to gather up-to-date information on plant genetic resources DNA banking activities and outlooks. The 816 institutions included both national and international institutions working with plant genetic resources, botanical gardens, universities and the private sector. 243 institutions replied and the survey showed that only 20% of those keep DNA as a genetic resource. Most of the replies mentioned lack of knowledge about the subject as well as budgetary constraints and lack of capacity (equipment and expertise). Most people requested information about protocols, standards, documentation, etc. but also about legal issues involved in exchange of DNA. The need for coordinating activities was also mentioned. IPGRI is at this moment finishing up a multi-authored publication, with the aim of establishing a point of departure by assembling information on different aspects related to DNA banking in general. Authors of the publication include some of the names who have been mentioned in this conference. I'm sure FAO will be happy to announce the publication when ready. [These are exactly the kind of publications included in the FAO-BiotechNews e-mail newsletter, posted roughly once a month - http://www.fao.org/biotech/news_list.asp?thexpand=1&cat=131 ...Moderator].

M Carmen de Vicente
International Plant Genetic Resources Institute (IPGRI),
Office for the Americas,
c/o CIAT, A.A. 6713, Cali,
Colombia
c.devicente (at) cgiar.org

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:17
To: 'biotech-room1@mailserv.fao.org'
Subject: 47: DNA bank versus seed bank

This is D. Vijay from India, again.

I totally agree with Kioumars Ghamkhar (Message 34, June 10). I had a brief discussion about the use of DNA banks with Dr. A.D.H. (Tony) Brown during his recent visit to IPGRI, New Delhi Office. We came to a conclusion that even though there are lot of advantages for DNA banks compared to traditional seed banks, they cannot replace seed banks, at least in the near future. Already Kioumars has mentioned some advantages and disadvantages of DNA banks, but here I want to emphasize why they cannot replace the traditional seed banks in the near future:

- From seeds, entire plants can be regenerated which is not possible from the DNA stored.
- For the use of DNA as replacement to the live plant, we should know the sequence of it first. Sequencing all the existing species is a mega task and will take sufficient time and, once sequencing is successful, then comes the identification of genes.
- Thus, DNA bank is fully useful only when all the genes in a species are known, otherwise it can be used partially for the known genes. Identification of genes in various species is itself a very big task and needs lots of sophistication in the existing molecular techniques.

Even the Royal Botanic Gardens, Kew, who are having highest number of DNA samples (22,000) in their DNA bank, clearly mentioned on their website that "We thus make no claims about the quality or concentration of these samples nor how these samples can be used (degraded samples are not suitable for AFLP, for example)". This shows still there is a need to work on a foolproof method to get a high quality DNA from different kinds of tissues (?).

Thus, DNA banks are the technology for the future. They may not replace the seed banks in the near future but certainly can supplement them. To my knowledge, there are only two major DNA banks in the world with respect to plant species, one is 'Royal Botanic Gardens', Kew, and second one 'Nationaal Herbarium Nederlands', The Netherlands, both of which even supplies the DNA samples of the species available with them.

Vijay.D, PhD
Scientific Assistant
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012, India
Mobile: 09868412855
E-mail: vijaydunna (at) gmail.com
URL: http://www.geocities.com/vijaydunna

[The Kew Gardens website for their DNA Bank Database (http://www.kew.org/data/dnaBank/homepage.html), informs that: "The RBG Kew DNA Bank contains over 22,000 samples of plant genomic DNA, all stored at -80°C. DNA is extracted from particular taxa of interest that are then databased with information on names, collectors, localities etc. Each sample is vouchered (made into a herbarium specimen). DNA samples are currently sent to collaborators all over world. It is our aim to open up this resource to a wider audience in the future. DNA samples can be purchased from Kew using this site. The fees assessed do not imply that DNA samples are being purchased, but rather this fee is meant to offset the cost of producing the sample, maintaining it and shipping it. The great majority of these DNA samples are of high molecular weight and reasonable concentration. Some as noted in the comments column are somewhat degraded because the tissue from which they were extracted was not dried properly, whereas others are more dilute than desirable, but some taxa never produce much DNA. We thus make no claims about the quality or concentration of these samples nor how these samples can be used (degraded samples are not suitable for AFLP, for example). Samples, unless otherwise noted in the comments column, have been cleaned on a caesium chloride/ethidium bromide gradient, so they are reasonably free of RNA and Taq-inhibitory chemistry, but in some cases further cleaning and concentration by means of a silica-based column may be necessary before amplification can be achieved. We are happy to advise about problems, and if degradation during shipment occurs we will replace such samples without further charge. The amount of DNA sent is suitable for PCR-based techniques (typically about 25 µl). If you require a greater amount of DNA, this may be possible, but you should contact us to discuss this (dna@kew.org)"...Moderator]

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:17
To: 'biotech-room1@mailserv.fao.org'
Subject: 48: Re: DNA genebank

This is Kioumars Ghamkhar from Australia, again.

Regarding message 39 (June 10) from Glaucia S.C. Buso: The only well-established DNA bank that I am aware of is in the Kew botanic Gardens in UK. There is also another DNA bank at the Trinity College (Dublin, Ireland). I guess there is a project in Brazil at Jardim Botanico (Botanical Garden) in Rio de Janeiro to establish a DNA bank, as well.

Criteria for long term preservation is keeping them in -80 or even -20 degrees, with fresh leaves in silica gel as a back up.

In terms of publications, there should be, but I do not have any in my mind at present. Searching the web is a good idea.

With regard to Rajeev Varshney's message (within nr. 39) on an Australian DNA bank, many thanks for introducing the centre. This is one of the advantages of this email conference. Yet, this bank is not a well-established one and even the Irish DNA bank is more developed than the Australian one.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:18
To: 'biotech-room1@mailserv.fao.org'
Subject: 49: Re: Introducing biotechnology in rural areas = sausages to a new born baby

This is Vijay.D from India, again

Regarding Message 16 (June 8) and Message 29 (June 9) from Roger Djoulde Darman:

I agree completely with Carmen de Vicente (Message 27, June 9) and Kioumars Ghamkhar (Message 33, June 10). I want to elaborate it a little further. Here, we should understand that technology is not the problem but its adoption is the problem. Lab to Land is very crucial to make the technology useful for the common good. When the technology in the case of cassava fermentation has failed (as per Roger), it means we should check the reasons why it failed? (as emphasized by Carmen). If the complicated procedure itself made it a failure then one should work to develop an easier technology. For example, old world computers which are huge in size and too costly and are not so popular but the present scenario is completely different. How did this became possible? So with further research only the technologies developed can be made user-friendly and will one day reach the common man. Research and technologies are like stepping stones. A single technology may not yield every thing.

Yes, what Roger said is correct. PCR or NMR are not being used by rural persons but the possible output from them can be used in the right way for the benefit of the so-called common man. The best example is breeding. The farmer has nothing to do with the art and science of maintenance of numerous lines, crosses, testing for resistance in glass houses and in phytotrons, checking the dominance and recessiveness of characters etc. But the end result of these technologies is an improved variety or a new hybrid which will change his fate. The so-called green revolution which has changed the scenario of world food production, particularly in developing countries like India, is remarkable. But this has happened only when the farmers had adopted the new varieties. It did not happen all of a sudden or overnight, it took years for the farmers to accept the new improved lines.

Coming to the present topic: Use of modern biotechnology for the conservation and use of germplasm has its own relevance. With the drastic change in farm practices, which includes excessive monoculture, there is a need to preserve the existing diversity to use it for further development of existing populations. So, in the situation of dwindling on-farm maintaince of this naturally existing diversity, cryopreservation promises to a great extent.

Thus, the technology developed should be used properly with user friendly methodology along with adoption of proper extension techniques for its successful transfer from lab to land which should also be given proper emphasis. If it failed in one case (as Roger said in the case of cassava fermentation) it is not a permanent failure, it is only transitory. This shows that a more user-friendly methodology has to be developed but the basic technology that ferments the cassava remains the same. Here, we should understand the difference between technology and methodology used by the end user. The molecular markers, PCR etc. are technologies the end user does not use them - instead he will use the outcome of these technologies.

Vijay.D, PhD
Scientific Assistant
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012, India
Mobile: 09868412855
E-mail: vijaydunna (at) gmail.com
URL: http://www.geocities.com/vijaydunna

-----Original Message-----
From: Biotech-Mod1
Sent: 13 June 2005 12:19
To: 'biotech-room1@mailserv.fao.org'
Subject: 50: Learning a lot in this conference - Panama

My name is Jazmina Urriola and I am studying biotechnology at the Saint Martin University in Panama. I am currently attending the third year of the career and I would like to be a specialist in the agrobiotechnology field, which is quite interesting.

Here in Panama, agrobiotechnology is not as developed as in other developing countries. The state has not provided the financial support that is required, there are few well educated people and there is a lack of equipment and infrastructure. However, researchers are trying to take advantage of the resources available, focusing on the improvement of our main crops. They are conserving sweet potato and yuca, and are using micropropagation for pixvae and pineapple. They have already characterized two tubers, called otoe and name, and they have also worked with tomatoes, achieving excellent results. Panamenian researchers are also working with livestock. The results have been great!!! Actually, an agrobiotechnology laboratory was opened yesterday [June 10...Moderator] in order to help farmers and rural people, who have well accepted these new technologies.

Here in Panama there is a lot to do regarding to this topic. I am learning a lot in this conference and I would like to thank all the participants for sharing their experiences. I wish to be able to apply all this knowledge, in order to benefit my country, mainly the rural population.

Jazmina I. Urriola S.
Faculty of Biological Sciences
Universidad San Martin de Panama
Panama,
Panama
jazmina_ius (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 14 June 2005 12:38
To: 'biotech-room1@mailserv.fao.org'
Subject: 51: Re: Establishing a universal molecular marker data base

This is Ted Kisha, again. I failed to introduce myself in my initial message, so I will take that opportunity to do so now. I am the Plant Geneticist at the Western Regional Plant Introduction Station (WRPIS) in Pullman, Washington, United States. For information about the National Plant Germplasm System (NPGS) and WRPIS, see http://www.ars-grin.gov/npgs/ and http://www.ars.usda.gov/Main/docs.htm?docid=6637. Please remember that I am participating in this conference as an individual, and that my comments and views are not necessarily that of the NPGS [Note, unless they indicate otherwise, people posting messages in conferences of this FAO Biotechnology Forum are always assumed to be speaking on their own behalf and not on behalf of their employers...Moderator].

Thanks to everyone for comments regarding the establishment of a Molecular Marker Data Base. The comments have been thoughtful and informative.

I agree that the establishment of this data base would not be a simple task, but I also believe that it is well within the realm of possibility.

Some good points from Vijay D. (Message 18, June 8), who wrote:
" But before venturing into such development one has to look after certain issues like,
* Selection of a set of universally reliable and reproducible markers
* Consensus on the outcome from different markers
* Standardisation of methodologies including the mode of analysis etc. "

1. It would definitely need to be a curated data base. Even microsatellite markers can be problematic considering dye mobilities, M13 universal primers, Plus-A markers etc. A representative, "standard" (not a molecular weight standard) of an accession or group of accessions would have to be readily available for direct comparison using whatever procedure works best for the individual lab. A sample gel in image form would be helpful for alignment.

2. The establishment of a core set of primers for use with each marker type would be a big step in, at the least, making studies comparable for posterity, even without the establishment of a universal data base.

3. I agree that although SSR markers are generally robust and contain the most information per locus, they would not cover much of the genome, considering investment of time and money. Some laboratories may not have the resources for microsatellite analysis.

I wouldn't rule out AFLP markers. They can cover a large area of the genome with less cost than microsatellites. Although there are "quantitative" markers that can prove difficult and that are not highly reproducible, there are also a large proportion of highly reproducible, easy to score markers that can be used in the "core" analysis. If these are identified based on monomorphic bands and with accompanying gel images, as well as a standard genotype for reference, they could prove to be an inexpensive and easy to use marker system.

Theodore J. Kisha
USDA-ARS
Washington State University
Box 646402
Pullman, WA 99164-6402
United States
Phone:(509)335-6898
FAX: (509)335-6654
e-mail: kisha (at) mail.wsu.edu

-----Original Message-----
From: Biotech-Mod1
Sent: 14 June 2005 12:42
To: 'biotech-room1@mailserv.fao.org'
Subject: 52: Re: Livestock - biotechnology - Pakistan

This is from Dr. Quazi M. Emdadul Huque, Bangladesh.

The term biotechnology is very attractive in developing countries like Bangladesh but the work with animal biotechnology is not easy. The most important points are equipment, manpower, funding and the works what really need to do. What will be the purpose for this work? What immediate benefit will come from this work? The policy makers (politicians) want to invest in some areas where they can show the benefit in the next day. They cannot think of long term benefit.

The other point raised from Pakistan (Message 3, June 6, by Muhammad Subhan Qureshi) is really very important in the case of Bangladesh too. We are talking about farm animal genetic resources conservation and improvement. On the other hand, we need to feed a huge number of increasing population of the country that requires immediate increase of production, like milk, meat and eggs. The farmers' demand is high yielding breeds for maximum production. In cattle, artificial insemination was introduced in the country about 30 years back and started the programme in the areas where better cows were available. We can see now that the good quality cows are already diluted. Now the question, what will be conserved and the improvement program will be taken by which cows ? Again, poverty reduction is the priority issue and livestock and poultry are being used as good tools for this. To get high income, the farmers' demand is maximum yield of milk. In such a position, scientists are in a very bad condition with the indigenous animals.

Anybody has any good suggestion to find out the ways for moving further ? We know we need to do many things for local animals but resources are not allowing us for this. We have carried out some studies on Bengal Goat in our research institute on selection, characterization etc but we need a collaboration from the group who can provide us.

Dr. Quazi M. Emdadul Huque
National Coordinator, NCC and Director General
Bangladesh Livestock Research Institute
Savar, Dhaka 1341
Bangladesh
Tel. 880-2-7708326
Fax:880-2-7708325
Email: qmehuque (at) bangla.net

-----Original Message-----
From: Biotech-Mod1
Sent: 15 June 2005 18:04
To: 'biotech-room1@mailserv.fao.org'
Subject: 53: Re: Establishing a universal molecular marker data base

This is Kioumars Ghamkhar from Australia, again.

In support of Marilyn Warburton's suggestion, I think coordination of using different markers by different labs around the world to characterize a specific germplasm/species by an organisation such as FAO or IPGRI will be a great achievement. These data can be stored and analysed by IPGRI in collaboration with those researchers, after collecting all data. We should not worry about different results from different datasets. What is important is the combined analysis that gives us an almost consensus on all the data.

In terms of using single nucleotide polymorphisms (SNPs), although it is a good idea for wheat or maize it is not a good idea for other not very well-known and newly introduced crops because you will need heaps of sequencing work to have access to SNPs.

Also, supporting, we should not focus only on the protein-coding regions of DNA or markers such as microsatellites that only focus on particular parts of DNA. Because non-coding regions are not necessarily (so-called) junk DNA, we must use techniques such as AFLP and particularly its fluorescent technique which gives us up to 300 bands for each sample (it is a huge source of data). To prove how important the non-coding regions of DNA are, I draw your attention to the fact that coding regions are just "functional needles in a genomic haystack" (Bofkin, L. and S. Whelan. 2004. Functional needles in a genomic haystack. Heredity, 92, 363-364). Also, many "conserved non-genic sequences (CNGs)" have proved to be more conserved between genomes than protein coding sequences, leading to some valuable clues to evolution. More evidence? One study reports that parts of the non-coding DNA may be involved in embryonic development (Peaston A.E. et al. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Developmental Cell, 7. 597 - 606).

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 16 June 2005 11:38
To: 'biotech-room1@mailserv.fao.org'
Subject: 54: Molecular tools and aquatic biodiversity // Appropriate applications in developing countries

This is Ron Jones, from Canada, again.

Vijay D (message 49, June 13) reiterates some key considerations about the appropriate application of sophisticated technologies in developing countries. Who benefits along the chain of R&D (research and development) and how is the adoption of outcomes monitored? Are incentives to innovate tied to farmer adoption? Are end users (the poor, the marginalized, the women) consulted beforehand in developing research trajectories (planning) to find solutions to their problems? Have these methods, and any alternatives to expensive, capacity demanding biotech approaches, been fully risk-assessed and evaluated?

The application of molecular tools in the relatively unknown world of fisheries and aquatic biodiversity will continue to play roles in determining stock structures of multi-species fisheries (meta-population dynamics) and important taxonomic classification work. Apart from this very basic work, reminding us that the great majority of genetic diversity needed for any future breeding plans for fish hopefully lies in dynamic and evolving wild gene pools, work on microsatellite markers and single nucleotide polymorphisms (SNPs) for marker-assisted breeding and QTL identification and genomics will be important in those species with high commercial importance, such as salmon, carp, tilapia and oysters. I find it very interesting to include aquaculture/ranching and other culture-based capture fisheries along with wild habitats all part of in situ conservation work. Molecular tools to describe important intraspecific diversity for these differing environments will be important. There will a trend towards the integration of genomics; physiology/biology and quantitative genetics, in what H.M. Gjoen terms "Integrative Genetics" (Bulletin of the Aquaculture Association of Canada 104-2: 7-11. Aquaculture Biotechnology Workshop, 11-12 May 2004, St. Andrews, New Brunswick, Canada). This will also include diagnostics for fish health issues. Hopefully, a global database for markers can include key fish and crustaceans as well.

Ron Jones
Consultant,
International Development Research Centre (IDRC)
Ottawa,
Canada
channastri (at) netscape.net

-----Original Message-----
From: Biotech-Mod1
Sent: 16 June 2005 11:40
To: 'biotech-room1@mailserv.fao.org'
Subject: 55: Re: Molecular characterisation of animal genetic resources

This is from David Steane, retired leader of the FAO regional project for animal genetic resources in Asia, and now living in Thailand.

There have been several messages (e.g. 31 (June 9, by Ilse Kohler-Rollefson), 35 (June 10, by Hans Lenstra), 36 (June 10, by Olivier Hanotte) and 45 (June 13, by Chanda Nimbkar) referring to the use of biotech techniques and the apparent lack of effort put into the more traditional methods of achieving genetic change for the benefit of local farmers. I agree with the sentiments expressed - particularly those of Olivier Hanotte and Chanda Nimbkar. The latter points out the discrepancy in terms of money and effort between biotechnology and traditional methodology and refers to glamour and whether researchers keep application in mind. One of the problems is the manner in which research and development is funded - in most countries the emphasis is on research - where this aspect is paramount for the scientists' personal future prospects it is clear that application is not paramount in their thinking. Most developing country policy makers seem to think that research in modern biotechnology will provide for their future - and it may be so - but certainly not by ignoring the well proven and cost effective traditional improvement methods.

Regarding the incompatibility of molecular analysis results from different centres - the European Union pig project, from early experiences I believe, developed a system whereby different labs studied only a restricted set of markers but for all samples (also suggested in this conference). Adding this approach to the use of the International Society for Animal Genetics (ISAG) recommended list of markers (suggested originally by an FAO working group and published by FAO) for the major farmed animal species, will go a long way to maximise the usefulness of the data. The record to date is of considerable waste of resources due to the lack of co-ordination between scientists involved.

Hopefully, the comments in this conference will be brought to the attention of decision makers - this is perhaps the area in which all participants can act to achieve better understanding and use of the technology. In Thailand, the Dept. of Livestock Development now has a nucleus unit of Kao Lamphun cattle (in co-operation with Chiang Mai university) to provide breeding stock to the region as the dam of crossbred beef production. There are also herds of two Thai Native cattle in other regions. It is intended to both characterise and store samples from some of the original animals as well as to attempt to make genetic change in the future. There is also an application for funding for some research looking for quantitative trait loci (QTLs) of traits of interest in this population although population size is not large. Hopefully, the project can use all the techniques to assist improvement of efficiency of beef production in Thailand.

Certainly biotech has an important role but it will never be the sole criterion for decisions about conservation and characterisation of breeds - but then I don't know anyone closely involved who has realistically suggested that to be the case!

David Steane,
Consultant,
Chiang Mai 50140,
Thailand
Tel/fax (66) 53 42 99 18
desteane (at) loxinfo.co.th

[With respect to paragraph 2: Regarding across-lab collaboration, Marilyn Warburton (Message 42, June 10) wrote "We have concluded, both in AMBIONET and the Generation Challenge Program, where large scale genotyping projects are coordinated between several labs, that each lab should run a subset of the markers on all genotypes for the project, rather than each lab running a subset of the genotypes with all the markers. Any other way cannot guarantee no introduction of bias into the study". Regarding the FAO/ISAG lists of recommended microsatellite loci for genetic distancing studies, more information about them as well as an overview of their use in genetic diversity studies of domestic animals can be found in an information document prepared for the meeting of the Intergovernmental Technical Working Group on Animal Genetic Resources for Food and Agriculture, 31 March to 2 April 2004, Rome, Italy, entitled "Measurement of domestic animal diversity - a review of recent diversity studies" - available at http://dad.fao.org/en/refer/library/reports2/itwg/CGRFA_WG_AnGR_3_04_Inf3.pdf ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 16 June 2005 11:41
To: 'biotech-room1@mailserv.fao.org'
Subject: 56: Biotechnology in developing countries // Human resource development

This is from Made S. Prana, Indonesia. The discussions on biotechnology in the developing countries (Bangladesh, Pakistan etc. - messages 3 (June 6) and 52 (June 14)) caught my attention. I was once in charge of a biotechnology research center in a developing country, Indonesia. I am not a biotechnologist, though.

In my opinion at least there are two reasons why biotechnology is important for us, even for people in the developing countries. Firstly, to keep ourselves aware of and update our knowledge on any recent development/progress of Science and Technology (S & T). Secondly, to apply it optimally (based on the local conditions) for the benefit of our people i.e. for poverty alleviation, or at least to prevent our country from being used for hazardous experimental field trials, including of biotechnology products.

Biotechnology is just a tool, an alternative tool as many people would say. Not all problems have to be solved using biotechnology or molecular methodology. Besides, biotechnology has a lot of options to offer - from the simple and inexpensive to the highly sophisticated and costly techniques. Through creativity, the equipment, the chemicals etc. could also be simplified and made less costly. There is almost nothing impossible in this world. So let's think positively.

