[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.]
-----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