[For further information on the Electronic Forum on Biotechnology in Food and
Agriculture see Forum website.
Note, participants are assumed to be speaking on their own behalf, unless they state otherwise.]
Sent: 07 June 2005 16:25
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
Washington State University
Pullman, WA 99164-6402
kisha (at) @mail.wsu.edu
Sent: 07 June 2005 16:27
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
fassad9 (at) yahoo.com
Sent: 07 June 2005 16:28
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
Tel: 58-0212-903-5104v Fax:58-0212-903-5092
dinfante (at) idea.gov.ve
Apdo. 17606 Parque Central
Caracas 1015-A, Venezuela
Carretera Hoyo de la Puerta
Sartenejas, Caracas 1080
Sent: 07 June 2005 16:29
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
jcummins (at) uwo.ca
Sent: 07 June 2005 16:29
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
Tel: 264-61-206 3426
Fax: 264-61-206 3791
Email: kchinsembu (at) unam.na
Sent: 07 June 2005 16:30
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
International Plant Genetic Resources Institute
IPGRI Office for South Asia
NASC complex, Pusa Campus
New Delhi - 110 012, India
E-mail: vijaydunna (at) gmail.com
URL: http:// www.geocities.com/vijaydunna
Sent: 07 June 2005 16:31
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,
email: sgtan (at) fsas.upm.edu.my
Sent: 07 June 2005 16:32
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
jcummins (at) uwo.ca
[The term alloploid refers to a polyploid organism with sets of chromosomes derived from different species...Moderator].
Sent: 07 June 2005 16:33
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.
International Development Research Centre (IDRC)
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].
Sent: 07 June 2005 16:34
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.
International Development Research Centre (IDRC)
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].