Another way to cope with financial problems is to establish collaboration with scientists in the developed or more developed countries on mutual benefit applying the win-win principle. But, please, put human resource development highest in the priority list. I do realize that this sounds much easier said than done, but believe me I have gone through it and I felt that I have achieved something.

Made S. Prana
PROSEA Network Office,
Research Centre for Biotechnology,
Indonesian Institute of Sciences (LIPI),
Cibinong/Bogor,
Indonesia
pran (at) proseanet.org

-----Original Message-----
From: Biotech-Mod1
Sent: 16 June 2005 13:04
To: 'biotech-room1@mailserv.fao.org'
Subject: 57: Re: Molecular characterisation of animal genetic resources

This is Daniel Komwihangilo from Livestock Research Centre Mpwapwa (LPRI), Tanzania. My reseach areas are in ruminant nutrition. Particular interests are in the evaluation of indigenous feed resources and indigenous/local knowledge of feed evaluation and utilization.

I am quite interested with the proceedings of the conference. Of particular, comments today are on Ilse Kohler-Rollefson's comments (Message 31, June 9) and follow up comments such as those of Oliver Hannote (Message 36, June 10) and others.

Although I am not a geneticist, I agree that molecular characterisation of animal and plant genetic resources are one area through which understanding of diversity could be better understood for better utilization of plants and animals. However, farmers of all levels (small scale or large scale) are (among others) interested in quantity and quality of products delivered through diverse processes and technologies. For smallholder farmers in Subsaharan Africa, for example, their concern is not on 'characterisation'. Their concern is on how these farmers will continue to live and produce through the diverse populations of cattle and chicken etc. they currently own. These farmers are pressed upon by 'new' human and animal diseases, 'new' breeds and varieties, 'new' languages of globalization etc.

Therefore, molecular characterisation and all novel techniques will be of value to all farmers and their offspring if they deliver them from the present trials of life and assure them sustainable futures. Thus, whatever efforts are made by natural, social and other scientists will be welcome by farmers if they are not only affordable but also if they embrace sustainable development of their natural environments.

On the other hand, the low level of funding of agricultural research, especially for countries in the South, has also been raised by many contributors so far. I agree that this scenario is not only in biotechnology. However, I am convinced that global (concerted) efforts into technological development are necessary. This will be a way through which the benefits of "constructive biotechnologies" will be felt, especially for countries of the South.

Daniel M Komwihangilo, PhD candidate
Senior Livestock Scientist
LPRI Mpwapwa
P.O. Box 202
Mpwapwa,
Tanzania.
Tel/Fax 255 026 2320853
E-mail: dkomwihangilo (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 17 June 2005 16:54
To: 'biotech-room1@mailserv.fao.org'
Subject: 58: Re: Molecular characterisation of animal genetic resources

This is Made Sri Prana from Bogor, specializing in general knowledge, from the Research Centre for Biotechnology - LIPI, Indonesia.

I understand the desperate situation that scientists working at the grassroots level have to face, especially those working in developing countries. Lots of problems have to be dealt with whilst resources are quite limited. It is quite natural if some of them would think that many of us have been wandering far over the sky forgetting that the people that badly need our help are deep down on earth.

I would say that there is no harm in discussing sophisticated science or high technology so far as one should always remember that we are all living in a real world. Therefore, when it comes to application there is no choice other than appropriate technology, adjusted to our real capability (resources etc.), local needs, capability (education, etc.), and social economic factors (culture, resources etc.). Please fly as high as you wish but ensure that your feet remain on earth.

Made S. Prana
PROSEA Network Office,
Research Centre for Biotechnology,
Indonesian Institute of Sciences (LIPI),
Cibinong/Bogor,
Indonesia
pran (at) proseanet.org

-----Original Message-----
From: Biotech-Mod1
Sent: 17 June 2005 16:55
To: 'biotech-room1@mailserv.fao.org'
Subject: 59: Re: Molecular characterisation of animal genetic resources

This is Peta Jones, author of "Donkeys for development", Member of National Steering Committee, South African Network for Animal Traction (SANAT) and Member of Animal Traction Network of Eastern and Southern Africa - ATNESA http://www.atnesa.org.

I was interested by the points that Ilse Kohler-Rollefson raised (Message 31, June 9). She is, of course, quite right in most of what she says. There is, nonetheless, something to be said in favour of the "relevance of these methods for livestock keepers themselves, and especially for poverty alleviation", if one focuses on history and not on special breeds, an example being donkeys - not exactly a breed and hardly rare, of course. Recent work in molecular genetics, as far as I understand the reports, has substantiated the long-held belief that most of today's donkeys have their origins in north-east Africa, and that those in southern Africa reached there via southern Europe, specifically the Iberian peninsula, and not through Africa across the equator. Such a history has implications for management practices and technology transfer, and thus indirectly on poverty alleviation.

North of the Equator, this history gives donkeys a tremendous depth of tradition embedded in indigenous knowledge systems that can be tapped and utilized, but sometimes need to be overcome. In southern Africa (and, I suspect, in the Americas too), conversely, it means much shallower traditions, but also that donkeys carry a cultural baggage of colonialism, which even today needs to be overcome before they can fulfil their potential. On the other hand, they are not part of the older tradition that excludes women from the management of large animals, so this is an advantage.

For those of us engaged in technology transfer, all this is very important ! Viva history, and even more if molecular genetics supports it.

Peta A. Jones, MSc, PhD
Donkey Power CC
Facilitation and Consultancy Services
PO Box 414
TSHITANDANI/MAKHADO
0920
South Africa
+27 cell [0]83 686 7539
tel [0]15 517 7011
fax [0]15 517 7034
asstute (at) lantic.net

-----Original Message-----
From: Biotech-Mod1
Sent: 19 June 2005 12:03
To: 'biotech-room1@mailserv.fao.org'
Subject: 60: Re: Molecular characterisation of animal genetic resources

I am Salah Galal, Professor of Animal Breeding, Ain Shams University, Egypt and ex FAO Staff on Animal Genetic Resources, Rome.

I am in agreement with Ilse Kohler-Rollefson (Message 31, June 9) in asking "should genetic uniqueness really be the key criterion for deciding which breeds we should save?". The answer in my opinion is not necessarily "yes" but it is quite useful to know that if the population you are working with is not too varied from another, then genetic progress made in one population could be safely transferred to the other without running the risk of crossing and 'diluting' the recipient population. Using molecular techniques in population distancing is quite useful and effort-saving in situations where some seemingly similar 'breeds' are scattered in the same region. Examples are the Awassi sheep breed/populations of the East Mediterranean, Barbary/Barki in North Africa and even some common breeds alleged to belong to the same root between Egypt and Turkey. If we can verify that these 'breeds' are more or less similar, joint efforts can be made to improve them jointly. The problem with breed molecular identification, in my opinion, lies in the fact that availing primers and other material and equipment needed to characterize the breeds with any degree of accuracy is a task that is too expensive for the majority of local institutions in charge of such task. Some regional coordination, possibly with international input, is required to carry out such work.

Salah Galal, Ph.D.
Professor, Animal Production Department
Faculty of Agriculture
Ain Shams University
Hadaeq Shubra 11241
Cairo,
Egypt
sgalal (at) tedata.net.eg
Tel: +202 444 1711
Fax: +202 444 4460

-----Original Message-----
From: Biotech-Mod1
Sent: 19 June 2005 12:08
To: 'biotech-room1@mailserv.fao.org'
Subject: 61: Re: Molecular characterisation of animal genetic resources

I am W. Akin. Hassan from the Department of Animal Science, Usmanu Danfodiyo University, Sokoto, Nigeria.

I have been following with keen interest the on-going debate on the application of molecular genetics to livestock development in developing countries.

First and foremost, it is important to underline the fact that, in those countries, especially those in sub-Saharan Africa, we can hardly talk of livestock producers, except a few rich individuals in cities who pick interest in livestock production mainly for prestige. The vast majority of the livestock diversities are kept by smallholders in the remote areas. These keepers have for ages been involved in low input-low output husbandry systems, paying very little or no attention to cost.

Then comes the issue of the appropriateness of animal biotechnologies under the prevailing husbandry systems. No doubt, molecular genetics has great roles to play in revolutionizing livestock production in the developing countries, but the stage is not yet set for such - for numerous reasons, including the following:

It will be worthwhile to continue the on-going phenotypic characterization of the ecotypes of various livestock and poultry species in those countries while efforts are made towards addressing the problems that presently militate against the applications of animal biotechnologies, including molecular genetics, to livestock production in the area.

W. Akin. Hassan, Ph.D.
Department of Animal Science,
Usmanu Danfodiyo University,
Sokoto,
Nigeria
akinola19 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 20 June 2005 11:37
To: 'biotech-room1@mailserv.fao.org'
Subject: 62: Fish genetic resources - Malaysia

I am Subha, a research officer attached to the Department of Fisheries, Malaysia.

It is an interesting discussion raised in this conference. Biotechnology is indeed very important to address a problem in any area, whether it is plants, forestry, animal and lastly fishes. The discussion that has been held on the importance and its potential is indeed debatable. I have to say that it is a tool for most of us, but the impact of biotechnology in selective breeding, stock improvement and characterisation has taken off in fish.

The work done by Kocher's group in tilapia by isolating microosatellites and depositing in the gene bank, continued by creating linkage maps with the possible loci, helped us in my PhD where I screened almost over 100 microsatellite primers that they designed. It helped me to characterise the various red tilapia stocks that was used in the breeding (Bhassu et al, 2004). In the tilapia study, characterisation was done using allozymes then later continued with microsatellites. The results showed that most of the fishes were inbred and had low heterozygosity levels. The phenogram was the same using both kinds of markers. In terms of laboratory to laboratory problems, I had no problem as the same primers were also used by Mather's group in Australia. We even exchanged the primers annealing temperature condition. It all depends on how you look at it. [Publications from T.D. Koscher available at http://hcgs.unh.edu/Staff/kocher/kocherpubs.html ; The Bhassu et al reference is to Bhassu S, Yusoff K, Panandam JM, Embong WK, Oyyan S, Tan SG. 2004. The genetic structure of Oreochromis spp. (Tilapia) populations in Malaysia as revealed by microsatellite DNA analysis. Biochemical Genetics 42(7-8):217-29...Moderator].

In my personal experience, I know that many people use biotechnology as a tool to address many problems, but I feel with sound knowledge on genetics (population and quantitative), breeding plays more important role in improving stocks and for conservation. Take the giant freshwater prawns project - the culture of these prawns have increased rapidly. It is an alternative source of an economically important commodity that many developing countries are looking at. I have to congratulate Dr New who came out with concise information on the freshwater prawn farming in FAO. Did it spark interest among the breeders and geneticists? I would say, yes. I am collecting the various stocks from the various riverine sources looking at their morphology and genetic make up. The breeders in Malaysia, with collaborative efforts with the WorldFish Center, is looking at genetic stock improvement of this giant freshwater prawns. Geneticists in Thailand are also working on sex identification of this prawn using AFLP markers. This biotechnology information will indeed be of importance. Research information on morphology identification, molecular characterisation is done with selective breeding. Funding you may ask? Very little. But then efforts are being made to obtain financial support. [The reference is to New, M.B. 2002. Farming freshwater prawns: A manual for the culture of the giant river prawn (Macrobrachium rosenbergii). FAO Fisheries Technical Paper 428. (ftp://ftp.fao.org/docrep/fao/005/y4100e/Y4100E00.pdf or contact FI-Inquiries@fao.org for more information). The original manual on freshwater prawn farming was written by M.B. New and S. Singholka in 1982 and translated in several langauges...Moderator].

The recent publication by Mather 2004 has shown that M. rosenbergii (freshwater prawn) is classified into two form, the western and eastern forms. We need information that we can use, as now we know that Malaysian freshwater prawns are different from the Australian freshwater prawns. This information is indeed vital for prawn breeders when they want different stocks. Of course, the importance of phylogeny may be of no importance to a farmer, but people like me, being trained as a molecular geneticist and an officer in the Department of Fisheries, could advise the farmers of its impact of importing a divergent form of the same form like. [The reference is to de Bruyn, M., J.A. Wilson and P.B. Mather. 2004. Huxley’s line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. Molecular Phylogenetics and Evolution 30:251-257. Their paper used 16S rRNA mitochondrial gene sequence data to confirm that there is an east-west grouping of the prawn, that had been noted before using morphological and allozyme data...Moderator].

The impact of biotechnology is very limited in fish, yet fantastic work has been done on the common carp and salmon. I hope the recent news like depositing of expressed sequence tags (ESTs) of the tilapia genome, headed by Kocher's group, will give advancement in our future marker assisted programs in tilapia in Malaysia and other countries.

Subha Bhassu, PhD
Research Officer
Freshwater Fisheries Research Center,
Batu Bererendam,
Melaka
Malaysia
email: subhabhassu (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 20 June 2005 11:52
To: 'biotech-room1@mailserv.fao.org'
Subject: 63: Re: Molecular characterisation of animal genetic resources

I am Miguel A. Toro from the Department of Animal Breeding of INIA (Spain).

With respect to the message of Salah Galal (message 60, June 19), I would like to point out two things:

1) Establishing that two breeds are genetically similar does not guarantee that the genetic improvement program of one of them can be applied to the other, because this depends on the existence or not of genotype x environment interaction. For example, the Holstein is a universal breed but probably a different genetic improvement program should be implemented in a tropical or in a temperate climate.

2) I cannot see ‘exactly’ how molecular markers could be used to decide if two breeds are or are not the same. First: a) molecular markers refer to neutral or non-coding genetic variation; b) it is well known that genetic distances are not very useful in this context because they ignore within breed variation. An inbred line (just because a handful of animals became isolated in a small area during a few generations) would be classified as a very different breed despite not having interest at all.

3) I am not very sure that biotechnological approaches are being used in developed countries. For example, the genetic improvement program of dairy cattle in USA is considered highly competitive, but as far as I am aware, they are not using molecular information. Or am I wrong?

Miguel Angel Toro Ibanez
Departamento de Mejora Genetica Animal
Instituto Nacional de Investigacion y Tecnologia Agraria y Agroalimentaria (INIA)
Carretera La Coruna km. 7 28040 Madrid
Spain
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 11:52
To: 'biotech-room1@mailserv.fao.org'
Subject: 64: Re: Fish genetic resources - Malaysia

This is from Ron Jones, Canada, again.

Subha Bhassu's comments (message 62 June 20) make some key points when putting our discussion into a fisheries/aquatics context. Most of the molecular/biotech work in fisheries is done on commercial or potentially commercial species, such as Subha's work done on relatedness in tilapia stocks and the giant freshwater prawn. The expense of biotech analyses for developing countries will probably mean that the priorities will focus on those important commercial applications and species (breeding, disease diagnostics, genetics for re-stocking/supplementation. Who actually benefits from this is, of course, another question. Researchers from developed countries, with robust grants, will continue to explore the marvellous historical evolutionary relationships among interesting populations. How can we apply this knowledge to reducing hunger and alleviating poverty through better design (or conservation) of aquatic systems? Where are the salinity/cold tolerant; disease resistant; fast growing; tasty; tilapia stocks?

It will always be important to determine stock origins and levels of inbreeding/introgression in founder stocks for any commercial production of aquaculture species. I think that national/international organizations can play key supportive or facilitative roles in both the governance and capacity building for genetic technologies respectively through creative co-management arrangements. It is my opinion that the conservation of aquatic genetic resources will require simultaneous applications of good in situ natural resource governance AND strategic applications of technology to characterize, protect and intelligently use these genetic resources. There are niche roles to play by each level of government, academia and NGOs, which will require collective creativity and willingness to implement. I think academic researchers will have to venture out of the lab (we can publish your results later) and find some interesting genetic problems on which to apply this technology thereby rekindling scientific explorations in solving key problems related to hunger, poverty and biodiversity.

It was interesting to hear that the 2 (east/west) stocks of giant freshwater prawn were first determined by less charismatic methods of morphology and allozymes. We really do have to take a hard look why we choose a specific technological pathway.

Ron Jones
Consultant,
International Development Research Centre (IDRC)
Ottawa,
Canada
channastri (at) netscape.net

[The reference in the last paragraph is to the results mentioned in Subha's message showing that M. rosenbergii (freshwater prawn) is classified into two form, the western and eastern forms. While that 2004 paper, by de Bruyn et al. in Molecular Phylogenetics and Evolution, is available for subscribers only, a 2003 article in Naga (the WorldFish Center Quarterly) by P.B. Mather and M. de Bruyn, entitled "Genetic diversity in wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii): Implications for aquaculture and conservation" summarises the results, writing "We, therefore, set out to document genetic diversity in wild M. rosenbergii stocks from across the natural range from southern Asia, to SE Asia and into the Asia-Pacific region. Molecular genetic analysis of a 472 base-pair segment of the 16S rRNA mtDNA gene, sampled from individuals representing 18 wild populations of M. rosenbergii, supports previous allozyme and morphological work that has identified two distinct forms of M. rosenbergii (De Man 1879; Johnson 1973; Lindenfelser 1984). The boundary between the two major clades corresponds with Huxley’s extension (Huxley 1868) of Wallace’s Line (Fig. 2), a well-known biogeographical break that runs through Indonesia" (http://www.worldfishcenter.org/naga/naga26-4/pdf/naga-26-4-article1.pdf) ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 14:57
To: 'biotech-room1@mailserv.fao.org'
Subject: 65: Re: Molecular characterisation of animal genetic resources

I am M. S. Tantia, Senior Scientist working at National Bureau of Animal Genetic Resources, Karnal, India.

I certainly agree that molecular characterization with microsatellite markers, which are mostly neutral to selection, are excellent tools to study population parameters and identify unique populations/breeds requiring efforts for their improvement and conservation. But in most of the developing countries, like India, due to small size of the animal holding (1 to 3 for large ruminants), no field recording systems exist on the ground. The population sizes at organized herds for certain breeds are also very small. In such a situation, the molecular data can effectively be utilized for diversity studies but, due to lack of pedigree and phenotypic records, how can we use molecular markers (marker assisted selection) for improvement of livestock?

In India, we have some naturally existing breeds/populations which have the extremes of a trait - for example, milk production. You find populations which are milch type producing on average 1500-2000 kg per lactation and, on the other hand, there are draft populations hardly producing 300-500 kg. Can we use some methodology to find quantitative trait loci (QTLs) from molecular markers in the absence of pedigree or phenotype data?

M S Tantia
Senior Scientist,
NBAGR,
Karnal 132 001,
India
mstantia (at) nbagr.ernet.in

[This conference focuses on the use of biotechnologies (including molecular markers) for the characterisation and conservation of genetic resources for food and agriculture. Methods for using markers for QTL detection or for genetic improvement are not a theme for discussion in the conference, so anyone wishing to address M.S. Tantia's questions are requested to contact him directly. Conference 10 of this Forum (entitled "Molecular marker assisted selection as a potential tool for genetic improvement of crops, forest trees, livestock and fish in developing countries", that ran from 17 November to 14 December 2003) has already addressed this area. The Background Document, 85 messages posted and the Summary Document from the conference are all available at http://www.fao.org/biotech/C10doc.htm ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 14:58
To: 'biotech-room1@mailserv.fao.org'
Subject: 66: Re: Molecular characterisation of animal genetic resources

This is Salah Galal, again. In response to Miguel A. Toro (Message 63, June 20):

You picked the wrong example - Holstein. I am talking about breeds or populations where hardly no intentional breeding programs took place and they share similar, if not the same, origins and geographical zones. These are what are sometimes called 'landraces'. Of course molecular techniques can establish with a certain degree of probability if these populations are/are not the "same".

Salah Galal, Ph.D.
Professor, Animal Production Department
Faculty of Agriculture
Ain Shams University
Hadaeq Shubra 11241
Cairo,
Egypt
sgalal (at) tedata.net.eg
Tel: +202 444 1711
Fax: +202 444 4460

[Miguel Toro (Message 63) had written
"1) Establishing that two breeds are genetically similar does not guarantee that the genetic improvement program of one of them can be applied to the other, because this depends on the existence or not of genotype x environment interaction. For example, the Holstein is a universal breed but probably a different genetic improvement program should be implemented in a tropical or in a temperate climate.
2) I cannot see ‘exactly’ how molecular markers could be used to decide if two breeds are or are not the same. First: a) molecular markers refer to neutral or non-coding genetic variation; b) it is well known that genetic distances are not very useful in this context because they ignore within breed variation. An inbred line (just because a handful of animals became isolated in a small area during a few generations) would be classified as a very different breed despite not having interest at all"...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 15:00
To: 'biotech-room1@mailserv.fao.org'
Subject: 67: DNA banks - forest genetic resources

This is E.M. Muralidharan from India again.

I had in an earlier message (Message 22, June 6) asked about the relevance of DNA banks. My interest was in the context of conservation of forest genetic resources and, more specifically, tropical forest genetic resources (much of it in developing nations) that are in danger of mass erosion due to degradation of the habitat. The situation is perhaps quite different from that of the agricultural or domesticated animal genetic resources that are being discussed more often in this conference. These areas manage to attract attention and funds for obvious reasons. On the other hand, forest genetic resources, especially that of the wild species, fail to get priority. Other than through national parks or sanctuaries, I don't see how the multitude of species (including unidentified species with unknown economic prospects for the future) can ever be preserved without incurring a huge expenditure. It thus appears that a great extent of such resources are destined to be lost for ever in the coming years. And it appears that scientists alone cannot change the scenario.

If simple, rapid and cost-effective DNA extraction and storage procedures applicable to several taxa are developed, will DNA banks be the sensible way to keep something for posterity? The primary advantage that I see here is the possibility of rapid collection, inventorizing and long-term storage of genetic material with minimal space requirements. For the same reason, I don't find the storage of leaves, eggs or other tissue parts under silica gel, cryoproservation etc. as ideal. Wherever feasible, the more conventional conservation methods would of course be used. DNA banks would also mean that the disadvantages of storing DNA (Messages 34 (June 10, Kioumars Ghamkhar) and 47 (June 13, D. Vijay)) are overcome and we presume that having DNA is better than species going extinct - leaving nothing at all. How much of a priority should this activity be given?

