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Sent: 13 December 2003 11:03
Subject: 82: Re: MAS and bioinformatics for developing countries
I am Rajeev Varshney from the Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. At IPK I am working in the area of development of gene-derived molecular markers, especially microsatellites or simple sequence repeats (SSRs) in barley. During my Ph.D. I was engaged in development and identification of molecular (microsatellite) markers for some traits like grain protein content, preharvest sprouting tolerance, grain yield (1000 grain weight), etc. in bread wheat in India.
First of all I should mention that I really enjoyed the reading of messages from different people about MAS and role of developing countries. In fact the recent message (no. 81, December 12) from Alberto Davila prompted me to post the following message.
(1) I agree with Alberto Davila that integration of bioinformatics with MAS will prove very useful not only for development of molecular markers but also for effective utilization of MAS for crop improvement programmes. For instance, people have already started to use bioinformatics by writing some perl scripts or computer programmes to identify the microsatellites in the EST (expressed sequence tag) sequences (e.g. Kantety et al. 2002; Varshney et al. 2002). Thus development of microsatellite markers has become very inexpensive as compared to earlier techniques (Gupta and Varshney, 2000). Moreover, since these markers are derived from the ESTs/genes, they hold better potential for their applications across the species (Thiel et al. 2003). Furthermore, it has been advocated that the 'functional' markers are better resources for their use in breeding since they have developed from the expressed part of the genome and directly from the genes affecting a particular trait (Anderson and Lueberstadt, 2003). I am sure that many of the rice geneticists and breeders are already aware of the use of bioinformatics to saturate the map of rice with about 2200 SSR markers (McCouch et al. 2002).
In my opinion the availability of draft sequence of rice genome and its annotation can be a target for bioinformaticsts to identify the gene(s) which can be used as markers (like SSR, STS, CAPS or SNP, etc.) in breeding programmes of not only of rice, but also in other cereal species because of conservation of synteny of rice with other cereals. I would also argue to use those genes, identified for different traits (like abiotic stress, etc.) by using cDNA or microarray technology, as markers (of course, after converting them in appropriate marker systems, as mentioned above) in breeding programmes. So, I think that it is the time to go one step ahead from MAS to 'GAB' i.e. Genomics-Assisted Breeding.
(2) Generation of databases for storing the marker data, their protocols, etc. is also a task for bioinformaticists so that the available information can be disseminated successfully and duplication of similar efforts can also be avoided/minimized. In this direction, the USDA-IFAFS (Initiative for Future Agricultural and Food Systems) sponsored project MASWheat (http://maswheat.ucdavis.edu/) is an example, and there is a need to generate more databases for other crops, livestocks, etc.
I am sorry for the long message but I hope that it would inspire geneticists, breeders and bioinformaticsts to co-ordinate the efforts in the area of MAS or GAB aimed for crop improvement programmes.References:
Rajeev Kumar VARSHNEY, Ph.D.
Molecular Markers Group, Plant Genome Resource Centre,
Institute of Plant Genetics and Crop Plant Research (IPK)
D 06466 GATERSLEBEN
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/
Sent: 13 December 2003 11:14
Subject: 83: Integration of molecular markers with plant breeding
From David Reece, United Kingdom.
Several people have indicated that it is both difficult and important to integrate molecular markers with plant breeding programmes if the maximum benefits are to be realised. I would be very interested in hearing experiences and opinions about what constitutes "good practice" in achieving this kind of integration, and about the kind of difficulties that need to be overcome.
Incidentally, I recently gave a conference paper on this subject: the text version is not yet ready, but will shortly appear on our website at www.ex.ac.uk/egenis. I would appreciate comments from members of this conference. Unfortunately, the paper will not appear until after the end of the conference, but people can contact me directly.
Egenis (the ESRC Centre for Genomics in Society)
University of Exeter,
J.D.Reece (at) exeter.ac.uk