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Sent: 14 June 2005 12:38
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
Washington State University
Pullman, WA 99164-6402
e-mail: kisha (at) mail.wsu.edu
Sent: 14 June 2005 12:42
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
Email: qmehuque (at) bangla.net