Dr. E.M. Muralidharan
Scientist, Biotechnology
Kerala Forest Research Institute
Peechi, Thrissur, Kerala State
680653,
India
Email: emmurali (at) kfri.org

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 15:07
To: 'biotech-room1@mailserv.fao.org'
Subject: 68: Application of biotechnology in forest genetic resources conservation

I am Alice Muchugi, a lecturer in the Department of Biochemistry and Biotechnology of Kenyatta University, Kenya, with special interest in conservation of indigenous forest tree genetic resources. I am currently a PhD research fellow at the World Agroforestry Centre (ICRAF).

I agree with the Moderator's concern that little mention has been made about forestry despite the global concern on reduced forest cover and forest genetic erosion especially in developing countries. However, the debate on biotechnology application in forestry follows the same trend of crop plants. Forest resources are threatened by the increased population as more land is taken up for settlement and farming. The problem is compounded where there is commercial exploitation of indigenous species. Again, when new forests have to be established in most of these developing countries the focus is on exotics. There is therefore a great need to think seriously about the indigenous forest genetic conservation which also happens to be a rich biodiversity habitat (for flora and fauna). There are two areas where biotechnology is being employed in conservation of the forest tree genetics.

First, molecular markers can be used to identify areas of focus in conservation of genetic diversity for specific species. Deductions on gene flow will also guide in ex-situ establishment of species in conserving diversity. Secondly, where circa-situ and ex-situ conservation have to be practiced, planting material of good genetic base is a problem for most of these indigenous species. Some have recalcitrant seeds or very little is available. Here, tissue culture techniques can play a major role in multiplication of available propagules. Suspension cultures and cryopreservation may be another aspect that can be approached in conservation (though Message 22 (June 8, E.M. Muralidharan) discourages this) as well as the DNA bank in form of plant material. [With circa situ conservation, germplasm is collected from a site and conserved in sites nearby. Geneflow is therefore a possibility between the sites, unlike ex situ conservation, where germplasm is collected from a site and conserved in a completely different site...Moderator].

Compared to temperate species, there is very [little?...Moderator] work that has been carried out on tropical tree species, where most of these developing countries fall. As already highlighted, the major limitation in its biotechnology application is in both physical and human resources. Since the floral distribution cuts across political boundaries, molecular characterization is best approached from ecological/geographical perspective. This, therefore, calls for greater collaboration among scientists within the regions in exchange of plant materials and knowledge gathered. Maybe a tropical tree biotechnology forum, if formed, can help in networking. This will finally reduce the technology cost for individual countries. I also feel that due to the pressure on loss of forest biodiversity, cheaper applications such as the RAPD markers (which are being discontinued in well developed laboratories) can still be employed in the preliminary studies to form a basis of conservation strategies. The collaboration of the Consultative Group on International Agricultural Research (CGIAR) centers and the national agricultural research systems (NARs) has also helped to improve on the capacity building problems for developing countries (I have had my MSc and PhD training under this) and should therefore be greatly fostered.

Alice Muchugi
PhD Research Fellow
Genetic Resource Unit,
World Agroforestry Centre (ICRAF)
PO Box 30677-00100
Nairobi, Kenya
tel: +254-20-7224000 Ext 4273
fax: +254-20-7224001
email: a.muchugi (at) cgiar.org
http://www.worldagroforestrycentre.org

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 15:08
To: 'biotech-room1@mailserv.fao.org'
Subject: 69: Economic value of genetic diversity measure in aquaculture

This is S.G. Tan, again, a geneticist from the Dept of Biology, Fac. Science, University Putra Malaysia.

In Malaysia, it has been found through the use of molecular genetic markers (be they protein level ones like allozymes, whenever possible or DNA markers like microsatellites, when the need arises) that the level of genetic variation is low in many cultured stocks of prawns and seabass. This has resulted in low fertility levels and abnormalities being found in them. Such information has vast economic implications because if the situation is not remedied through the introduction of more genetic variation, the cultured stocks will continue to deteriorate with time and the aquaculture industry will suffer economically. Hence, in developing countries, it does make sense to invest in genetic marker studies of economically important species even though we do not have the luxury of studying the non economic species as well at this stage of our development.

Prof. Dr. S.G. Tan BSc.(Hons. Malaya), PhD. (Hawaii),J.S.M. (Malaysia).
Professor of Genetics.
Dept. of Biology,Faculty of Science,
Universiti Putra Malaysia,
43400 UPM Serdang,
Malaysia.
email: sgtan (at) fsas.upm.edu.my
Fax: 603-86567454/89432508

-----Original Message-----
From: Biotech-Mod1
Sent: 21 June 2005 17:38
To: 'biotech-room1@mailserv.fao.org'
Subject: 70: Molecular markers - genetic distances - livestock

Again from Hans Lenstra from Utrecht, Netherlands.

I would like to respond to the discussion of Salah Galal and Miguel Toro [Messages 60 and 66...Moderator] on the basis of observation on datasets of cattle, sheep and goat (European Union (EU) Resgen project (CT98-118) and EU Econogene project).

Miguel Toro is right that a large genetic distance often mainly reflects genetic isolation - examples are Danish red cattle, a subpopulation of Betizu cattle, Mallorquina cattle, fighting cattle. However, the large genetic distance of Italian Chianina cattle from other breeds seems to reflect an ancient history. Despite its reputation, Holstein populations are quite heterozygous and genetic distances to other breeds are not at all extremely long. Genetic isolation is not at all restricted to highly selected breeds and is also common for island breeds (e.g., Greek Skopelos sheep) or may be caused in the wild by habitat fragmentation.

On the other hand, short genetic distances may very well confirm that populations are closely related, if not identical, like German Brown Bavaria and German Brown Wuertemberg, or the Swiss Evolene and Eringer.

For the non-selected cattle breeds, a zebu component may create a large genetic distance, but as pointed out by Salah Galal, breeding is not strict and there may be considerable overlap between breeds.

In general, in all three species we see a clear difference between phenotypic distinctness and molecular diversity. North-Western European breeds are clearly distinct with long genetic distances. However, allele richness as a measure for molecular diversity is clearly higher in South-Eastern Europe and still higher in Asia, where uniqueness of breeds is less conspicuous (but certainly valuable, like local adaptation and disease resistance). So phenotypic distinctness and molecular diversity may both be valid reasons for conservation, but are often negatively correlated.

Dr. J.A. Lenstra
Faculty of Veterinary Medicine
Yalelaan 8
3584 CL Utrecht
Netherlands
+31-30-2534992, fax 2518126
at home +31-30-6375622
J.A.Lenstra (at) vet.uu.nl

-----Original Message-----
From: Biotech-Mod1
Sent: 22 June 2005 15:01
To: 'biotech-room1@mailserv.fao.org'
Subject: 71: Molecular markers - Populations the same? - Inbreeding

This is Miguel A. Toro, again.

1. In Message 65, M.S. Tantia says: "I certainly agree that molecular characterization with microsatellite markers, which are mostly neutral to selection, are excellent tools to study population parameters and identify unique populations/breeds requiring efforts for their improvement and conservation".

I have two comments: a) Which are ‘exactly’ these tools and how should be applied?
b) I think that the important parameters to consider are the phenotypic ones: adaptation to specific environments, possession of traits of economic importance or unique traits, cultural or historical values, etc..(see "Genebanks and the conservation of farm animal genetic resources", 1999, edited by J.K. Oldenbroek). To use molecular markers is not harmful as long as we recognize its subordinate relevance in this context.

2. In Message 66, Salah Galal says: "Of course molecular techniques can establish with a certain degree of probability if these populations are/are not the "same". "

My comment is again: Are there molecular techniques that allow us to establish objectively that two populations are/are not the same with a certain probability? Which are these molecular techniques ?

3. In message 69, S.G. Tan says: "In Malaysia, it has been found through the use of molecular genetic markers (be they protein level ones like allozymes, whenever possible or DNA markers like microsatellites, when the need arises) that the level of genetic variation is low in many cultured stocks of prawns and seabass. This has resulted in low fertility levels and abnormalities being found in them. Such information has vast economic implications because if the situation is not remedied through the introduction of more genetic variation, the cultured stocks will continue to deteriorate with time and the aquaculture industry will suffer economically. Hence, in developing countries, it does make sense to invest in genetic marker studies of economically important species".

My comment is the following: Inbreeding depression is well known since 1900 (at least) and, in all conservation (and genetic improvement) programs in domestic species, precautions are taken to avoid this problem. In general, the optimal strategies require the knowledge of pedigree, but some other more simple things can be done (for example, subdividing the population and interchanging individuals among them). Obviously, these things are well established and were utilized before molecular markers existed. Also, from experimental work (with mice, Drosophila, pigs, trout etc.) it has been many times verified that if you do deliberate inbreeding (by brother-sister mating, for example) you will observe the catastrophic consequences of inbreeding. I cannot see what molecular markers can add to this huge amount of information (obviously in some of these experiments people also observe a decrease in the heterozygosity of microsatellites). On the other hand, molecular markers hardly can be useful in the management of a conservation program. However, I do not want to be totally negative. I think that molecular markers could be useful in some settings to obtain or verify pedigree information (by paternity analysis for example) that is the crucial information for a correct management of a conservation program.

Miguel Angel Toro Ibanez
Departamento de Mejora Genetica Animal
Instituto Nacional de Investigacion y Tecnologia Agraria y Agroalimentaria (INIA)
Carretera La Coruna km. 7 28040
Madrid
Spain
Tel: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es

[As part of an European Union (EU) Concerted Action, 3 meetings were held in 1997 and 1998 in which several aspects of conservation of genetic variation in farm animal populations in Europe were presented and discussed in order to develop guidelines for the cryoconservation of farm animal genetic diversity. Much attention was paid to the integration of the ex situ conservation in a genebank in programs for in situ conservation in EU circumstances. Geneticists from Scotland, Norway, Finland, France, Italy, Spain, The Netherlands and from FAO participated in these meetings. In a fourth meeting in 1998, they synthesised these aspects and discussions for publication in the 8-chapter book edited by J.K. Oldenbroek, referred to near top of the message - available at http://dad.fao.org/en/refer/library/reports/GenebanksNL.pdf ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 23 June 2005 10:35
To: 'biotech-room1@mailserv.fao.org'
Subject: 72: Markers - Characterisation - Biopiracy

This is from Vladimir Magalhães. I'm a biologist and lawyer, graduated at University of São Paulo (USP) in Brazil. I'm a coordinator of a postgraduate environmental law course. My PhD thesis at USP was about "Intellectual Property, Biotechnology and Biodiversity", where I discussed that patents on DNA natural sequences and other natural biological molecules, even when they are isolated from the animal or human tissues, are discoveries and not inventions, because there is not human creative activity in the natural chemical biological structures which are described, like DNA, and patented in the United States and the European Union (EU).

Section 2 of the Background Document says that characterisation, using example molecular markers, can be important for promotion and control of bioprospecting. [The relevant part of Section 2 reads "Characterisation of genetic resources goes hand in hand with their conservation as it is fundamental both for understanding what is being conserved and for choosing the genetic resources that should be conserved. Characterisation enables us to identify the key features (both the strengths and weaknesses) of the available genetic resources, and this knowledge can also be used to develop breeding programmes for sustainable use of the genetic resource to harness and/or disseminate the positive attributes identified in the population. Characterisation can also play an important role regarding issues of access to, and benefit sharing from, agricultural genetic resources, as well the promotion and control of "bioprospecting" (i.e. biodiversity prospecting, the search for commercially valuable compounds, substances or genetic material in nature). If a country has characterised its genetic resources, it should be appropriately positioned to develop and implement conservation strategies for targeted species, and to promote and oversee any potential commercial or other enterprises arising from the knowledge generated; to protect the resources (or any of their products) from inappropriate bioprospecting, including that carried out by foreign companies or countries; and to negotiate appropriate compensation for use of these resources by third parties, be they national or foreign"...Moderator].

It's virtually impossible to characterize every natural biological molecule with real or potential commercial value in the Brazilian biodiversity, for instance, because our biodiversity is very huge and we even don't know all the plant, animal and microrganism species we have in our ecosystems. And we do not have money to do it well. The ecosystems are being destroyed for an agricultural model using monocultures for exportation to the first world countries (as 200 years ago).

Sure, it is very important do these characterization. But it is more important to discuss what is behind the international agenda. It's clear the movement of developed countries (USA and EU) to monopolize the biological resources of developing countries through the patent law for using them in their biotechnology industries.

The question is to criminalize in the developed countries biopiracy in other countries using an international agreement to define a international crime of biopiracy against the sovereignty of the countries over their biological resources as defined by the Convention on Biological Diversity. I doubt whether USA and EU countries would accept to sign a agreement like this but the countries with megadiversity would forbid enterprises from these countries to access their biodiversity if they do not sign the agreement.

In this moment, the role of biotechnology would be very important as a way to probe that a biological material described in a patent had an origin in the biopiracy done in a determinate country, in the case of endemic species material, or in some countries, when these biological materials exist in more than one country. It is related to agricultural activities because many of the biological materials subject to biopiracy are utilized for agricultural biotechnology.

The FAO would be a forum to begin to discuss the importance of criminalization of biopiracy as an international crime like drugs trade and terrorism. The use of biotechnology to conserve the biodiversity cannot be considered as a solution but only a palliative when the biodiversity in the developing countries is being destroyed by an economic model built by developed countries, through the International Monetary Fund (IMF), for instance, based on the economic exploitation of developing countries and their natural resources. As always, since the Spanish began to plunder the Incas and Mayas nations. In these models, the developing countries are supposed to have a monoculture agriculture for export with low economic value, to have industries activities that are highly polluting, and sending the semi-manufactured products to the developed countries to do the less polluting activities which export the final products with higher aggregated economic value to the developing countries (I'm simplifing to show the big picture of this questions). In this way, the commercial balance will always favour the developed countries while the developing countries will never have economic resources to develop their technologies, including biotechnology, what is not in the developed countries interest, because their higher developed technology makes the difference in the international commerce.

Vladimir Magalhães
São Paulo University,
São Paulo,
Brazil.
vlad (at) usp.br

-----Original Message-----
From: Biotech-Mod1
Sent: 23 June 2005 10:39
To: 'biotech-room1@mailserv.fao.org'
Subject: 73: Diversity and conservation

It is again D. Vijay from India.

The conservation of genetic diversity has a lot of economic value. Even though it is not having direct impact, it is the basic source for the further development of the existing species as through conservation itself we can store the existing diversity from extinction. All means of possible techniques should be adapted both for assessment and preservation of existing diversity i.e. either through seed banks, sperm banks, DNA banks, cryopreservation etc. Already there was lot of damage to the natural diversity and now it is high time not only to preserve but to use the conserved diversity. Both conservation and usage should go hand in hand. Certainly molecular markers will help in this aspect, even though they have their own lacuna. The usage of new technologies like DNA bar-coding (Message 23, June 8, from P.K. Gupta) have to be given importance along with time tested techniques like molecular markers.

The modern techniques are certainly resource drenching and it is difficult for the developing countries to work on them. But with the advancement of technology we have to move along with it. Developing countries cannot stay aside from the mainstream knowledge as most of the diversity and its end users belong to them. The international organisations like CGIAR institutes and UN institutes are lending their helping hand in this extent, let them try to hold it and move along.

It's the right time to move together and for framing international guidelines for the use of these technologies. I wish this conference may provide an outcome in this direction e.g. some concrete steps like zeroing a suitable marker and steps towards establishing the universal data bases etc.

Vijay D., PhD
Scientific Assistant
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012,
India
Mobile: 09868412855
E-mail: vijaydunna (at) gmail.com
URL: http://www.geocities.com/vijaydunna

-----Original Message-----
From: Biotech-Mod1
Sent: 23 June 2005 10:44
To: 'biotech-room1@mailserv.fao.org'
Subject: 74: Capacity building // Decentralised banks

I am Dr P S Janaki Krishna, working as a ‘consultant’ in the Andhra Pradesh Netherlands Biotechnology Programme being implemented at the Biotechnology Unit, Institute of Public Enterprise, Hyderabad, India.

I always enjoy the FAO e-mail conferences wherein participants come up with rational views. I have been following the excellent messages placed during the first half of the conference. The issue of characterization and conservation of species are, although very important in the context of developing countries, rarely considered as priority problems. More often than not, enhancing crop/animal productivity is considered as a felt need and the necessity of conservation of some of the species is given a priority only when particular species became endangered. (Note: Identification and deposition of large diverse genetic base is equally a priority issue for breeding better varieties). This is one of the reasons why agricultural biodiversity is declining and many of the landraces are being lost in developing countries. We become alert to the situation only when our kitty is going to be emptied. It’s fortunate that FAO has come up with this conference and thrown some light on it.

Biotechnological tools like ‘molecular markers’ and ‘in vitro conservation’ can play a great role in characterisation and conservation of genetic resources. However, capacity building and availability of financial resources are major stumbling blocks in harnessing the potential of these expensive tools. Firstly, it is high time that massive capacity building programmes in these areas are conceived at national and international level. Secondly, establishment of decentralized DNA/germplasm/seed banks are more economical and feasible rather than establishing one/two centres at global level. The international and national agencies should give priority to setting up local genetic resources units at district/state level. However, complying with the intellectual property rights on such materials is yet another important issue to be considered in the new patent regime.

P S Janaki Krishna,
Consultant,
Biotechnology Unit, Institute of Public Enterprise,
Hyderabad - 500 007,
India
Email: jankrisp (at) yahoo.com
Phone: 040 - 27097018/27098148

-----Original Message-----
From: Biotech-Mod1
Sent: 23 June 2005 11:20
To: 'biotech-room1@mailserv.fao.org'
Subject: 75: Re: Molecular markers - Populations the same? - Inbreeding

My name is Menchie Ablan and I am with the WorldFish Center based in Penang, Malaysia. I've used molecular markers of marine fish, mainly to see where it can help with fisheries questions on stock structure, restocking programs, marine protected area design and connectivity. I am slowly diversifying into cultured fish, but not yet. We've had cases where molecular genetics provides answers, others where it simply validates observation of the phenotype, local knowledge, value judgements, or even gut feel. And yes, sometimes its usefulness can be forced.

Population genetic models define how genes have to be organized if there was one single population. By testing our observed gene frequencies (based on molecular markers) of populations aginst the Null Hypothesis of unity, we determine if populations are significantly different from one another. This analysis compares population parameters. The terms "same" or "different" here do not refer to phenotypic traits. Because of that, such molecular marker analyses are not as meaningful for cultured (farmed) populations as for wild populations. For cultured populations, an individual from the "same" population as one that grows fast should also grow fast. For wild populations, though, "same" and "different" refer to the way in which individuals of the population interact with the environment and continue to do so. It defines the spatial dimension of stocks. For restocking programs, it provides guidance for where the broodstock should come from.

More recent analysis methods, however, allow assignment of individuals to populations. That is different from comparing populations. With these analyses, we look at an individual's genotype and compute a probability that it is generated by the allele frequencies of population A, B or C using maximum-likelihood or a Bayesian approach. The analysis provides a different perspective because it says individual 1 is most likely to come from population A with an associated probability as opposed to population B with an associated probability. A cut off for the probability value can be set (e.g. 0.9 or 0.8) to say the population assignment is statistically supported. Maybe you were looking for something like this, Dr Toro ? [Message 71, June 22..Moderator] We've started using this analysis with wild stocks as an alternative way to determine population structure and assess migration. I have no idea how well it will work for cultured species with a long histories of domestication. Some useful references are given below.

Ma. Carmen A. Ablan (Menchie)
Head, Molecular Genetics Laboratory
WorldFish Center Jalan Batu Maung, Batu Maung
Bayan Lepas, Penang 11900
Malaysia
m.ablan (at) cgiar.org

Pritchard JK, Stephens M and Donelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155. pp 945-959 [Available at http://www.genetics.org/cgi/reprint/155/2/945 ...Moderator].

Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin A and Estoup A. 2004. Geneclass2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95(6):536-539

Manel1 S, Gaggiotti OE, Waples RS. 2005. Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology and Evolution 20(3):136-142

-----Original Message-----
From: Biotech-Mod1
Sent: 23 June 2005 16:48
To: 'biotech-room1@mailserv.fao.org'
Subject: 76: Re: DNA banks - forest genetic resources

This is Kioumars Ghamkhar from Australia, again.

E.M. Muralidharan (message 67, June 21) has mentioned that there is no priority for conservation of the genetic resources of the wild species of the forests (trees). I agree with him that there is not enough effort and funding for the conservation of forest genetic resources. I think that DNA banks can play a very important role in conserving the genes in a condition that genetic erosion is happening so fast and the lack of sufficient funding does not let us conserve these precious sources of diversity. When we are not able to conserve the trees where they are (I wish we could, as an evolutionist), there is no other option than ex situ conservation and it can work either by seed banks, storing tissues, or DNA banks. Doing any of these is better than nothing.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 23 June 2005 16:53
To: 'biotech-room1@mailserv.fao.org'
Subject: 77: Simpler techniques for molecular characterization of forest trees

This is Alice Muchugi from Kenya, again.

A few points I am still pondering on - still on molecular characterization of forest trees and their conservation:

In my previous message (nr. 68, June 21), I mentioned the use of random amplified polymorphic DNA analysis (RAPD) and other simpler techniques, such as isozymes, in molecular characterization of tropical tree species. Apart from equipment costs, RAPD offers a fast method of assaying large sample sizes of previously unstudied taxa. Despite several authors giving comparable results of RAPDs and other techniques and recommending their use (among them Kjolner et al, 2004, Molecular Ecology, 13, 81-86; Garcia et al, 2004, Genetics and Molecular Biology, 27, 579-588), I am saddened that renowned molecular genetics journals refuse to publish work studied using RAPDs even as preliminary results. The volumes of work done and published in the 1990s attest to the reliability of RAPD analysis (Hadrys et al, 1992, Molecular Ecology, 1, 55-63). This is placing scientists in the developing world with simple labs in a tricky position; we would love to employ the modern state of art sequencers but financial limitations will not allow it. What is the way out then considering the need to study these taxa before we lose them on the earth's surface? I see a position where, by the time we acquire the current technology in the developed world laboratories, again they will have written off what we have taken so long to acquire!

Secondly, I am also wondering what would be the best way of properly conserving the characterized forest tree germplasm apart from 'protected reserves'. I know bringing forest on farms is being greatly advocated but this is only for species with promising uses that are already known. What of the unknown ones and those with less valued uses? Have botanical gardens worked well in developed countries? If so, can we create regional ones within the tropics then with combined resources from several countries? For most crops which are mainly annuals, collected germplasm can be multiplied with ease. Forest trees have longer lifespans and will therefore take long to mature. This is a drawback too as the developing countries may not have the back up for the research continuity. Just thinking out loud about how we can utilize biotechnology to save our forest genetic resources.

Alice Muchugi
PhD Research Fellow
Genetic Resource Unit,
World Agroforestry Centre (ICRAF)
PO Box 30677-00100
Nairobi,
Kenya
tel: +254-20-7224000 Ext 4273
fax: +254-20-7224001
email: a.muchugi (at) cgiar.org
http://www.worldagroforestrycentre.org

[The articles referred to here are
1) Kjølner, S., Såstad, S. M., Taberlet, P. and Brochmann, C. (2004). Amplified fragment length polymorphism versus random amplified polymorphic DNA markers: clonal diversity in Saxifraga cernua. Molecular Ecology 13 (1), 81-86. The anstract ends: "We conclude that although AFLP analysis is superior in terms of efficiency, RAPDs may still be used as reliable markers in small low-tech laboratories".
2) Antonio A.F. Garcia1, Luciana L. Benchimo, Antônia M.M. Barbosa1, Isaias O. Geraldi, Cláudio L.Souza Jr. and Anete P. de Souza. 2004. Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genetics and Molecular Biology, 27, 4, 579-588 http://www.scielo.br/pdf/gmb/v27n4/22428.pdf
3) Hadrys, H., M. Blaick, and B. Schierwater. 1992. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Molecular Ecology 1:55-63...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 23 June 2005 17:19
To: 'biotech-room1@mailserv.fao.org'
Subject: 78: Re: Capacity building // Decentralised banks

This is Kioumars Ghamkhar, again.

In agreement with Janaki Krishna (message 74, June 23), I believe that state and national genetic resource centres (GRCs) must be established but there must be a regional director for each region comprising up to 10 countries to coordinate these centres and assure the end users that there is enough interaction among these centres. These coordinating centres must be funded by international organisations such as FAO and IPGRI/GCP. Training and capacity building can be achieved by making connections between the researchers from developing countries who are working and living in the developed world and who are interested to serve their original countries and/or cooperate with the researchers in their original countries. The researchers in these local/national GRCs can then be trained either in the homeland or in the regional offices on the characterisation (either conventional or molecular) and the data will be saved in the national centres with a backup in the regional centres or the mother organisations (i.e IPGRI or FAO).

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

[Just to give a bit more background to some of the acronyms mentioned above and that have been used frequently throughout this conference:
The Food and Agriculture Organization of the United Nations (FAO) is an inter-governmental organization representing 187 member countries plus the European Union (http://www.fao.org/UNFAO/about/index_en.html).
The International Plant Genetic Resources Institute (IPGRI) is one of the 15 research centres supported by the Consultative Group on International Agricultural Research (CGIAR) (http://www.ipgri.cgiar.org/index.htm).
The CGIAR is an informal association of 63 members that supports agricultural research and related activities of an international public goods nature carried out by 15 autonomous research centres. The CGIAR partnership includes 24 developing and 22 industrialised countries, 4 private foundations and 13 regional and international organisations that provide financing, technical support and strategic direction. FAO, the International Fund for Agricultural Development (IFAD), the United Nations Development Programme (UNDP) and the World Bank serve as cosponsors of the CGIAR (http://www.cgiar.org).
In 2003, the CGIAR approved for implementation 3 pilot Challenge Programmes (defined as a "time-bound, independently-governed program of high impact research, that targets the CGIAR goals in relation to complex issues of overwhelming global and/or regional significance, and requires partnerships between a wide range of institutions in order to deliver its products"). One of them, the Generation Challenge Programme (GCP), aims to "harness the rich global heritage of plant genetic resources and create a new generation of crops that meet the needs of resource-poor people" (http://www.generationcp.org/index.php) ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 24 June 2005 13:22
To: 'biotech-room1@mailserv.fao.org'
Subject: 79: Re: Simpler techniques for molecular characterization of forest trees

This is D. Vijay again

This is in reply to Alice Muchugi's message (message 77, June 23). I agree that random amplified polymorphic DNA (RAPD) is comparable with the other techniques but its important drawback is the absence of reproducibility, as the technique itself implies it is a random technique and its sensitivity to chemicals and conditions is also another factor. In general, the decamer primers used in RAPD have a lower annealing temperature thus in such low stringent conditions the reproducibility is doubtful. With the advancement of technology, new techniques which are more robust, reliable and reproducible have been developed and we have to adopt them. Even the articles which Alice Muchugi mentioned have references for the non reproducibility of RAPD markers (e.g. Neale and Harry, 1994; Demeke et al., 1997; Karp et al., 1997) and the excerpt from Garcia et al, 2004, Genetics and Molecular Biology, 27, 579-588 “Our results indicate that, apart from the RAPD markers, the other DNA marker systems provided consistent information for diversity studies on tropical maize populations and produced genetic distance estimates which were in good agreement.” Thus, this is the main reason why the leading journals are not accepting the RAPD data. [In RAPD analysis, DNA primers of an arbitrary 10 base pair sequence (decamer) are generated and the polymerase chain reaction (PCR) is used to amplify DNA segments in the genome that are flanked by sequences which anneal (pair with) to the primers...Moderator].

I agree that funding is the main problem for scientists in the developing world but use of outdated technology because of its low cost is not the answer. Here, we should take the help rendered by several international organisations to the developing world. Another important aspect is the concentration of resources rather than their excessive distribution - like use of common laboratories/facilities rather than individual laboratories, so that we can really work out something productive.

Coming to the conservation of forest genetic resources, as E.M. Muralidharan said earlier in his message (message 67, June 21) the usage of DNA banks could be helpful along with other methods of conservation like seed banks, gene sanctuaries, circa-situ and ex situ conservation (Alice Muchugi, message 68, June 21).

Vijay D., PhD
Scientific Assistant
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012,
India
Mobile: 09868412855
E-mail: vijaydunna (at) gmail.com
URL: http://www.geocities.com/vijaydunna

References used in text:
- Neale DB and Harry DE (1994) Genetic mapping in forest trees: RFLPs, RAPDs and beyond. Ag Biotech News Inf 6:107N-113N.
- Demeke T, Sasikumar B, Hucl P and Chibbar RN (1997) Random Amplified Polymorphic DNA (RAPD) in cereal improvement. Maydica 42:133-142.
- Karp A, Edwards K, Bruford M, Vosman B, Morgante M, Seberg O, Kremer A, Boursot P, Arctander P, Tautz D and Hewitt G (1997) Newer molecular technologies for biodiversity evaluation: Opportunities and challenges. Nature Biotechnol 15:625-628.
- Antonio A.F. Garcia, Luciana L. Benchimo, Antônia M.M. Barbosa, Isaias O. Geraldi, Cláudio L.Souza Jr. and Anete P. de Souza. 2004. Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genetics and Molecular Biology, 27, 4, 579-588 http://www.scielo.br/pdf/gmb/v27n4/22428.pdf

-----Original Message-----
From: Biotech-Mod1
Sent: 24 June 2005 13:27
To: 'biotech-room1@mailserv.fao.org'
Subject: 80: Re: Simpler techniques for molecular characterization of forest trees

Just answering Alice Muchugi's concern (message 77, June 23):

I suggest inter-simple sequence repeat (ISSR) techniques, as I did in my previous messages. It is more efficient, still cheap and it is not based on random selection of primers.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

[For more information on ISSR markers, see Kioumars' message 28, June 9...Moderator]

-----Original Message-----
From: Biotech-Mod1
Sent: 24 June 2005 13:31
To: 'biotech-room1@mailserv.fao.org'
Subject: 81: Re: Molecular markers - Populations the same? - Inbreeding

This is S.G. Tan, geneticist, Dept of Biology, Faculty of Science, Univ. Putra Malaysia.

With reference to message 71 (June 22) from Miguel Toro, I totally agree with him that inbreeding depression is a well known phenomenon. However, unfortunately many of our aquaculturalists seem to be unaware of it or choose to ignore it. They usually also do not keep breeding records. Thus, it is often a surprise to them when molecular typing results show that their problem stocks are inbred. After being shown the molecular typing results, then only will they follow the suggestion that they do outcrossing to improve their stocks. Such is often the reality on the ground level in developing countries.

Prof. Dr. S.G. Tan BSc.(Hons. Malaya), PhD. (Hawaii),J.S.M. (Malaysia).
Professor of Genetics.
Dept. of Biology,Faculty of Science,
Universiti Putra Malaysia,
43400 UPM Serdang,
Malaysia.
email:sgtan (at) fsas.upm.edu.my
Fax:603-86567454/89432508

-----Original Message-----
From: Biotech-Mod1
Sent: 24 June 2005 17:22
To: 'biotech-room1@mailserv.fao.org'
Subject: 82: Animal genetic resources - Documentation, evaluation, conservation and utilization

I am Mahmoud Abdel Aziz, Professor of animal breeding and genetics, Alexandria University, Egypt. This is my second contribution to the conference.

Work needed for the future:

The complete study of animal genetic resources involves documentation, evaluation, conservation and utilization. In developing countries, I assume there is no systematic efforts that have been made so far to ensure collection and conservation of animal genetic resources. I also assume that most research work has been conducted on experimental herds of research centers and universities. Experimental data are completely different from field data. Although the former should be more accurate and organized, they are small in number. Therefore, the results and recommendations obtained from experimental herds cannot be applied and generalized on field data. In my opinion, comprehensive breeding plans should be developed. These plans should broadly fall under the following functions: 1. Identification and classification of native breeds based on ecological, genetic and economic criteria. 2. Preservation and conservation 3. Utilization.

1. Documentation: There may be a great deal of information on the distribution, population number and production performance of the various types of livestock. However, much of this information is not readily available to research workers because it is unpublished or published in local documents, reports and journals that have a very restricted and limited distribution. It is imperative that this information be collected and collated in a readily available form to identify gaps of knowledge, and areas where research efforts should be maximized, to fully document productivity of local strains and to assess their adaptation to specific climate-management-production systems to ensure that such strains are not displaced by so-called improved breeds (exotic breeds and crosses) before their present or potential value is known, to allow research workers to know the extent of information in their area of interest, and hence, to minimize the chance of repetition and to allow planners and administrators to make rationale decisions with regard to national development programs to maximize rates of improvement. There is no room for complacency, and the need for action is urgent.

2. Evaluation: While documentation will provide basic information on the indigenous types of livestock, there is a vital need for comparative evaluation studies. The conditions under which such evaluation is made must be the normal environment. Further evaluation should be performed in a potential environment. Such conditions might be available on experimental stations or larger commercial enterprises. It should be noted that large enterprises are basically established on importing exotic breeds, with no attention given to native livestock. The evaluation experiments must be carried out to a properly designed and prepared plan. Evaluation must be made on total performance, including not only productivity measures but also reproductive rate, mortality and disease resistance. Overall economic merit should also be considered. Studies on biochemical genetic polymorphisms are one of the ways to study the population in order to express their genetic differences and/or similarities by detection of alleles that are genetically conserved during the evolution process. Based on the expected results, native animals can be judged, evaluated and then, morphological, conformation and production standards ought to be established for each.

3. Conservation: The task of conservation of livestock is very complex problem. In any developing country, I assume that 90% of the animals are owned by small farmers. In addition, socio-cultural conditions make the problem more complicated. Under these circumstances, it is necessary to identify individuals, families and groups of specific genetic importance. Individuals that show promise for selecting breeding should be conserved by appropriate means. They must be maintained in an adequate number in well managed units. Distinctiveness is a difficult quality to define. A breed can be defined as a population which conforms to stipulated standards, which breed true for type, and which is distinct from other breeds. There are no recognized measures of distinctiveness. There are two questions that need answers. Are local breeds worth conserving ? Are local breeds in certain region similar? Small farmers or farmers of limited resources are abundant in any developing country. They are easily visible. They are located in remote areas lacking the necessary infrastructure, and hence, the exposure to modern technology. There should be some consideration to the small farmers who keep the majority of livestock resources.

4. Utilization: In developing countries, there is not any breeding program operating nationwide for improving productivity of any livestock species. It is necessary to design breeding programs for that purpose. These programs require the rapid assembly and evaluation of large amount of information. Its full development depends on the evaluation of data processing machinery and analytical methods. However, the environment may adversely affect the design aspects in two aspects: a) There may be severe limitations to animal productivity by a combination of climate, nutrition, health, and management practices. b) The infrastructure which supports such programs is entirely lacking. Difficulties of cost, literacy, communication may greatly inhibit the consistent operation of these programs. Both aspects must be taken into consideration in designing the program. Improved local populations must be initiated from within. This naturally requires a domestic selection program. Any crossbreeding strategy may be required at some point in the program, but it must not replace it. The genetic model underlying the selection program requires a knowledge of heritabilities, genetics and phenotypic correlations, phenotypic variances and appropriate economic weights. A key element in the implementation of any selection scheme is the new breeding and reproduction technologies including, of course, artificial insemination.

Mahmoud Abdel Aziz
Department of Animal Production
Faculty of Agriculture
University of Alexandria
Alexandria,
Egypt
fassad9 (at) yahoo.com

[Further messages on this subject should focus more on the potential role that biotechnology can play for the characterisation/conservation of the animal genetic resources...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 26 June 2005 13:49
To: 'biotech-room1@mailserv.fao.org'
Subject: 83: Re: Capacity building // Decentralised banks

I am Sylvia Uzochukwu from the Biotechnology Center of the University of Agriculture, Abeokuta, Nigeria.

I agree with Kioumars Ghamkhar (Message 78, June 23) that capacity building should feature strongly in any talk of modern biotechnology in developing countries and that international bodies should be interested in funding these training activities.

What obtains now is that the big funding bodies are interested in research proposals in biotechnology and will give preference to any such proposals from developing countries, but they are not interested in enabling the native scientists in developing countries to come up with such proposals. By enabling, I mean, making it possible for these scientists to re-train themselves and get to know what the new technology is all about before they can articulate research proposals that will use the technology to solve local problems.

In our center, we are doing what I think the Kioumars is suggesting: running short training courses to teach our scientists basic molecular biology techniques. We keep writing for support funds, but nobody wants to listen to training proposals, only research proposals. We are hoping this will change.

Dr. Sylvia Uzochukwu
Acting Director and Associate Professor
Biotechnology Center
University of Agriculture
Abeokuta,
Nigeria
E-mail: suzochi (at) yahoo.com
Phone: +234-803-353-1178

-----Original Message-----
From: Biotech-Mod1
Sent: 27 June 2005 11:46
To: 'biotech-room1@mailserv.fao.org'
Subject: 84: Re: Capacity building // Decentralised banks

I am Emma K. Sales, again, of the University of Southern Mindanao, Philippines.

This is in response to message 83 (June 26) of Sylvia Uzochukwu. I agree that there is really a need for scientists from developing countries to be regularly updated on the current trends and innovations in biotechnology through capacity building. I applaud and am pleased to inform everybody of the innovations done by the Asian Maize Biotechnology Network (AMBIONET). AMBIONET is a collaborative research and training network that was established to strengthen the biotechnology capacity of national maize research programs in Asia. Most scientists from member countries were trained on the applications of biotechnology tools. The network also conducted a proposal development workshop - in that way, the participating members were trained in how to write research proposals for fund/grants. Also through these initiatives, member scientists were able to establish our own biotech labs which opened doors and funding opportunities as well as linkages with other maize scientists in Asia. [Some of the molecular marker characterisation work carried out through AMBIONET was previously mentioned in Message 42 (June 10) by Marilyn Warburton...Moderator].

In this regard, I'm calling the attention of concerned scientists from developed countries to spearhead the same innovations especially for livestock. From the exchange of ideas and comments, I think there is a need to do the same network collaboration so that livestock research can move in the less developed and developing countries like the Philippines. As far as I know, the Philippines does not have an existing biotech or molecular work on livestock. As had been pointed out, the developing countries are swamped with new breeds of livestock and poultry but nothing has been done to preserve and conserve the native breeds.

Emma Sales
Department of Plant Breeding and Genetics,
University of Southern Mindanao,
Kabacan, 9407
Cotabato,
Philippines
ekalaw (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 27 June 2005 11:47
To: 'biotech-room1@mailserv.fao.org'
Subject: 85: Re: Capacity building // Decentralised banks

This is Kioumars Ghamkhar, again.

In response to Sylvia Uzochukwu (message 83, June 26), although I am not writing on behalf of any organisation, I would like to mention that there are yearly training programs in Africa, Asia, and Latin America covering a wide range of activities, from research proposal writing to molecular characterisation, marker assisted selection, and bioinformatics. I suggest having a look at Carmen de Vicente's message and the links therein and also the Generation Challenge Program's (GCP) website to get some idea about what is going on. However, we should not misunderstand the message. The message is that GCP and similar programs are committed to helping the developing countries for capacity bulding but we should not expect them to plan, organise, fund, practice, and deliver everthing. What about the developing countries themselves? They must be productive and supportive, too. [Carmen's message 26, June 9, provides more details on the GCP (www.generationcp.org) ...Moderator].

If scientists and policy makers in the developing countries do not put enough time and effort into these activities and do not prepare a strategic plan for these purposes, there is nothing programs such as GCP can do. Scientists in the developing countries are the right arm of the international organisations for development programs and, knowing the extraordinary diversity in the existing germplasm collections of crops and their landraces and wild relatives, these scientists must push and influence the policy makers to cooperate in establishing national germplasm centres, making connections with other germplasm centres around the world, characterisation of the germplasm, developing carefully structured core collections within the existing collections (preferably using molecular technques due to their preciseness), and providing the best cores to the breeders for conventional and/or molecular breeding.

The developing world must not expect the international organisations to go all the way from training the researchers at the regional level to training at the national level. They must put further effort to transfer this knowledge to their national research centres/universities by preparing a focused strategic plan and funding national training programs by their senior scientists that have been already trained or will be trained by the international organisations, otherwise the image that we are making of the future will be an undeliverable ideal or even a dream.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 27 June 2005 11:50
To: 'biotech-room1@mailserv.fao.org'
Subject: 86: Biotechnology and genetic resources in war-hit countries

I am Janaki Krishna from India, again.

I agree with Sylvia Uzochukwu (Message 83, June 26). The projects on training on higher end biotechnologies should also be given due consideration by the funding agencies in order to obtain quality research proposals and output.

Also, I wish to flag a strange situation (though not discussed in the Background Document) wherein characterisation and, especially, conservation of genetic resources may play an important role. Similar to the special emphasis on developing countries situation, the war affected countries or war (endemic!) zones should also be considered as a special category in this regard. I feel there will be some effect on genetic resources in the war-hit zones. Special task projects may be funded to establish genetic resources centres or seed/sperm/DNA banks with specific safety measures in these areas to conserve and retrieve the germplasm. In vitro/cryopreservation techniques can be useful tools in this regard. It is just a stray suggestion as I am ignorant of the statistics with regard to the affect of war(s) on genetic resources. If it is insignificant, kindly ignore this message.

P S Janaki Krishna
Consultant
Andhra Pradesh Netherlands Biotechnology Programme
Institute of Public Enterprise
Hyderabad - 500 007,
India
Phone 91 - 40 - 27097018/27098148
Email: jankrisp (at) yahoo.com

[War and civil strife do indeed have an impact on genetic resources for food and agriculture. For example, Section 1.2 of FAO (1998), notes that there are several primary factors responsible for diminishing animal genetic diversity in the developing world and that one of them is "Wars and other forms of political unrest and instability" (http://dad.fao.org/en/refer/library/guidelin/sml-popn.pdf). Regarding plants, in their Country Reports for the State of the World's Plant Genetic Resources for Food and Agriculture (SoW-PGR), nearly all countries said that genetic erosion was taking place and was a serious problem. They cited a number of main causes for the genetic erosion, one of which (cited by 6 countries) was war and civil strife, where "In some countries, war and civil strife have contributed significantly to genetic erosion. In Rwanda and Somalia, they have resulted in the neglect of fields and the consumption of seed, while in Angola and Cambodia, they contributed to the loss of many traditional varieties as people moved from one area to another in search of safety. Farmers were unable to preserve their local varieties. In Viet Nam, genetic erosion was one of the consequences of the large-scale use of defoliants during the war in that country". (Section 1.5.2 in the SoW-PGR http://www.fao.org/ag/AGP/AGPS/Pgrfa/pdf/swrfull.pdf) ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 27 June 2005 15:00
To: 'biotech-room1@mailserv.fao.org'
Subject: 87: DNA barcoding // Inadequacy of using a single molecular marker system

I am PK Gupta from Meerut University, India, again.

I had earlier raised two important issues, which have not been discussed at any length during the conference. Therefore, I want to reiterate these two issues again:

The first (raised in Message 23, June 8) is the use of DNA barcoding for characterizing germplasm. No developing country has tried it, but they need to consider whether or not this technology will be useful. If it seems to be useful, we need to start using it without wasting any time.

The second (raised in Message 44, June 13) deals with the inadequacy of a single molecular marker system (e.g. simple sequence repeats (SSRs)) for estimation of genetic diversity in the germplasm, so that either the data from several marker systems (SSRs, SAMPL, AFLP, etc.) need to be pooled and used for estimation of genetic diversity, or else we should revert back to morphological traits for estimation of genetic diversity, because there are reports that a number of morphological traits together give a better estimate of genetic diversity.

I hope that the above two issues will receive the desired attention of those participating in this e-conference.

P.K. Gupta
Honorary Emeritus Professor and INSA Senior Scientist
Molecular Biology Laboratory
Department of Genetics and Plant Breeding
Ch. Charan Singh University
MEERUT-250 004
India
Tel (Lab): 91-121-2768195
(Resi): 91-121-2762505
TeleFax : 91-121-2768195
e-mail : pkgupta36 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 10:40
To: 'biotech-room1@mailserv.fao.org'
Subject: 88: Using different molecular marker systems

This is Ted Kisha in Pullman, United States, again.

First, I would like to thank everyone not only for the discussion of a universal molecular marker database, but on the subject of molecular markers for the estimation of genetic diversity in general. These two topics, of course, are inseparable.

I would like to say that ANY molecular marker data is useful, and no marker type should be discounted. It's true that random amplified polymorphic DNA (RAPD) markers have some problems with reproducibility. Any molecular marker system that is a multi-order chemical reaction is going to be subject to competition among annealing sites for primers. Problems can result from symplasty, repetitive DNA, or differences in the reaction conditions. This is a problem with AFLP (amplified fragment length polymorphism) also. It's not as noticeable using AFLP, because ignoring non-reproduceable, quantitative markers still leaves many more very strong, scoreable markers. I would ask anyone who has used AFLP to review their work. They will see that there is variance from gel to gel for every run. It is just so much easier to ignore this variability when there are so many more "good" markers to choose from. This problem is exacerbated when researchers use software to score gels, instead of an eyeball and some common sense. [The symplast is the continuum of cytoplasm within a plant tissue connected by plasmodesmata (fine protoplasmic threads that connect adjacent plant cells). Repetitive DNA is DNA sequences that are present in a genome in many copies...Moderator].

It is true that microsatellite data is more reproducible, and usually has a higher information content per locus, but the number of loci analyzed is limited by time and money.

Any marker system can also be subject to other problems like clustering about the centromere or telomere, or being in tight groups within heterochromatin. That's why the database should be curated, and a select "core" of markers, even within a select core of primer sets (AFLP), should be adopted for universal comparison. [The centromere or telomere are specific regions of the chromosome. Heterochromatin are regions of the chromosomal material that are stained intensely by certain dyes...Moderator].

I would also agree that it would be useful to compare at least two different marker systems for agreement in the resulting relationships.

I am going to pursue the establishment of a database locally, with hopes that it might someday be adopted on a larger scale. I would encourage anyone interested to keep in touch following this conference.

Thank you everyone,

Theodore J. Kisha
USDA-ARS
Washington State University
Box 646402
Pullman, WA 99164-6402
United States
Phone:(509)335-6898
FAX: (509)335-6654
e-mail: kisha (at) mail.wsu.edu

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 10:46
To: 'biotech-room1@mailserv.fao.org'
Subject: 89: Biotechnology in animal genetic resources research - Philippines

I am Dr. Sonwright B. Maddul, professor at the Benguet State University in La Trinidad, Benguet, Philippines.

I fully agree with my compatriot, Emma Sales (Message 84, June 27), that much innovation is desired in less developed and developing countries when it comes to biotechnology, considering the huge investment that it requires. This is especially true in livestock research and development (R&D). While there are people trained in biotechnology, inadequacy of equipment in laboratories or the lack of it, has stiffled the progress in this field. Our University, being government-owned, does not even have a biotech lab for livestock. But this has not dampened our interest nor our spirit to do simple R&D on livestock. Since 2003, we have started The Animal Genetic Resources (TANGERE) Conservation Program which established the Highland Pig Farm and Native Chicken Farm. Our research included physical characterization of the native pigs and chickens found in the highlands of northern Luzon, and monitoring their productive and reproductive performance ex-situ. We have not yet done the molecular characterization due to absence of a lab. In fact, we are waiting for collaborators.

Dr. Sonwright B. Maddul,
Department of Animal Science,
Benguet State University
La Trinidad, Benguet,
Philippines.
smaddul (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 10:55
To: 'biotech-room1@mailserv.fao.org'
Subject: 90: Re: Capacity building // Decentralised banks

This is Dr. Seetharam Annadana, India, replying to Kioumars Ghamkhar (Message 85, June 27):

Capacity building is a two way process between developed and developing countries. Developed countries have an arrogance that they know all, and their way is the way to do it. However, such attitudes have failed in really developing nations as a lot of socio-economic considerations have to be taken into consideration for any developmental activity. Developing countries are also complex. Sometimes they grumble saying the fund is not enough so why put an effort, otherwise they make unnecessary delays in moving files and getting approvals making the donor feel the recipient is not interested.

Both donors and recipients, I think, must work under some international framework and, if necessary, make use of a body for monitoring.

Dr. Seetharam Annadana
CTO: ASR BIOTEC and ASR HERBALS
Director Technical: AgriGrowMore (M) Sdn. Bhd.
71/2, 21st A Main, Marenahalli, JP Nagar,
Bangalore 560078,
India
seetharam (at) hotmail.com
Ph: 0091-80-26493204
Fax: 0091-80-26651157
Cell: 0091-9845006451
Wageningen University: http://www.wageningen-ur.nl
Contract Research: http://www.plant.wageningen-ur.nl
Molecular Markers: http://www.keygene-genetics.com
Biologistics International: http://www.biologistics.us
ASR HERBALS: http://www.asrherbals.com
AGRIGROWMORE: http://www.agrigrowmore.com

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 13:22
To: 'biotech-room1@mailserv.fao.org'
Subject: 91: Re: Biotechnology and genetic resources in war-hit countries

This is Edo Lin, independent consultant.

Janaki Krishna (Message 86, June 27) brings up the issue of the management of genetic resources in war and conflict. Although strictly speaking outside the scope of this conference, I would like to contribute to this topic as, in several parts of Africa and elsewhere, war and low intensity conflicts tend to become endemic and threaten not only genetic resource conservation but directly affect the livelihoods of millions of people.

In many developing countries, genetic resources conservation takes place in-situ by small scale farmers and is supported by seed exchange between individuals and communities (the informal seed sector). This system of conservation and exchange is based on trust and loyalty which is threatened when, through conflict, trust is destroyed, people and communities are,displaced, seed stores in villages are looted and crops in the field are destroyed. In addition conflicts may destroy (and have done so in several countries) institutional genebanks.

Participants interested in this issue and also the problem of genetic resource rehabilitation post conflict can find a free report at the IPGRI website: http://www.ipgri.cgiar.org/publications/pdf/245.pdf (660 KB). The 1997 report, by Paul Richards and Guido Ruivenkamp, entitled "Seeds and survival: Crop genetic resources in war and reconstruction in Africa", gives three detailed case studies concerning rice genetic resources during conflicts in Sierra Leone, Guinea Bissau and Liberia and proposes a reorientation of the rehabilitation efforts post conflict.

Edo Lin
Ceres Consulting International
309, rue de Bombon
77720 Bréau
France
tel and fax: +33 164387844
e-mail: ceres.consult (at) free.fr

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 15:36
To: 'biotech-room1@mailserv.fao.org'
Subject: 92: Capacity and economic issues - Madagascar

This is from Xavier Rakotonjanahary, plant breeder at FOFIFA, a national research institute, Madagascar.

I followed with interest the debate on the role of biotechnology on characterization/conservation of crop, forest animal and fishery genetic resources in developing countries. I would like to contribute on capacity and economic issues.

Many people in their messages have emphasized the weak capacity of using biotechnology in characterization/conservation, in developing countries. It is understandable that, in general, national policy is poverty alleviation, food self sufficiency and increased agricultural productivity and that research activities are not a priority. However, characterization and conservation activities which are the basis for any breeding progam are included in the national research sector. It will take time for the developing countries to reach a level where biotechnology could be used as an efficient tool for this purpose. International organizations, like FAO, the World Bank and the international centers should have an efficient way to promote and support the application of biotechnology in characterization/conservation in developing countries. This could be done by organizing at the regional level some group trainings, workshops or seminars,...and by funding some projects. They also could play a role in disseminating information, give recommendations on how a molecular technique is suitable, simpler and low cost.

Public private partnerships in developing countries could play an important role, but only on the condition that characterization and conservation has an evident economic impact, which is not the case for the moment. In most cases, the private sector is more interested in genetic material from outside, which has proven better performance in the country of origin.

About weighting genetic differences with respect to non-genetic differences, the former should be ranked at a lower level because socio-economic traits such as culture, market value, degree of endangerment are more related to humankind, which is to be considered the top priority.

From my personal view, genetic differences for traits which have been under selection are also more important than genetic diversity at neutral loci, even for characterization and conservation purposes. The best combination is that there is linkage between adaptative trait or trait of economic importance and a molecular marker.

Before I end my contribution, I would like to address my appreciation to the moderator of the conference for providing an updated and insightful background and to all participants for sharing their experience or giving recommendation and useful comments.

Xavier Rakotonjanahary
Plant breeder
National Center for Applied Research for Rural Development (FOFIFA)
BP 1690, Antananarivo, 101
Madagascar
E-mail: r.xavier (at) simicro.mg
Tel office 261 20 22 238 35
Mobile 261 33 12 060 08

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 16:18
To: 'biotech-room1@mailserv.fao.org'
Subject: 93: Re: Using different molecular marker systems

This is Glaucia S. Cortopassi Buso, from Brazil, again.

I agree with all of the observations of Ted Kisha (Message 88, June 28). Sometimes we don't have much time to choose or apply the best marker. In our lab, in some cases, we have to analyse the diversity of plants which were never studied before as fast as we can, because the site where these species are will be flooded. The faster marker is still random amplified polymorphic DNA (RAPD) and we think that if we take some precautions to choose the robust and reproducible bands (doing repetitions) and to perform an accurate data analysis (applying bootstrapping to check the confidence of marker number, etc) we have trustful results.

I agree that amplified fragment length polymorphism (AFLP) have the same problems as RAPD and it is more expensive and difficult to implement.

In addition to the case of flooding, we have many species for which simple sequence repeats (SSRs) have not been developed, and not enough funds for research, therefore we have used RAPD as a marker and the analysis frequently corroborates the morphological one, giving more confidence in our results.

I also agree with Alice Muchugi (Message 77, June 23) that renowned journals are refusing to publish studies with RAPDs and this may be harmful for the research with species that are not in the focus of developed countries where the best marker systems are developed and applied.

Glaucia Salles Cortopassi Buso, Ph.D.
Laboratorio de Genetica
Embrapa - Recursos Geneticos e Biotecnologia
Parque Estacao Biologica 70770-900
Caixa Postal 02372
Brasilia - DF
fone: 61- 448-4647
448-4645
fax: 61-340-3624
buso (at) cenargen.embrapa.br

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 16:29
To: 'biotech-room1@mailserv.fao.org'
Subject: 94: Use what the countries have to make decisions on conservation

This Alice Muchugi from Kenya, again.

If we address the application of biotechnology (especially of molecular marker technology) in developing countries, D. Vijay (Message 79, June 24) will agree with me that it is not possible in the near future to say that we will be at a par with the developed countries. His options of pulling resources together, as well as using laboratories of international organizations are okay (and I also suggested it previously). As Ted Kisha (Message 88, June 28) comments, every marker system has its disadvantages. My question is; With the unavailability of the two above solutions, and considering the threat to biodiversity, would it not be advisable to use what the countries have to make decisions on conservation? This can be combined with morphological traits as suggested by PK Gupta (Message 87, June 27).

We are lucky that, in Kenya, we have several international organizations with very good laboratories and our national research institutes have a few advanced equipments too. These have made a great contribution to the application of biotechnology in various fields of medicine and agriculture locally. However, I do know the problems being experienced by colleagues in other African countries as we interact while visiting these laboratories.

Finally, on pooling of resources, as several participants are suggesting: A good example is the Biosciences East and Central Africa (BECA; www.biosciencesafrica.org) facilities located in the International Livestock Research Institute (ILRI). I do hope that developing countries in other regions will, in future, have such a facility to help in the advancement of biotechnology.

Alice Muchugi
PhD Research Fellow
Genetic Resource Unit,
World Agroforestry Centre (ICRAF)
PO Box 30677-00100
Nairobi,
Kenya
tel: +254-20-7224000 Ext 4273
fax: +254-20-7224001
email: a.muchugi (at) cgiar.org
http://www.worldagroforestrycentre.org

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 17:46
To: 'biotech-room1@mailserv.fao.org'
Subject: 95: Characterization of genetic resources using molecular markers

This is from Hubert Dulieu, Professor Emeritus of Plant Genetics, University of Burgundy, Dijon, France. I have done developmental genetics studies on somatic mutations in plants (in vivo and in vitro) since the 1960's and molecular/population genetics since 1989.

Many messages concern the first topic of the conference: Characterization of genetic resources. This is an important point where DNA technology must be used. One of the problems is the repeatability among different labs. We agree with the observations that some markers (microsatellites, sequence tagged sites (STS), inter-simple sequence repeat (ISSR))) are more faithful than others (amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD)). Unfortunately, microsatellites and STS, which are sequence-based markers, require more preliminary research: cloning, screening, sequencing and, finally, genetic mapping. Remember that fingerprinting kits are produced for human DNA that are used universally. Some biotech companies should be encouraged to produce kits for the most important species used in the world. Nevertheless, AFLPs are highly informative and can now be performed without radioactive elements for many actual applications of fingerprinting cultivars, varieties and species.

I would like to point out a property of hypervariable markers which does not seem to have been discussed by our colleagues (probably except P.K. Gupta, Message 44, June 13): Many molecular markers reveal intraspecific/populational polymorphism which is not highly correlated with performances nor with phenotypic characters. Indeed, the level of polymorphism in panmictic (random mating) populations revealed by microsatellites is so high (number of alleles per locus can reach 40 or more) that it leads to overestimations 1) of genetic distances and 2) of the part of polymorphism of interest for the breeders, i.e. concerning the regulatory/structural genes responsible for the realization of the characters/phenotypes. Molecular characterization of genetic resources used for breeding should be more pertinent if sequences from functional genes could be used, many of which are not identified at the DNA level today. Remember, however, that increasing databanks of expressed sequences exist, as well as complete genes from which primers can be chosen freely and applied to related species. Remember also that genetic distances can be calculated from phenotypic characters if the observer is attentive and able to correctly code the alternative forms of each character - I doubt that such distances should be less efficient than molecular distances for preparing the use of germplasm to be bred.

Hubert Dulieu,
Emeritus Professor of Plant genetics,
University of Burgundy,
(personal address: 6, rue des roses, 21 110 France
tel : 0032 380 37 82 88).
hdulieu (at) u-bourgogne.fr

-----Original Message-----
From: Biotech-Mod1
Sent: 28 June 2005 18:06
To: 'biotech-room1@mailserv.fao.org'
Subject: 96: Germplasm conservation and conservation of endangered species

This is from Hubert Dulieu, France, again.

Concerning the second topic of this conference i.e. conservation of genetic resources, it is necessary to distinguish between a) germplasm conservation and b) conservation of endangered species, which refers to population genetics.

My opinion tends to remain simple and realistic: if a germplasm (associated or not with molecular data) cannot be maintained alive and reproduced normally in culture or at least in collections, its probability to be lost in a next future remains high (many species disappear as well as ancient cultivars), in spite of sophisticated processes used (in vitro culture, DNA banks, cryopreservation). Simply because the probability of technical problems, catastrophes, etc. is of the same order of magnitude as losses due to human destruction by abandonment or to environmental changes. Concerning DNA banks, I should prefer phage genomic libraries, relatively easy to prepare and to preserve, from which every gene can be isolated in the future. However, I am tempted to think that using more technology to try correcting counter-effects of misuses of technology (mainly the destruction of traditional agricultural systems), resembles the eternal promethean dream of humans, unable to resolve the crucial dilemma of pursuing the logics of the intensive production of consumer goods at the expense of the environment. This remark is not contradictory to the development of scientific projects for identifying characters (physiological, ecological, molecular) of resources species and varieties whose culture and use must be maintained and/or radiated in all the favourable countries possible.

Population analyses with highly informative neutral markers (namely microsatellites) should be recommended for endangered wild species (animals, fish, forest trees, etc.). Such studies should allow us to evaluate the genetic polymorphism which is necessary to maintain, in order to suppress or delay the risks of extinction. There are typical examples where bottlenecks have been detected by molecular markers, leading to decisions favouring protection. These very important applications of molecular biotechnology to population genetics and management are true for all countries. One single example: forest trees of indigenous species in Europe were subjected both to phenotypic counter-selection during their multi-secular history and efforts are presently encouraged to regenerate populations naturally. It must be demonstrated that such populations have maintained their genetic basis sufficiently large, both to maintain diversity and to apply directed phenotypic selection (two apparently antagonistic goals, except for forest geneticists). This must be done by molecular analyses of populations.

Hubert Dulieu,
Emeritus Professor of Plant genetics,
University of Burgundy,
(personal address: 6, rue des roses, 21 110 France
tel : 0032 380 37 82 88).
hdulieu (at) u-bourgogne.fr

-----Original Message-----
From: Biotech-Mod1
Sent: 29 June 2005 09:21
To: 'biotech-room1@mailserv.fao.org'
Subject: 97: Conservation requires a long term commitment

I am Made Sri Prana, senior researcher, R&D Centre for Biotechnology, Indonesian Institute of Sciences.

Being trained in conservation and utilization of plant genetic resources, I fully agree with the importance of genetic resources conservation of whatever organism it is (plant, animals, microbes) and appreciated the effort of my colleague Sonwright Maddul of the Philippines (message 89, June 28). However, I should say that even just for maintenance of the collection already requires sufficient amount of budget which is not always available in institutions of a developing country. Therefore, it is not uncommon to notice that the whole collection may gradually disappear due to lack of financial support or loss of interest from the boss.

I tend to believe that conservation requires a long term commitment (policy, human resource, funding etc) and certainly it should not be based on personal interest (except in an extreme case). Besides, experience tells us that conservation is best linked with a programme on utilization of the resources conserved. Otherwise, sooner or later, they will disappear simply because it is felt as a mere burden.

Yes, I agree that the key word is "collaborator" or collaboration. Please promote your programme and germplasms collection to the world who knows that at one time somebody from somewhere would be interested to collaborate with you. Let's cross our fingers.

Made S. Prana
PROSEA Network Office,
Research Centre for Biotechnology,
Indonesian Institute of Sciences (LIPI),
Cibinong/Bogor,
Indonesia
pran (at) proseanet.org

-----Original Message-----
From: Biotech-Mod1
Sent: 29 June 2005 10:44
To: 'biotech-room1@mailserv.fao.org'
Subject: 98: Re: Characterization of genetic resources using molecular markers

This is Ted Kisha in Pullman, Washington, United States, again.

Hubert Dulieu (Message 95, June 28) brings up an important characteristic of molecular markers to which I had previously alluded (Message 88, June 28), and which has been the subject of considerable research (see K. Weising et al., 2005, DNA Fingerprinting in Plants: Principles, Methods, and Applications, CRC Press). They may reside in neutral, unexpressed regions of the genome, and even be clustered in these regions. I would like to emphasize again the need for a curated set of "core" markers (for each different marker technology) that uniformly and randomly sample the genome, especially in regions of euchromatin where the functional differences of diversity reside. More microsatellite primers are being developed using expressed sequence tags (ESTs) where these become available in GenBank. AFLP markers can be generated using PstI, which preferentially creates markers in unmethylated DNA. Markers should be mapped where possible to ensure uniform distribution.

I agree that measurement of functional diversity is the ultimate goal, but strict adherence to this goal where it may lead to extra expense or delay in germplasm characterization may be unnecessary. Since much of the genetic diversity is a result of adaptation within isolated environments, especially in wild, ancestral germplasm, there could very well be a high correlation between clusters identified by random molecular markers and unique functional characteristics. I believe that an inexpensive, high throughput technology should be the first and most serious consideration. Information from many loci, I believe, is preferential to highly diverse information from only a few loci.

Theodore J. Kisha
USDA-ARS
Washington State University
Box 646402
Pullman, WA 99164-6402
United States
Phone:(509)335-6898
FAX: (509)335-6654
e-mail: kisha (at) mail.wsu.edu

[To give more details on points made in paragraph 1: Following the classic biology textbook of John W. Kimball, within a cell, the nucleus contains the chromosomes. Each chromosome consists of a single molecule of DNA complexed with an equal mass of proteins. Collectively, the DNA of the nucleus with its associated proteins is called chromatin. The density of the chromatin (that is, how tightly it is packed) varies throughout the nucleus. The dense regions are called heterochromatin (referred to in Message 88, June 28) while the less dense regions are called euchromatin. Heterochromatin is found in parts of the chromosome where there are few or no genes, such as centromeres and telomeres; is densely-packed and is greatly enriched with transposons and other "junk" DNA. Those genes present in heterochromatin are generally inactive; that is, not transcribed. Euchromatin is found in parts of the chromosome that contain many genes and the genes are active (http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleus.html). DNA methylation, where methyl groups (-CH3) are added to DNA, can directly or indirectly silence gene expression. AFLP markers are DNA markers generated by the amplification using the polymerase chain reaction (PCR) of fragments of DNA, cut using restriction enzymes (such as PstI). GenBank was discussed in Message 6...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 29 June 2005 14:26
To: 'biotech-room1@mailserv.fao.org'
Subject: 99: Genetic diversity studies: Too much emphasis on markers

This is Miguel Toro, again.

Going back to the question of whether molecular markers can provide an 'objective' method to establishing the 'similarity' between breeds and an objective way of claiming that two breeds are or are not different (raised in several messages - numbers 63, 65, 66, 70, 75, 82, 89, 95, 96 etc.), I would like to point out the following:

If I understand correctly Hans Lenstra's message (nr. 70, June 21), genetic distance based on molecular markers are only partially informative because:
a) they do not take into account within-breed variability;
b) they can reflect or not phenotypic distances;
c) they can reflect or not ancient history.

Therefore it seems that at least three pieces of information are needed: phenotypes, markers and history (and common sense probably). However, I think that there has been too much emphasis on markers, probably because this information is much more easy to obtain. There are hundreds of papers on genetic distances but very few on phenotypic distances (could someone quote some paper on that?).

Miguel Angel Toro Ibanez
Departamento de Mejora Genetica Animal
Instituto Nacional de Investigacion y Tecnologia Agraria y Agroalimentaria (INIA)
Carretera La Coruna km. 7 28040 Madrid
Spain
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro (at) inia.es

[To respond to Miguel's question, in Stephen Hall's recent book, "Livestock biodiversity: genetic resources for the farming of the future", he refers to a study where phenotypic information (morphology) was used to create phylogenetic trees. The study (Crepaldi, P. et al, 2001. Diversity in five goat populations of the Lombardy Alps: comparison of estimates obtained from morphometric traits and molecular markers. Journal of Animal Breeding and Genetics, 118, 173-180) considered phenotypic variability (estimated on the basis of six somatic measurements on 60-140 adult goats per Italian breed) whereas genetic variation was measured on the basis of 201 AFLP loci. Results showed that morphometric and molecular marker data produced unrelated distance values and different topology of UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clusters...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 30 June 2005 08:14
To: 'biotech-room1@mailserv.fao.org'
Subject: 100: Re: Genetic diversity studies: Too much emphasis on markers

This is Kioumars Ghamkhar, again, addressing Miguel Toro's concerns (Message 99, June 29).

However, exactly for reason number 5, it is a good idea to do both molecular and morphological characterization if there is enough time and money.

Regarding the need for some knowledge on the ancient history, I assume Miguel means some knowledge on the phylogenetic relationships. If so, then some knowledge on the sister groups of the study group is all the researcher needs unless it is a 'molecular clock" and/or population genetic study.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 30 June 2005 13:36
To: 'biotech-room1@mailserv.fao.org'
Subject: 101: Conservation/depletion of forest biodiversity - Nigeria

I am Adegoke Adedayo Oluawsegun, from the Centre for Energy Research and Development, Obafemi Awolowo University, Ile-Ife, Nigeria.

In Nigeria at present the destruction of natural habitats continues apace, resulting in the depletion of the country's biodiversity. For example, the Nile crocodile (Crocodylus niloticus) which was once found in the Nigerian coastal waters right up to Lake Chad, is fast disappearing due to loss of habitat and the hunting of the crocodile for their meat, eggs and hide. Also in Southern Nigeria, the forest elephant, chimpanzee, leopard, yellow-backed duiker, the royal phyton, the Nigeria quenon (Cercophithecus erythorgaster) are among the animals on the endangered list. Forestry experts have reported that about 65 of Nigeria's 560 species of trees are now faced with extinction while many others are at different stages of risk. Every year a considerable part of the nation's forest resources are destroyed through industrialisation, commerce, agriculture and the activities of rural dwellers, thereby disturbing the balance that nature maintains with the living and non-living resources.

It brings some comfort to know that some governmental agencies and non-governmental agencies like the Nigerian Conservation Foundation (NCF), the Federal Environmental Protection Agency (FEPA), the National Resources Council (NARECO) in collaboration with the United Nations Environmental Programme (UNEP) and the World Wide Fund (WWF) and several other Agencies have embarked on programmes to protect and preserve the nation's biodiversity. This is a good step in the right direction since there is an ethical demand on society to preserve the Nation's biodiversity for the future generations, for aesthetic values, for its economic and commercial value, for its pharmaceutical and medical prospects and also to protect and maintain the balance in the ecosystem.

This implies that biodiversity provides mankind with the source of food, fuel, clothing, medical and a host of other uses. For years, micro-organisms have been used for fermentation, drugs, preservation, DNA research, biotechnology, genetic engineering, tissue culture and a host of other purposes. An example is the armadillo. A leprous Armadillo showed response to leprosy drug tests. This animal is now being used to test efficacy of these drugs. It does not take much imagination to realise what the world would be like if these flora and fauna had been destroyed before their usefulness was discovered.

In Nigeria today a large population resides and works in rural areas. These rural dwellers are a major contributor to forest depletion. Agriculture is dominant in these areas. It has the greatest concentration of poverty, landless workers, small tenant farmers, small farm owners, the rural unemployed, and the poor of the poor in the nation. As a result of the poverty level in these areas, biodiversity provides for 90% of their needs, a fact which plays a major role in the destruction and depletion of native flora and fauna. One major way these rural dwellers affect the biosphere is through the use of firewood as the major source of household energy. 95% of these dwellers use firewood as they cannot afford fossil fuel. The demand for firewood has recently increased since the introduction of the Structural Adjustment Programme (SAP) in July 1986. This programme resulted in a move of more people back to the rural areas into agriculture. Poverty in this group further increased the demand for firewood.

The agricultural practices of peasant farmers brings further destruction to biodiversity. Slash-and-burn or shifting cultivation provides a basis for subsistent agriculture bringing about the burning of forests and bush, the depletion of nutrients and organic matter in the soil. This is inimical to the conservation of forests. The use of outdated equipment and low-yielding agricultural materials makes room for an over demand for land, resulting in more forest being cleared for planting crops and pasture.

Exploitation of the forest resources to generate (monetary) income in order to survive has resulted in the hunting of wildlife on an enormous scale. It is very common to see wildlife (bush meat) being hawked on our roads in Nigeria. These peasants are forced to hunt and trap animals in search of income, selling about 80% of the bushmeat they trap and consuming the rest. Most of those hunting wildlife in Nigeria have little or no economic alternative. The most hunted species is what is known as "The Grass Cutter" (Thryonomys swinderianus), followed by the African giant rat (Cricetomysgambianus) and then small antelopes.

Hunting, trapping and bush-burning to smoke out rodents from burrows brings about further devastation to the forest, to nature's biological web. Small-scale forest-based enterprise such as the use of bamboo for making baskets, canes for making furniture all contribute their own quota to the destruction of the biosphere. Indeed, most of the materials required for making cooking utensils, musical instruments, weapons, implements for fishing and hunting, clothes, adornments and games all come from the forest. Construction and maintenance of household structures in the rural areas also place their demand on wood, bamboo and grass.

The need for food - protein and other nutrients are mostly supplied through the forests. Many wild animals, fish and birds are caught for protein; providing up to 70% of their protein diet. Children collect termite, snails, and the caterpillars of several insects. They also collect ripe fruits, vegetables, mushrooms and different kinds of leaves from the forest in order to supplement their diet, while bees are smoked out of their hives for their honey.

Knowledge of the many uses of flora and fauna in their environment are passed down over generations. The seed of the wild mango (Irvingia gabonensis) is a very important delicacy for making sauces (Ogbono) in the Eastern and Western part of Nigeria. The baobab tree widely distributed through the savannah in Nigeria has several uses. The young leaves are used in sauces, the powdery pulp of the fruit capsules are fermented to make beverages while the bark and rind are used for rope fibre and for fuel. Many plants gathered serve as additional income. The leaves of Theumatococcus danielli is widely sold and used in the western part of the country as a wrapping material for food. Furthermore, about 80% of these rural dwellers depend on plants for treating ailments since many of them know no other medicines. Although hunting and gathering of animals and plants are necessary for survival, it is the unsustainable use of these resources that creates the problem for species threatened with extinction as these are not replaced.

Conservation programmes have been greatly hindered in Nigeria as a result of poaching. Compounding the problem is the simple fact that the communities in these reserve areas have a need for monetary income and they see little or no direct economic return to them as a result of the protection of these reserves. And many see the reserves as rightfully part of their land.

The Nigerian government remains preoccupied with economic problems such that they are unable to allocate enough resources for conservation, for research and monitoring of conservation programmes, for the creation of gene banks and education of the public concerning the importance of preserving the biosphere. However, it is in the field of creating wildlife reserves and forestry through tree-planting that Nigeria has made the most conscious and discernible effort towards conservation. But, tree planting only preserves a part of the original biodiversity in an environment, it does not result in a return of the vast and varied flora and fauna hitherto destroyed.

Fuelled by poverty, low levels of education and a weak knowledge of conservation, the rural poor cannot appreciate the need for preserving our environment. The same group the depends on the environment for many of its needs is thus often unrestrained in causing its destruction.

For any meaningful and lasting conservation programme to be effectively carried out there must be a conscious effort in involving the local people in maintaining and managing their environment since the needs of these dwellers must be respected. Any action to limit the use of the forests without providing an alternative to them or alleviating their poverty or lack of education will meet with a lot of problems as can be seen from the incessant activities of poachers on our wildlife reserves.

Adegoke Adedayo Oluawsegun,
Centre for Energy Research and Development,
Obafemi Awolowo University, Ile-Ife,
Nigeria.
+234 803 403 1411
aoadegoke (at) yahoo.com

[Further messages on this topic should focus on the potential role (if any) that biotechnology could play for the conservation/characterisation of these forest genetic resources...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 10:14
To: 'biotech-room1@mailserv.fao.org'
Subject: 102: Review of issues concerning aquatic genetic resources

This is Ron Jones from Canada, again.

I have been going through the archives of this conference picking out those contributions relating to biotechnology applications to the conservation of aquatic genetic diversity and other messages useful to a general focus on key concerns for aquatic systems. I think that Adegoke`s messages (nr. 101, June 30), although a bit off topic for this conference, is an excellent contextual setting for most of the drivers of change and pressures facing those who are working on conservation of genetic resources in developing countries, be it in any wild or culture-based system. This context, I feel, really forces us to ask serious questions on how we are going to prioritize our efforts. On what natural resources are we going to concentrate these wonderful tools and techniques we have been discussing over the last few weeks.

In the developed world we can concentrate time and money on applied microbiology and molecular genetics to discoveries from bioprospecting in extreme environments (hotsprings, deep sea vents, deep caves etc) with the aim for a cure to cancer or perhaps a better adhesive. Where do our values for the natural world reside? Decisions on what we save and what goes extinct will, in this man-driven epoch, for the time being be based on livelihood decisions and all the fancy science and explorations will be used primarily for finding new materials or using our knowledge of genetics to improve (intensify) existing food production systems and the commercial health care industries. With 6 billion+ people on this planet we no longer have the luxury to try and conserve everything. We should focus on those organisms and processes which have/may have direct application and utilization in ecological food and livelihood systems, based on applied research from key biogeographic regions. If we can lovingly, intelligently and ethically apply an inclusive form of sustainable livelihoods approach we will save a good deal (NB. re-read Aldo Leopold). What is an acceptable resolution of understanding needed to solve immediate problems? [Information on the American naturalist Aldo Leopold's work available e.g at http://gargravarr.cc.utexas.edu/chrisj/leopold-quotes.html ...Moderator].

For applied issues in aquatic systems, Devin Bartley`s Turin paper, asks questions such as "How to choose aquatic species for domestication?" or "How to manipulate genetic resources to increase and improve domestication?". This will involve the recognition of the risks of losing potentially valuable (social, economic and ecological) genetic material for future considerations. What is not "valuable" today may be important sources of genetic diversity in breeding or stocking programmes in the future. These are key questions and concerns. S.G. Tan`s message (nr. 69, June 21) and Subha Bhassu (Message 62 June 20) emphasize the important concept of using molecular techniques in the elucidation of, and prevention of, inbreeding (low hetrozygosity effects) in aquaculture stocks, which is a persistent result from breeding of highly fecund and small founder populations, whether in a hatchery programme or from an unknown wild source considered for breeding. Inbreeding (depression and introgression) prevention and the separation of family (full and half sib) mating systems will always be a challenge for hatchery set ups. I refer readers interested in applied biotechnology in aquaculture to Han Magnus Gjoen`s Introduction to the Proceedings of the Aquaculture Biotechnology Workshop, 12-12 May, 2004, St. Andrews, Canada (Bulletin of the Aquaculture Association of Canada 104-2 (2004). The introduction, plus the papers within, contain a good overview of issues facing developed world aquaculture with perhaps eventual implicatons for global aquaculture in general. [Devins's paper (entitled "Status of the the world's fishery genetic resources") was presented at the international workshop held on 5-7 March in Turin as part of the preparations for this e-mail conference (proceedings available at http://www.fao.org/biotech/torino05.htm). I assume the 2004 proceedings from the Canadian aquaculture biotechnology workshop will be made available at http://www.aquacultureassociation.ca/bulletin/pub.html ...Moderator].

Once choices are made, hopefully via enlightened political will free of corruption and entrenched cultural biases and dogma, on where and what we are to focus our limited resources, we will have to face the challenges in conserving the in situ aquatic genetic resource base (through forms of creative co-management governance), as little aquatic domestication has ocurred, and using both evolutionary biology and our molecular tools to pin down areas and species of high genetic relevance for aquaculture, inland water fisheries enhancement, and potential areas for bioprospecting. Molecular and evolutionary tools must be used when contemplating the introduction of any potentially disruptive aquatic species. We should develop methodologies and apply OIE (World Organisation for Animal Health), EIFAC (European Inland Fishery Advisory Committee) and CCRF (Code of Conduct for Responsible Fisheries) guidelines as soon as possible because aquatic species will continue to be introduced deliberately and unintentiionally all over the world, so let's use this dynamic to strategically produce more from our diversity of waterbodies.

I guess in the end, the issues and impacts on aquatic ecosystems and the genetic diversity they contain may prove more difficult and pressing to manage than terrestrial systems, for many reasons, not the least our fundamental dependence on unpolluted water and general lack of understanding of aquatic environments (freshwater and marine, although this is improving) but perhaps, more importantly, the complex, non-linear and multi-scale/multi-use relationships which occur in these highly connected enviornments. The physio-chemical and biotic worlds are intricately linked to the socio-ecological worlds of the people who live there. These spheres are linked through complex webs of resource, information and energy feedback which are difficult to highlight and generalize. I think that building the local or national capacities to study and manage these systems must go beyond providing new tools and lab space (this infrastructure and training is surely needed to some extent), but creative governance approaches must be found which inspires researchers beyond "publishable science" to work with resource users and managers to find out how these biologically diverse systems work. Maintaining the structural and functional integrity of aquatic habitats and the key factors which foster evolution and systems resilience will provide the genetic diversity for any future designs we have. Humans are the the foremost "ecological engineers" and if assumptions concerning the existence of alternate stable states and bifurcation thresholds for marine and feshwater systems exist, then our political choices in how we manage these social-ecological relationships will have direct consequences on the quality of the ecological inheritance we leave for future generations.

The incresing complexity of today`s conservation problems requires us to forge bridges between many of the scientists participating in this conference and those in the social sciences, law, politics and spirituality to develop equitable approches to alleviating poverty and the sustainable use of natural resources

Ron Jones
Consultant,
International Development Research Centre (IDRC)
Ottawa,
Canada
channastri (at) netscape.net

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 10:22
To: 'biotech-room1@mailserv.fao.org'
Subject: 103: Curated molecular marker data base

This is from Ted Kisha, again.

Responding to a question from the Moderator, I can clarify that the use of the term "curated" in my messages was in the context of the data base itself for which the term means to "organize and oversee". In that context, the markers should be "organized" by someone who has a significant interest in the species being analyzed, and who has mapped the markers to ensure that they:

Curation of incoming data generated by these markers is, of course, very important to ensure that the markers are accurately labelled for comparison to other data.

A set of standards (not just molecular weight standards, but standard plant tissue to generate known fragment sizes (microsatellite) or known fragment patterns (AFLP)) for comparison should be readily available for distribution to interested researchers.

Theodore J. Kisha
USDA-ARS
Washington State University
Box 646402
Pullman, WA 99164-6402
United States
Phone:(509)335-6898
FAX: (509)335-6654
kisha (at) @mail.wsu.edu

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 10:28
To: 'biotech-room1@mailserv.fao.org'
Subject: 104: Re: Capacity building // Decentralised banks

I am Dr. Isaac Osakwe, a Senior Lecturer in the Department of Animal Production and Fisheries Management, Ebonyi State University, Abakaliki, Nigeria. My area of specialisation is animal nutrition. Ebonyi State University just started a four-year degree programme leading to a Bachelor’s Degree in Biotechnology. As a nutritionist, I would like to see gene-based technology that would develop transgenic forages or use molecular genetics to breed, select and conserve forages with specific nutritive qualities such as reduced anti-nutritional factors e.g. lignin, tannin, toxins etc. in grasses, legumes and browse plants. Also enhance resistance of forages to diseases and drought.

Frankly, there is no meaningful characterisation and conservation of genetic resources using biotechnology in animals in most developing countries. Some progress has been recorded in plants, especially in countries where international research centres have their headquarters or country programmes. This is possible because of the huge funding made available to these research centres from donors from developed countries.

I agree with Sylvia Uzochukwu (Message 83, June 26) that funding bodies are not reluctant to release funds for biotechnology proposals but very reluctant to release funds for training and updating scientist at national levels. I think and believe that some governments and national stakeholders, private foundations and NGOs in developing countries should be able to fund this aspect and then take advantage of the funding from big funding bodies/agencies for research proposal. Governments in developing countries should be able to show their will and determination that they are sincere and committed to capacity building in biotechnology. Money stashed away in foreign banks by corrupt leaders at all levels and those used by warlords should be diverted to research in biotechnology and we shall see developing countries come at par with developed countries.

Dr. Isaac I. Osakwe
Department of Animal Production and Fisheries Management
Ebonyi State University, PMB 053, Abakaliki
Ebonyi State,
Nigeria
Phone: +234-803-4910687
E-mail: osakwe_I (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 10:48
To: 'biotech-room1@mailserv.fao.org'
Subject: 105: Re: Markers - Characterisation - Biopiracy

My name is Bocar Oumar Kante. I´m a volunteer to the legal office of FAO. My nationality is Senagalese. I have been living in Paris since October 2003, where I did a DESS in cultural heritage law. Now I´m doing a PhD and my thesis title is: Cultural heritage law in Africa. I include in this research the study of local community rights.

I first join my opinion to the message (nr. 72, June 23) from Vladimir Magalhães who said that "The use of biotechnology to conserve the biodiversity cannot be considered as a solution but only a palliative when the biodiversity in the developing countries is being destroyed by an economic model built by developed countries, through the International Monetary Fund (IMF), for instance, based on the economic exploitation of developing countries and their natural resources." And I add the reference of an note from the UNCTAD secretariat (UNCTAD and the civil society: Towards our common goals, 10th session, Bangkok, 12-19 February 2000) which recognises that article 27.3(b) of the TRIPS agreement encourages biopiracy. It´s then a real paradox when some states argue that if the developing countries recognise patents they cannot claim benefit sharing.

Bocar Kante
Volunteer of FAO
Legal Office
Room A 441
Viale delle Terme di Caracalla,
00100 Rome,
Italy

[This topic can be continued only if focusing on the role that biotechnology can play for the characterisation/conservation of genetic resources. The note by the secretariat referred to above is a statement to the 10th session of the United Nations Conference on Trade and Development (UNCTAD). The statement "reflects the outcome of the NGO Plenary Caucus held at UNCC-ESCAP, Bangkok, on 7-8 February 2000. It was adopted by acclamation at the meeting, which was attended by approximately 160 participants representing around 120 non-governmental organizations from over 40 countries". http://www.unctad.org/en/docs/ux_td390.en.pdf ...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 10:59
To: 'biotech-room1@mailserv.fao.org'
Subject: 106: Root crop diversity and local tissue culture

I am Ann Marie Thro, National Program Leader for Plant Breeding and Genetics in the Cooperative State Research, Education, and Extension Service (CSREES) of the U.S. Department of Agriculture. CSREES manages funding approriated by the U.S. Congress for agricultural research in the 50 states. I have also served as Commissioner of the USDA Plant Variety Protection Office and as Coordinator of the international Cassava Biotechnology Network (CBN).

I have been following the conference with interest and would like to add an additional concept. This was proposed to CBN by a Colombian NGO called FIDAR (Fundación para la Investigación y el Desarrollo Agrícola). In the Andean countries, many lesser-known root and tuber crops (such as canna and oxalis) are indigenous. Most have been grown less and less frequently. Jose Restrepo of FIDAR observed to CBN that because fewer and fewer of the vegetative planting stocks of these crops remain, they tend to be weakened by systemic pathogens carried in the propagation materials. FIDAR proposed a low-cost rural-level tissue culture project, using local materials, to propagate these indigenous roots and tubers. The stocks would have been cleaned up first at an expert lab using thermotherapy. Tissue culture would allow pathogen-free propagation materials to be multiplied and distributed rapidly, allowing farmers to explore possible renewed interest in these indigenous crops in the urban markets of South America. This would have been a form of in-situ germplasm preservation, combined with using the germplasm, and providing an additional income source for farmers, made possible through tissue culture. When last I heard, this project had not yet found a donor. Perhaps someone else following this e-conference?

The primary FIDAR proposal was for developing low-cost rural-level tissue culture methods for cassava, a major indigenous root crop that also suffers from pathogen build-up in planting material. The cassava proposal was funded by the Participatory Research initiative of the Consultative Group on International Agricultural Research (CGIAR). Low-cost tissue culture methods using locally-obtainable materials were successfully developed, and the project is now in its second phase. Information about the cassava tissue culture can be found at www.ciat.cgiar.org/biotechnology/cbn/colombia.htm ("Application of low-cost in vitro propagation techniques to conserve native varieties and produce quality cassava seed in southwestern Colombia"), or by contacting Alfredo Alves, the current CBN Coordinator (at a.alves (at) cgiar.org, see the same web site).

Ann Marie Thro
USDA CSREES
800 9th St. SW
Washington DC 20024
United States
202 401 6702
athro (at) csrees.usda.gov

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 11:22
To: 'biotech-room1@mailserv.fao.org'
Subject: 107: Biotechnology and conservation of livestock - Pakistan

I am Dr. Masroor Ellahi Babar, Associate Professor of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan. I am currently working as a visiting scientist at the Nova Scotia Agricultural College, Nova Scotia, Canada and engaged in genomic studies of Livestock.

I read most of the messages of very learned scientists who sent their messages from all over the world about this emerging field of science “Biotechnology”. First of all, I want to say that no nation can progress unless it improves its educational standards especially in applied sciences which are directly related to human welfare. In Pakistan, there are some of the world famous breeds of livestock. Sahiwal and Red Sindhi cattle have a great potential for milk production. Nili-Ravi is the world’s best buffalo breed and can also be used for meat production. Lohi and Kajli sheep and Beetal, DDP, Kamori and Teddy goat can make revolution in livestock sector.

In the developing countries there is lack of planning for livestock sector, resulting in little promising results. Due to lack of specialists in the public sector, there is no continuity in research work. If a person speaks in favor of importation of pure Friesian cattle, the officials import big flocks of pure breeds without debating its demerits. Similarly, by listening to a few advantages of crossbreeding, all the people start crossbreeding without seeing the merits of selection of indigenous germ plasm. Due to ill planned cross breeding more than 60-70% of the native breeds of cattle, sheep and goat have not been evaluated in Pakistan and the purebred are only available at government livestock farms. There is a dire need for long term planning in developing countries especially in Asia.

I think the need of conservation or even the preservation of local breeds of livestock is essential for the future of developing countries especially in Pakistan. All the methods of cryoconservation, including embryo and semen preservation and establishing DNA banks, should be started immediately otherwise we will lose some of the precious breeds of the world. In this aspect, the University of Veterinary and Animal Sciences in Lahore took a leading step in establishing a DNA bank having 300 DNA samples of nine local breeds of sheep of Pakistan. It is our future strategy to increase the number of species and samples from different breeds in this bank in the near future.

Now as regards the biotechnology or genomic studies in the animal sector, there is severe shortage of trained manpower in the developing countries. In Pakistan, no specialized institute is engaged in livestock genomic studies. Only a few institutes are engaged in plant genomic studies. During my stay in Canada, I saw that even the farmers of the developed countries are aware of the genetic resistance against diseases like scrapie and BSE but in developing countries nobody even knows about these problems and what to talk about their detection at DNA level, precautions and remedies. I think organizations like FAO should put more emphasis towards developing countries as compared to developed countries regarding capacity building and establishment of institutes for genomic studies. The universities of the developed countries should make linkage programs and have close liaison with developing country universities. This will also be helpful for the developing countries as they have the knowledge and access to genetic variability which is not available in their animals. There are many countries like Canada which have not their own genetic resources. The universities of such countries should make sister relationships with the universities of densely populated areas of subcontinent and should initiate some solid research projects related to genomic studies. [To say that Canada does not have their own animal genetic resources does not seem a fair comment. See e.g http://dad.fao.org/cgi-dad/$cgi_dad.dll/selsimp or http://www.cfagrf.com/ ...Moderator].

I am of the strong opinion that unless the developing countries start learning new techniques of biotechnology, they can never bridge the gap of science that currently exists between developed and developing countries. Even this gap will become wider with the passage of time. Use of DNA markers and marker assisted selection are very powerful tools and should be used more and more with traditional quantitative genetics procedures. All of us know that such type of research needs long term adequate financial support. This money should be spent on capacity building and establishment of solid institutes for genomic studies. Source of funding is the question of time. World reputed organizations should think on this serious issue.

Dr. Masroor Ellahi Babar,
Nova Scotia Agricultural College,
PO Box 550
Truro, Nova Scotia
Canada B2N 5E3
MBABAR (at) nsac.ns.ca

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 12:32
To: 'biotech-room1@mailserv.fao.org'
Subject: 108: Capacity building for biotechnology

This is Kazhila Croffat Chinsembu, from Namibia, again.

I must say I have enjoyed this FAO e-conference on biotechnology, and wish all those that participated could receive some form of certificates for remembrance. Biotechnology is now a buzz-word here in Africa. I came face to face with the realities of biotechnology ten years ago when as a young African student in Brussels, I was isolating and analyzing Salmonella genes that are induced under iron starvation. This work is now prominent in the development of DNA vaccines. In future, I wish the FAO e-conference would also involve biotechnology in disease analysis, prevention and therapy. But that is for the FAO to decide.

On the question of molecular characterization of biodiversity, the FAO should take the lead in implementing some of the suggestions and recommendations from this conference. We have had many conferences and workshops here in Africa without any follow-up action. This is a waste of time and resources. We need to see movement in the establishment of a DNA resource bank. We need to see movement in training. We need basic infrastructure for biotechnology. We need training materials and courses up and running in our universities.

As a molecular biologist, I have been working with biotech for the past ten years now, first at the University of Zambia (UNZA) from 1996-2002 and now at the University of Namibia (UNAM) from 2002 to-date. My experience over the years is that biotechnology is an expensive business. At UNZA, it was difficult to even extract DNA. Here at UNAM, we have the basic facilities to isolate and amplify DNA and run a gel. We can only go as far as RAPDs since we do not have sequencing equipment. But our budget for consumables is very high. Yet, because Namibia is an arid country, we are presented with the most important biotechnological challenge, that is to screen for drought-tolerance using molecular markers, or better still to find drought-tolerance genes. We also have indigenous resurrection plants from which we could out-source drought-tolerance genes for development of our own “smart plants”. But this is all wishful thinking if we do not have the capacity to do so.

The option is to collaborate with those that have equipment and the know-how. South African Universities have the capacity, like the University of Cape Town where I have visited already. The problem is that we are not at the same level, they are too far ahead. So we are left to tackle the challenge of this biotechnological divide, which is widening day by day, within Africa and without Africa.

This is why international research organizations must step in to help. We also need our own initiatives at the level of NEPAD (New Partnership for Africa’s Development), African Union and regional groupings such as the Southern African Development Community (SADC). Most often, because of having few trained people in the field of biotechnology, we do not have serious engagement with policy decision-makers to approve biotechnology projects. That is why we see a plethora of useless agronomic and breeding field projects across Africa, without a sound biotechnological base.

Without biotechnology, efforts to solve Africa's hunger and poverty shall take long; in the end, we as scientists shall become irrelevant, and our sciences shall be useless. Our skills in the labs should be as sharp as our skills to negotiate for space and capacity for our science to flourish and make a positive contribution to our people. This is the unique challenge for us the biotechnologists of Africa, to be seen and heard. But we see most often that even at the level of political representation, while African Presidents have political and economic advisors, very few if any have scientific advisors. Shame!

So again, there is a lot we can do from within. We must summon the necessary political will to encourage the growth of biotechnology in Africa. The political will is also important to solve the problem of brain-drain of biotechnologists from Africa to the rich north, or from one African country to another. When I left Zambia three years ago, I could count genuinely trained molecular biologists, including myself, on my ten fingers. A friend I trained with in Brussels who later went to the US has never returned to Zambia or Africa, largely because of poor working conditions, apart from the peanut salary. To attract and retain biotechnologists must become a political undertaking at the level of governments.

That is where I end this debate: we need a leadership that will create capacity for biotechnology in Africa, maybe we should "clone" one - ha ha ha. Thank you very much to the moderator and all the participants.

Kazhila Croffat Chinsembu
Lecturer, Molecular Biology
Faculty of Science, Dept of Biology
University of Namibia
P/B 13301, Windhoek, Namibia.
Tel: 264-61-206 3426
Fax: 264-61-206 3791
Email: kchinsembu (at) unam.na

[Regarding e-conferences in this FAO Biotechnology Forum, a total of 13 have been held so far. None have dealt solely with the topic of biotechnology for disease analysis, prevention and therapy, although these issues have come up in different conferences e.g. in Conference 11 on food processing (involving the use of biotechnology to address food safety and product quality). Secondly, a meeting of the FAO Working Group on Biotechnology was held yesterday and it was decided that the next e-mail conference will deal with the potential role of biotechnology for improving use of water in agriculture. We will come back to the Forum members with more details on this at a later stage...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 14:04
To: 'biotech-room1@mailserv.fao.org'
Subject: 109: Not depending heavily on a single type of marker

This is E.M. Muralidharan from India, again.

For me, one happy outcome of participating in this conference has been the relevation that one should not depend too heavily on molecular markers of a particular type alone. Usually, the literature abounds with statements that only praise what is, for the time being, the latest method and claiming how useful it is in overcoming the disadvantages of the older methods. Words of caution are rarely given. The fact that, even with amplified fragment length polymorphism (AFLP) markers, conclusions can be misleading means that a critical evaluation should be done by researchers regarding the suitability of a particular system vis-a-vis the costs and ease of use for routine purposes.

It will be useful for many participants here, including me, if a few recent references were listed which comprehensively review the advantages and limitations of the different markers. This will help us choose judiciously the combination of marker systems and help pool together information to suit a particular purpose e.g. characterization of genetic resources. [If participants wish to send me the citations of relevant references, I will compile them and send as a single message before the conference ends. Include any weblinks if the articles are freely available on the web...Moderator].

E.M. Muralidharan
Scientist, Biotechnology Division
Kerala Forest Research Institute
Peechi, Thrissur, Kerala State
680653, India
Phone: +91-487-2699061, 2699037
Fax : +91-487-2699249
Email: emmurali (at) kfri.org
emmurali (at) sancharnet.in

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 14:26
To: 'biotech-room1@mailserv.fao.org'
Subject: 110: Benefits of the conference - Bosnia and Herzegovina

My name is Belma Kalamujic. I'm a postgraduate student and an employee of the Institute for genetic engineering and biotechnology in Sarajevo, Bosnia and Herzegovina.

I'd like to thank the FAO organization for setting up this conference. Since I'm working in the laboratory for molecular genetics of natural resources and my fields of interest for the time being are microsatellite markers and restriction fragment length polymorphisms (RFLPs), I had an opportunity to learn a lot from people with various experiences and background.

A lot of participants were from the developing countries so I also had an opportunity to see what kind of problems they face regarding the role of biotechnology in the characterisation and conservation, and to see what is the current position of our Institute, since Bosnia is not a rich country at all.

We were lucky, by participating in various projects with other partner countries, to receive an up-to-date technology and get an education in respectable laboratories in Europe and USA.

Our ongoing project is genetic characterisation of salmonid species in Bosnia and Herzegovina, using microsatellite markers and RFLPs. That our work wasn't worthless. After the first genetic testing of fish farms breeding stocks in 2003 confirmed earlier hypotheses on their alochtonous origin, a new law on freshwater fisheries was adopted, which included provision on obligatory genetic control of material provided for stocking.

I enjoyed being a part of this conference and I hope there will be many more like this one.

Belma Kalamujic
Institute for genetic engineering and biotechnology
Kemalbegova 10, 71000 Sarajevo
Bosnia and Herzegovina
http://www.ingeb.ba
belma_kalamujic (at) ingeb.ba
phone/fax ++387 33 442 891

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 15:27
To: 'biotech-room1@mailserv.fao.org'
Subject: 111: Re: Capacity building for biotechnology

From Alice Muchugi, Kenya, again.

On a small note before the conference closes, I would like to respond to Kazhila's message (nr. 108, July 1). Good comments. Just to let you know that I have just come from a meeting where I have learnt that there is a World Bank supported initiative to start up an African Institute of Science and Technology (AIST) with at least five regional centers; western, eastern, northern, southern and central. It is hoped that this will contribute to technological advancement in the region especially in capacity building. (That's good as we have all being suggesting pooling of resources and donor support!). There is also hope that the African scientists in Diaspora will greatly support the initiative even if it's on consultancy basis. Already the west and east centers have been identified and will be Nigeria and Tanzania respectively. So Kazhila can you front your country for southern block. I hope if the initiative materializes all those who have been contributing in this e-conference will assist to make biotechnology advancement a reality in Africa and other developing countries.

Finally it has been good reading all your contributions and I am truly gaining a lot. I look forward to further sharing news in the field with you all. To FAO organizing group, keep up the good work!

Alice Muchugi
PhD Research Fellow
Genetic Resource Unit,
World Agroforestry Centre (ICRAF)
PO Box 30677-00100
Nairobi,
Kenya
tel: +254-20-7224000 Ext 4273
fax: +254-20-7224001
email: a.muchugi (at) cgiar.org
http://www.worldagroforestrycentre.org

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 16:06
To: 'biotech-room1@mailserv.fao.org'
Subject: 112: Biotechnology, conservation and nature

I am Adediran Adeniyi Samuel, a research scientist (nutritionist) at the International Trypanotolerance Centre (ITC) in Banjul, The Gambia.

I am not a biotechnologist by training so please pardon my ignorance. I have been following with great interest all the various contributions and I would like to join issues with Vladimir Magalhães (Message 72, June 23) to raise some ethical issues.

It would seem to me that genetic characterisation and conservation via gene banking cryopreservation, vis a vis in-situ conservation should be considered within the context of the resources, human and materials, available to each country. Granted that the entire human race has a duty to conserve the environment for the use of present and future generations, developing countries should adopt approaches that are most sustainable for them.

The issue of capacity to use this technology has been raised, then there is the financial aspect. On both fronts, the developing country lags far behind. Therefore, for us, conventional conservation approaches cannot be jettisoned without dire consequences. Responsible use of natural resources, control of over exploitation, consciousness for the environment, curbing the over materialistic and capital build up tendencies of modern societal developmental approaches (western economic models) without due consideration for the eco-balance. All these will continue to play vital roles in conservation efforts. Of course, characterization is always good and necessary. We need to know what we have, where we are, where we want to be and how to get there. I therefore share the views of Vladimir that there is a need for international legislation on biopiracy. Until such control measures are in place, the developing countries in particular stand to lose in a biotech race having neither yet the capacity, infrastructures, sense of commitment, on the one hand nor the capital to pursue this mainstream science on the other hand.

Secondly, the entire ecosystem is in a state of constant evolution, if not in the short term in the long term (I stand corrected) with gene by environment interaction continually leading to the evolution of new species and naturally, extinction of certain species. Considering the alarming rate at which our physical environment has been changing, principally through human activities, it is time to reappraise the implications of these events and take thought of how to become partners in progress with nature.

Therefore, whilst not discountenancing the immense benefits of biotechnology and its conservation tools, these cannot be the license for unrestrained exploitation of the natural resource base.

Adediran Samuel Adeniyi
Research Scientist
International trypanotolerance Centre (ITC).
Bag 14, Banjul,
The Gambia.
Tel:220 - 4462928 (off)
220 - 9945154 (cell)
Fax: 220 - 4462924
Web: www.itc.gm
niyi.adediran (at) itc.gm

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 16:36
To: 'biotech-room1@mailserv.fao.org'
Subject: 113: Decision-support tools for conservation of livestock

I am Mizeck Chagunda, an animal geneticist from Malawi, currently doing a Postdoc at the Danish Institute of Agricultural Sciences in Denmark. I have followed with great interest the discussion in this e-conference. A lot of illuminating and constructive contributions.

My contribution, as the conference is going towards its close, is on decision support tools in as far as conservation strategies for farm animal genetic resources is concerned. I agree with the previous contributors that there might be no comprehensive databases available in different countries. Further, I agree that decision for conservation should not be done based on one source of information e.g. molecular markers alone. However, there seems to be a general lack of decision-support tools (computer programs, etc) that would combine information from different sources (molecular, phenotypic, genotypic, production system, indigenous knowledge, social economic, etc) in a meaningful way to support decision for conservation strategies. These tools could be used for monitoring degree of biodiversity, degree of risk and even progress made in different populations. Such tools would even be more useful if they had features that would make them adaptable to local environments and situations. I hope some research and development efforts can be focused in this area so as to utilise the available data where it exists and any future datasets being generated.

Mizeck Chagunda, PhD
Project Scientist
Research Unit for Disease Mechanisms, Biomarkers and Prevention
Dept. of Animal Health, Welfare and Nutrition
Danish Institute of Agricultural Sciences
Research Centre Foulum
P.O. Box 50
DK-8830 Tjele
Denmark
Dir.tel. +45 8999 1477
Cell: +45 5056 3892
Fax +45 8999 1500
email: Mizeck.Chagunda (at) agrsci.dk
http://www.agrsci.org

-----Original Message-----
From: Biotech-Mod1
Sent: 01 July 2005 16:46
To: 'biotech-room1@mailserv.fao.org'
Subject: 114: Re: Root crop diversity and local tissue culture

This is Nagib Nassar, again.

I refer to the proposal by Ann Marie Thro (Message 106, July 1) of using tissue culture as a means to avoid pathogen contamination in cassava. In an early message (nr. 4, June 6), I proposed apomictic clones to be more effective and cheaper. What do my colleages think in this? Your discussion and argument certainly will enrich our knowledge on the subject.

Nagib Nassar
Departamento de Genetica e Morfologia,
Instituto de Ciencias Biologicas,
Universidade de Brasilia,
Campus Universitario Darcy Ribeiro, Asa Norte.
CEP: 70910–900, Brasilia – DF,
Brazil.
Phone: (+55.61) 349.3253
Fax: (+55.61) 349.3562
nagnassa (at) rudah.com.br
www.geneconserve.pro.br

-----Original Message-----
From: Biotech-Mod1
Sent: 03 July 2005 10:42
To: 'biotech-room1@mailserv.fao.org'
Subject: 115: Preservation of livestock genetic resources

Again, I am Dr. Masroor Ellahi Babar.

I would like to express my regret for making a comment that I made in my previous message (nr. 107, July 1) “There are many countries like Canada which have not their own genetic resources”. I am aware of the fact that Canada has its genetic resources and is committed to the preservation of livestock genetic resources, and has devoted a considerable amount of funding to this initiative. What I wanted to say was that many breeds of livestock originated from Europe, Africa and Asia and these areas have wild type breeds. Most of the livestock species are kept in these areas for more than 5000 years. There are a few references to sheep rearing in Bible. Similarly, the Holy Prophet Muhammad (peace be upon him) used to take sheep for grazing. So these areas have original genetic resources. Other areas have some modified or migrated breeds as many areas are discovered much later than these three areas.

The conservation of farm animal genetic resources and biodiversity are growing concerns in all countries. The preservation of agro-biodiversity is important for sustainable agriculture and food security globally. The problem that I see is that most of the funds dedicated to genetic preservation are committed by the developed countries. A considerable number of livestock breeds that are considered rare and are thus preserved in these countries originated from Europe, Asia and Africa, many of them may not be rare in the country of origin. Second, a very large number of local breeds in developing countries are disappearing and are being replaced by more productive imported breeds. Many of these breeds may have valuable genetic characteristics that will become useful in the future. Very little or no attempt is being made to preserve these breeds.

My suggestion was for each institution in the developed countries to make a sistership relation with an institution in the developing countries, and develop joint genetic evaluation and conservation programs. The long-term outcome of such activities with respect of understanding the genetic merit of various breeds and preservation of genetic resources will be, in my opinion, immense.

Dr. Masroor Ellahi Babar,
Nova Scotia Agricultural College,
PO Box 550
Truro, Nova Scotia
Canada B2N 5E3
MBABAR (at) nsac.ns.ca

-----Original Message-----
From: Biotech-Mod1
Sent: 03 July 2005 10:44
To: 'biotech-room1@mailserv.fao.org'
Subject: 116: End of e-mail conference - India

I am Janaki Krishna from India again.

Though these conferences are a bit informal, I would like to thank FAO formally for organising this conference. I always enjoy the FAO conferences as they inspire and give lot of insights. I would also like to thank the Moderator for the nice moderation throughout the conference. The conference has generated very useful leads for further follow up and necessary actions. Looking forward to more such conferences in the area of biotechnology.

P S Janaki Krishna
Consultant
Andhra Pradesh Netherlands Biotechnology Programme
Institute of Public Enterprise
Hyderabad - 500 007,
India
Phone 91 - 40 - 27097018/27098148
Email: jankrisp (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 03 July 2005 11:15
To: 'biotech-room1@mailserv.fao.org'
Subject: 117: Using biotechnology to conserve and characterise life support species

I am Promila Kapoor-Vijay, an ecologist with special interest in population biology. My research work covers biodiversity and genetic resources of underutilized species. My recent work has been to provide concept and framework for developing a web-based Biodiversity Thematic window for the South, in which biotechnology has a sub theme.

I wish to reaffirm my support to the voices of all those who supported various contributions emphasizing use of biotechnology tools for conservation of plant and animal genetic resources in terrestrial and aquatic environments. I am very pleased to see emphasis being placed on the need to use of appropriate tools, techniques and practices for developing both conventional and advanced methods of cataloguing genetic diversity and variability of annual, perennial plant (trees) and animal genetic resources. There is no way one can put value on genetic resources as their importance transcends economic, social and ecological values. Ecological services rendered by biodiversity; economic value generated by biomaterials embedded in bio-wealth cannot be calculated and the few estimates that are available only give a clue as to future worth of naturally available biological resources.

It is well known that all developed countries invest heavily in biotechnology and it is becoming one of the key economic growth areas of the world and will have the next wave of major environmental impacts.

The knowledge and expertise related to biotechnology for the use of local and indigenous plant, animal and microbial resources is missing in the countries of the South where millions suffer from poverty, hunger and disease. Where and when people do not have resources to meet even their basic needs, the world does not focus on building their scientific and technological capacities as priority is to save lives at the given moment. However, the missing links of knowledge, building of competence and capacities, when not attended to at the right time, become the source of more of future problems and disasters.

The natural disasters (Tsunamis, land based earthquakes, volcanoes), whether caused by natural factors or driven by human actions, affect the poor most, as they do not have access to economic resources for coping with emergencies. The richer community, somehow, suffers lesser damage as they have easy access to social and economic instruments that can spread the impact of disasters. The poor, especially those living in the marginal environments, rely most on unique life support species for their food, nutrition security and survival of their communities in emergencies. These species have ability to grow in extreme environments and habitats such as saline, water logged lands (both coastal and non coastal) after disasters such as Tsunami, floods, land slides, drought. For example, some populations of Chenopodium album are used in emergencies by mountain people. Studies on genetic relationships among cultivated and wild populations of Chenopodium species using random amplified polymorphic DNA (RAPD) profiles has given new direction in characterization and conservation of this important pseudocereal. [Chenopodium album, also known as lambsquarter, is in the same genus as quinoa. Pseudocereals are plants, such as quinoa, that do not belong to the cereal grains grasses but produce fruits and seeds that can used as flour for bread and other staples...Moderator].

The genes which are unique to such life support species could be useful in developing future varieties of plants, animals and microbes in building food, nutrition, health, and ecological security for the people of the South. The use of biotechnology to catalogue and conserve diversity of life support species will safeguard humanity from poverty and hunger and impending threatening global climate change, increasing soil stresses such as from chemicals, salinity and desertification.

My considered view is that information, knowledge, and expertise associated with biotechnology which is relevant and needed to conserve unique plant, animal and microbial species thriving in diverse and especially extreme environments should be strengthened.

Developing countries of the South need to become part of this revolution. If they cannot, then they will become technologically excluded and lose out on the economic growth that is within their reach as the critical ingredient needed for using biotechnology, the vast pool of genetic material, is owned by them. If they do not take part, the benefits, so greatly needed by them, will be missed.

Dr Promila Kapoor-Vijay
Affiliated Scientist,
Institue of Environmental Sciences,
Zurich University,
Zurich
Switzerland
pkv (at) bluewin.ch

Professor (Hon.) in Environmental Sciences,
GB Pant University of Agriculture and Tchnology,
Pant Nagar-263145
Uttaranchal,
India

-----Original Message-----
From: Biotech-Mod1
Sent: 03 July 2005 11:22
To: 'biotech-room1@mailserv.fao.org'
Subject: 118: Re: DNA barcoding // Inadequacy of using a single molecular marker system

This is Kioumars Ghamkhar, again.

Regarding the 2 issues reiterated in P.K. Gupta's message (nr. 87, 27 June):

1. For the for first issue, I was hoping someone would address his comment on DNA barcoding before the e-conference ends but no one did. So, I do it:

There is no doubt that DNA barcoding can help taxonomists to classify, re-classify, or even identify taxa or new species within the current known taxa as well as the unknown taxa, which will be discovered in future (only 15% of all species have been identified so far). However, it does not mean that it is, or must be, an alternative to the traditional taxonomy based on morphological data/information. There is already an agreement among many taxonomists in the world to harmonise the DNA barcoding activities and because of a need for consistency, the gene that must be, or is, used should be a gene that exists in all taxa and while it is variable among taxa, it should not be too variable among (evolutionarily) very close taxa (sister groups). That is exactly why the genes responsible for coding the cytochromes have been mostly selected for this purpose. So, if anyone has got the facilities and the material (plant specimens), it is recommended to start doing barcoding sooner rather than later.

2. Regarding the second issue in his message (also mentioned by E.M. Muralidharan, Message 109, July 1):

Sure. No single molecular method has been ever claimed to be solving the world's problems. Basically, more molecular techniques/data, more resolution or better results. Also, using molecular data does not mean that morphology must be ignored or forgotten. The best approach (as I have mentioned in my previous email) is to analyse your single (each molecular and morphological) data, obtain the results, compare the results of separate datasets in pairs with the single results and, finally, the combined whole (single molecular plus morphological data) data with each separate and paired results using statistical analyses. If you have enough time and funding and you looking for the best outcome, you must do all this because there is (most of the time) inconsistency between different data sets.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

-----Original Message-----
From: Biotech-Mod1
Sent: 03 July 2005 11:33
To: 'biotech-room1@mailserv.fao.org'
Subject: 119: Re: Not depending heavily on a single type of marker

This is Kioumars Ghamkhar, again.

Concerning E.M. Muralidharan's message 109 (July 1) about amplified fragment length polymorphism (AFLPs):

Although I am doing (fluorescent) AFLPs myself, and I am pretty much convinced it is a great method, he is right about the fact that the results of AFLP (or any other whole genome fingerprinting technique) must be checked before jumping to any conclusion. This can be done either by using other more consistent techniques (such as sequencing of, for example, internal transcribed spacer (ITS) or a coding region of the genome) or by testing the results using different analytical methods. To get more information on this issue please read this article:
Phylogenetic signal in AFLP data sets, W.J.M. Koopman (2005), Systematic Biology, 54:2, p.197-217.

Dr Kioumars Ghamkhar
Research Associate
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au

[The abstract to this article reads "AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative"...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 03 July 2005 11:40
To: 'biotech-room1@mailserv.fao.org'
Subject: 120: Use of DNA microarrays for study of genetic diversity

I am PK Gupta again from Meerut University in India;

I would like to point out that one aspect, which still remains uncovered in this conference is the use of DNA microarrays for the study of genetic diversity. This subject is covered in detail in the recent Special Issue of "Chromosome Research" Volume 13, # 3, which is exclusively devoted to DNA microarrays. The DNA oligonucleotide arrays, already available in some plant systems, would allow the study of genetic diversity at the whole genome level utilizing information on diversity at the nucleotide level. Since these microarrays are being procured in several labs in the developing countries also, the participants in this conference should be aware of this powerful tool for the study of the germplasm, at least in some crop plants (e.g. rice, brassicas, etc.). Interested participants may consult the above Special Issue of Chromosome Research and the literature cited therein.

P.K. Gupta
Honorary Emeritus Professor and INSA Senior Scientist
Molecular Biology Laboratory
Department of Genetics and Plant Breeding
Ch. Charan Singh University
MEERUT-250 004
India
Tel (Lab): 91-121-2768195
(Resi): 91-121-2762505
TeleFax : 91-121-2768195
e-mail : pkgupta36 (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 03 July 2005 11:54
To: 'biotech-room1@mailserv.fao.org'
Subject: 121: Re: Preservation of livestock genetic resources

It is D. Vijay from India again.

I truly agree with Masroor Ellahi Babar (message 115, July 3) with regard to cooperation between developed and developing countries. What he said is true not only for Livestock but also for other resources like plants and fisheries. It's the right time to have a global understanding of the problem of loss of biodiversity and its conservation. Keeping the borders aside and united, the individuals can do a lot towards achieving this target. With the advancement of technology (like use of molecular markers for conservation) there should be a proper collaboration between these two parts of the world.

Being a first time participant of an e-conference, I am totally delighted by its concept and the way it was conducted. I thank the moderator for a nice moderation and FAO for organising such a worthy conference. This conference has helped me to brighten my understanding and gave me an opportunity to learn new concepts in the field of molecular biology with respect to conservation. I appreciate the way the participants responded and shared their experiences. Simply saying I like it very much. Thank you all.

Vijay.D, PhD
Scientific Assistant
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC Complex, Pusa Campus
New Delhi - 110 012, India
Office: +91-11- 25847537/46/47
Mobile: +91- 09868412855
Email: vijaydunna (at) gmail.com
URL: http://www.geocities.com/vijaydunna

-----Original Message-----
From: Biotech-Mod1
Sent: 04 July 2005 16:41
To: 'biotech-room1@mailserv.fao.org'
Subject: 122: End of e-conference - Cameroon

It's Roger Djoulde Darman, once more.

I just want at the end of this e-conference to acknowledge all of those who have been participating actively. I have really enjoyed it as I have learned a lot about biotechnology, especially concerning DNA data banks. I hope some of the ideas given here will be further materialised and be beneficial, particularly for preserving natural resources of developing countries. Anyway, I’II be happy to know more about the World Bank supported initiative to start up an African Institute of Science and Technology (AIST) mentioned by Alice Muchugi (Message 111, July 1). I am really interested and could you tell me where and what are the criteria to deposit a DNA in this bank? [Alice might be kind enough to respond directly to Roger about this...Moderator].

A special thanks to the moderator, he has done a great huge job!!!!.

Hope to participate again in the next e-conference.

Roger Djoulde Darman (PhD)
Researcher
IRAD/CRRAD
B.P 33 Maroua
Cameroon
Tel: 0032477236041
Email: djoulde (at) gmail.com

-----Original Message-----
From: Biotech-Mod1
Sent: 04 July 2005 16:42
To: 'biotech-room1@mailserv.fao.org'
Subject: 123: Summing up - Nigeria

I am Olayinka Edema, a food and applied microbiologist from Nigeria.

I had thought I would not contribute to this conference as the topic wasn’t directly related to my field. I have however enjoyed the messages tremendously and couldn’t help chipping in these words as the conference rounds up.

The first message by Charles Nkhoma (Message 1, June 6) and the seventh by Mahmoud Mohamed Ahmed Abdel Aziz (June 7) said it all and I thought those messages presented a good summary of the situation in the developing world.

I, however, do not totally agree with messages 16 (June 8) and 29 (June 9) by Roger Djoulde Darman. I believe that molecular techniques can even be used to modify the genes responsible for cyanide formation in cassava or even remove it totally. I’m sure fermentation improves the protein content of cassava, but I also know that it cannot be comparable to the increase by hybridization as reported by Nagib Nassar in message 5 (June 6). If the new techniques are too complicated, then it is our duty to present them in simpler ways. I do not agree that rural illiterate populations do not have the technical background to use starters. Some bread bakeries are owned by such categories of people and they handle and use baker's yeast quite effectively. Message 33 (June 10) by Kioumars Ghamkhar is very explicit and takes care of Roger’s concerns.

We do not have funds and resources to, on our own, advance in biotechnology. Neither can we afford to be left behind. I will advocate that we use all available opportunities at our disposal, provided by the more technologically advanced (as stated by D. Vijay in message 79, June 24), to learn and then come back home to work out appropriate ways of presenting the new technologies to our rural people in the forms they will understand and appreciate. If we fail to get the technical know-how as far as these technologies are concerned, we will be unable to control what happens to our countries in terms of food security in the near future.

In all, I think this has been a very informative and interesting conference.

Dr. Mrs. Olayinka Edema
Microbiology Department,
University of Agriculture,
Abeokuta,
Nigeria
moedemao (at) yahoo.co.uk

-----Original Message-----
From: Biotech-Mod1
Sent: 04 July 2005 16:43
To: 'biotech-room1@mailserv.fao.org'
Subject: 124: Gene banks and the role of biotechnology

This is Denis Murphy, a biotechnologist at the University of Glamorgan in the UK.

Firstly, as we draw to the end of this conference, I wish to thank the moderator and all participants for a most interesting and wide ranging discussion. It is especially good to hear from crop science colleagues whom I would never normally get a chance to meet, and from those in related disciplines, like animal breeding, where I am less aware of current progress. I have learned a lot in this conference and wonder if it would be possible to create a more permanent moderated forum for our community?

My specific points for the present discussion relate to gene banks and the role of biotechnology.

It is really a matter of priorities because, as we know from the current situation at CIMMYT (the International Maize and Wheat Improvement Center) and IRRI (the International Rice Research Institute), there are serious resource shortages even in the flagship centres of the CGIAR (Consultative Group on International Agricultural Research). The situation in many national research centres in developing countries is much worse, with failings in basic infrastructure like refrigeration sometimes causing the loss of irreplaceable genetic stocks. Then we have the dreadful situation of the effect of civil conflict and environmental disasters on genetic resources. Just to cite a few recent examples, the work at WARDA (the Africa Rice Center) on the new rice for Africa (NERICA) was seriously disrupted when its headquarters in Bouaké in Côte d’Ivoire was bombed in November 2004, and breeder Robert Carsky killed. The main Iraqi seed bank at Abu Ghraib, near Baghdad, was pillaged and destroyed after it was left undefended in the wake of the invasion of Iraq in 2003. Luckily, Iraqi colleagues had foreseen such a risk and had removed some of their precious seed across the border to safety at ICARDA (the International Center for Agricultural Research in the Dry Areas), near Aleppo, Syria. ICARDA is now helping to rebuild Iraqi agriculture by sending seed back to Iraqi farmers - over 20 tonnes has been sent so far in 2005. A further twist to this story occurred in mid-2005, when it was reported that hostility of the US government to the Syrian government was in danger of jeopardising efforts to ensure the future of ICARDA itself as an international repository of plant germplasm (editorial in Nature - http://www.scidev.net/pdffiles/nature/435537b.pdf).

IRRI has also provided new seed to countries such as Afghanistan, Rwanda and Cambodia, where seed banks had been destroyed during recent civil conflicts, and to Honduras, Nicaragua and Cuba were crops had been devastated by hurricanes. However, such efforts are merely the tip of a very large iceberg, as was shown in a 2005 report from CGIAR entitled "Healing wounds; How the international research centers of the CGIAR help rebuild agriculture in countries affected by conflicts and natural disasters" (http://www.cgiar.org/publications/HealingWounds/index.htm). This report documents dozens of examples, from about 50 countries around the world, where the CGIAR network has provided seed and breeding advice following a succession of environmental and manmade disasters. Examples range from famine in North Korea to post-hurricane assistance in the Caribbean.

We need to ensure that the world accepts the need for genetic resources to be available to all as a public good, as well as available for private exploitation as appropriate. Unless we have a stable, secure and genuinely accessible global system, it is difficult to think about progressing to the more sophisticated high-tech methods like markers and tissue culture, outside of those favoured countries that already have access to both the technology and the guaranteed resources to enable them to deploy it in the long term. There are many agronomic traits and crops where molecular markers can make a huge difference to crop breeding, but they require significant investment in both skills and infrastructure. In places where seed banks are being destroyed by looters who are just after the plastic bottles, or where stocks are dying from want of electricity to refrigerate them, we need to question our priorities.

A final point about progress in biotechnology. We have recently spent tens of millions of dollars on sequencing the rice genome. Out of the 60,000 computer-predicted genes in the rice genome, roughly half of them have been assigned an as-yet uncertain role on the basis of their DNA sequences, while only about ONE HUNDRED genes (0,166% of the total) have a known and verified function (Cyranoski D 2003, Rice genome: a recipe for revolution? Nature 422, 796–798 - www.nature.com/uidfinder/10.1038/422796a ). It will probably take many decades for plant physiologists and breeders to catch up with all this new information - maybe we should rethink our priorities and focus more on assimilating and exploiting the immense amount of information that we already have than in generating ever more terabytes of new data.

I will be exploring these and other issues in a forthcoming book on Agriculture, Plant Breeding and Biotechnology, to be published in 2006.

Prof. Denis Murphy
School of Applied Sciences
University of Glamorgan
Pontypridd
Wales
UK
CF37 1DL
dmurphy2 (at) glam.ac.uk

-----Original Message-----
From: Biotech-Mod1
Sent: 04 July 2005 16:44
To: 'biotech-room1@mailserv.fao.org'
Subject: 125: Thanks a lot!

It is Rajeev Varshney from IPK-Gatersleben, Germany again.

By this mail, I would like to thank FAO in general and John in particular for organising this wonderful conference. Like many other participants, I have enjoyed very much this conference and I have been benefited a lot by listening to the experiences and ideas of many participants. Without any doubt, the conference has witnessed the critical assessments of presently available tools for conservation of biodiversity and has provided many new ideas for further follow up and necessary actions.

I look forward to participating in such FAO's conference in the area of biotechnology.

Thanking John (Moderator) and all the participants once again.

Rajeev Kumar VARSHNEY, Ph.D.
Institute of Plant Genetics and Crop Plant Research (IPK)
Correnstrasse 3,
D 06466 GATERSLEBEN
Germany
Tel: ++ 49 39482 5594(off.),5231 (lab) Fax: ++ 49 39482 5595
E-mail: rajeev (at) ipk-gatersleben.de / rajeevkvarshney (at) hotmail.com
Web: http://www.ipk-gatersleben.de/en/ ; http://pgrc.ipk-gatersleben.de/

-----Original Message-----
From: Biotech-Mod1
Sent: 04 July 2005 16:44
To: 'biotech-room1@mailserv.fao.org'
Subject: 126: Capacity building for biotechnology - Suggestion for a global biotech programme

I am John Caesar, a senior lecturer in biology at the University of Guyana and presently Project coordinator for Guyana's UNEP-GEF (United Nations Environment Programme-Global Environment Facility) National Biosafety Framework Project.

This conference has been very rewarding. FAO and the moderator must be commended for this very enlightening forum. Please permit me to add to the discussion on capacity building. We in the Caribbean have similar biotechnology capacity problems akin to most developing countries with the exception of Cuba which is very far ahead. Additionally, the small size of countries comprising the Caribbean Community (CARICOM) necessitates harmonization of efforts and collaboration. To this end, the community's agricultural research organization, the Caribbean Agricultural Research and Development Institute (CARDI), recently coordinated an effort on the harmonization of biotechnology policy - www.cardi.org. The CARICOM Charter requires regional consultation on key developmental issues confronting member states. A CARICOM Single Market and Economy framework is to be implemented early next year. As we have been advised by some experts, this century is the bioeconomy century. Information technology has been a key developmental construct to date, with its attendant digital divide syndrome. Perhaps developing countries can learn from those experiences and leapfrog the biotech/bioeconomy age without compromising the safety of the technology. As has been pointed out by a number of participants, developing countries lack adequate capacity for biotechnology development. Where do we go from here? Should bilateral arrangements be the only means? Or should we look at a current model for capacity building in biosafety and adapt its process to facilitate all developing countries in the process?

Such a global project may go a long way in helping all developing countries to narrow the impending biotechnology-divide.

Thank you for this opportunity

John Cartey Caesar BSc(Hons) MSc
National Project Coordinator, UNEP-GEF National Biosafety Framework,
[Commissioner (part-time), Public Utilities Commission of Guyana; Secretary, Caribbean Academy of Sciences;
Senior Lecturer and former Dean of Natural Sciences, University of Guyana, Box 10-1110, Georgetown]
Environmental Protection Agency,
IAST Building,
University Campus,
Georgetown,
Guyana
Tel.: 592-222-5784 or 5785 ext.31 ext. 40(messages) or 6004(messages), 592-222-6610 (h); Cell: 592-623-8773
PhoneFax: 592-222-4180 or 2442
Email: jccaesar (at) yahoo.com

-----Original Message-----
From: Biotech-Mod1
Sent: 04 July 2005 16:46
To: 'biotech-room1@mailserv.fao.org'
Subject: 127: Re: Not depending heavily on a single type of marker

From Edo Lin, some references as requested in Message 109, July 1, of E.M. Muralidharan:

Edo Lin
Ceres Consulting International
309, rue de Bombon
77720 Bréau
France
tel and fax: +33 164387844
e-mail: ceres.consult (at) free.fr

[Articles 1 and 2 have abstracts, that are reproduced below
1. "A variety of different molecular techniques can be used for the study of botanical diversity. Restriction fragment length polymorphism (RFLP), arbitrary primed DNA, amplified fragment length polymorphism (AFLP), variable number of tandem repeats (VNTR), sequence-tagged simple sequence repeats (SSRs) and polymerase chain reaction (PCR) sequencing are briefly reviewed here. These techniques differ in the way that they resolve genetic differences, in the type of data that they generate and in the taxonomic levels at which they may be most appropriately applied. It is imperative to understand the different ways in which the data from the different molecular techniques can be utilized before embarking upon a programme of applying them to any particular diversity study".
2. "The ability of populations to undergo adaptive evolution depends on the presence of quantitative genetic variation for ecologically important traits. Although molecular measures are widely used as surrogates for quantitative genetic variation, there is controversy about the strength of the relationship between the two. To resolve this issue, we carried out a meta-analysis based on 71 datasets. The mean correlation between molecular and quantitative measures of genetic variation was weak (r = 0.217). Furthermore, there was no significant relationship between the two measures for life-history traits (r = - 0.11) or for the quantitative measure generally considered as the best indicator of adaptive potential, heritability (r = - 0.08). Consequently, molecular measures of genetic diversity have only a very limited ability to predict quantitative genetic variability. When information about a population’s short-term evolutionary potential or estimates of local adaptation and population divergence are required, quantitative genetic variation should be measured directly"...Moderator].

-----Original Message-----
From: Biotech-Mod1
Sent: 04 July 2005 16:50
To: 'biotech-room1@mailserv.fao.org'
Subject: End of FAO conference on biotechnology and genetic resources

Dear Colleagues,

The last message, (number 127, from Edo Lin), has been posted so Conference 13 of the FAO Biotechnology Forum, entitled "The role of biotechnology for the characterisation and conservation of crop, forest, animal and fishery genetic resources in developing countries", is now officially closed.

I personally found it an extremely interesting conference and I learned a lot. I was particularly glad to see that all sectors were covered in the conference, with excellent inputs about crop, livestock, fisheries and forest genetic resources, and that messages came in from so many people in nearly 40 different countries.

FAO established this Biotechnology Forum in 2000 with the aim of providing quality balanced information on agricultural biotechnology in developing countries and to make a neutral platform available for people to exchange views and experiences on this subject. We hope that you also found this conference informative, interesting and of value.

All the messages posted will remain on the Forum website for people to read in the future, at http://www.fao.org/biotech/logs/c13logs.htm. I will also put all the 127 messages into a single webpage and send a message to you with the weblink in the next couple of days. NB - We strongly encourage you, as Forum Members, to widely disseminate information from this conference so that the voices of the people that participated can be heard.

For your interest, we can provide some figures about the conference. It ran for four weeks, from 6 June to 4 July 2005, and a total of 645 people subscribed, the highest number for any of the Biotechnology Forum conferences held so far. Of the 645 people, 64 (i.e. 10%) submitted at least one message. Messages were received from all major regions of the world - 35 of the 127 messages posted (i.e. 28%) came from participants in Asia, 20% from Africa, 17% from Europe, 13% each from Latin America and the Caribbean and from North America and 10% from Oceania.

Messages came from people living in 38 different countries - the greatest proportion was from participants in India (15%), followed by Australia (9%), Canada (7%), Brazil and the United States (6% each), France (5%) and Kenya, Malaysia and Nigeria (4% each). A total of 78 messages (i.e. 61%) were from participants in developing countries and 49 (39%) from participants in developed countries. Most messages came from people working in research centres, including six CGIAR centres, (45%) and in universities (43%).

This conference was a success due to the active participation of the 64 people who sat down and invested their time and effort in sharing their views and experiences on the many diverse issues raised in this conference, such as the potential role for molecular markers in prioritising populations for conservation purposes; the potential role for markers in characterisation of different populations; the advantages and disadvantages of different marker systems; the potential importance of DNA banks; international collaboration and capacity building etc. etc. To each one of you, a special thanks.

John Ruane, PhD
FAO Working Group on Biotechnology,
Moderator, Conference 13
E-mail address: Biotech-Mod1@fao.org
FAO website http://www.fao.org
Forum website http://www.fao.org/biotech/forum.asp
FAO Biotechnology website http://www.fao.org/biotech/index.asp

p.s. I would like to remind you that that the next e-mail conference (number 14) of this Forum will deal with the important issue of the efficiency of water use in agriculture, and the potential role that biotechnology can play there.

p.p.s. I would also like to inform you that FAO-BiotechNews, the free FAO e-mail newsletter containing news and event items relevant to applications of biotechnology in food and agriculture in developing countries, already available in English, French and Spanish, is about to be launched in a Russian version.