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Sent: 12 December 2003 10:11
Subject: 80: MAI from wild species, other issues
This is from N. Sarla, Principal Scientist, Directorate of Rice Research, India. I am working on identification and introgression of yield-enhancing QTLs from wild species of rice.
My comments are on marker aided introgression from wild species and some of the 11 issues put up for discussion. [refers to Section 6 of the Background Document to the conference...Moderator].
1. Marker aided introgression of QTLs for complex traits from close wild relatives to crops would be useful for developing countries as the genetic gains (e.g. high yield, drought tolerance, etc.) are enormous. Such QTLs, stable over different genetic backgrounds and environments, have been reported. The advanced backcross (BC) method for identifying QTLs from the wild species helps save time. I might add that it is possible to get plants looking like the recurrent parent in BC2 itself (all the chromosomes may not undergo recombination in each meiotic cycle) from elite cultivar x wild species crosses.
2. Marker-aided allele mining (for specific traits or QTLs) from the vast germplasm is also a distinct possibility. Assuming synteny (colinearity) one can look for beneficial alleles in the germplasm using markers for specific traits. Since many developing countries have large germplasm resources, it will be useful to develop competency in these areas for accelerating utilization of germplasm by breeders. FAO can play a catalytic role in the process.
3. As long as all information on mapping and marker development is kept in the public domain, benefits are sure to follow, either in the form of reduced costs or time saved to researchers in developing countries. To give an example, working with limited resources we were trying to introgress, map and identify QTLs for yield from a wild species O.rufipogon using the advanced backcross method. Knowing that certain chromosomes have more QTL-rich regions than others, the mapping work was then confined to polymorphic SSR markers on 5 chromosomes (instead of 12, cost cutting!) and getting a dense linkage map to increase the likelihood of identifying significant QTLs in these chromosomes. We thus mapped a QTL with significant effects on yield on chromosome 2. Secondly, inclusion of some unmapped multilocus markers (RAPDs, ISSRs which are cheaper to use) along with mapped SSR markers (which are costlier, if proprietary) in mapping studies helps in placing cheaper (per polymorphism) markers on maps. [Inter-simple sequence repeat (ISSR) techniques are nearly identical to random amplified polymorphic DNA (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. SSR markers are also called microsatellites...Moderator].
4. The limiting factors for successful application of MAS in some developing countries may not be costs alone. The cost of mapping, marker development, and their use is coming down. Simpler, quicker and high throughput methods of DNA extraction are being reported. Use of multiplex PCR (polymerase chain reaction), multiplex PAGE (polyacrylamide gel electrophoresis), cheaper staining methods may cut costs further. The application requires a close synergy between the user of MAS and the developer of markers, the need and value of MAS should be obvious to both. Successful conventional breeding programs should be linked right from the beginning of a MAS program.
5. The issue raised by Dr Williams regarding communication between breeders and lab personnel is significant. From my earlier experience as faculty of Genetics at Indian Agricultural Research Institute, New Delhi, I would say PhD students who work with both and appreciate both are an asset. They could help "bridge the gap", so to say. FAO could provide PhD scholarships for MAS application studies especially in crops of regional importance, which are nutritionally important but may not attract much funds otherwise. [The messages referred to is message 70 (December 5) by Manilal William, who wrote "Another key aspect of marker applications and utilization of markers in the breeding programs is the need for close collaboration between the field personnel such as pathologists, entomologists, breeders with the personnel working in the laboratories"...Moderator].
Tanksley SD, Nelson JC, 1996. Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding line. Theoretical and Applied Genetics 92, 191-203
Tanksley SD and SR McCouch, 1997. Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277: 1063-1066
N Sarla PhD
Crop Improvement Section
Directorate of Rice Research
Hyderabad 500 030
email: sarlan (at) operamail.com
Sent: 12 December 2003 11:16
Subject: 81: MAS and bioinformatics for developing countries
This is from Alberto Davila, molecular biologist and bioinformatician, from Instituto Oswaldo Cruz-Fiocruz, Brazil.
I have followed with great interest the discussion about MAS and developing countries. Some points that have not been addressed are:
a) While MAS could be a bit expensive for some developing countries, it is something that can be done without major problems in "less" poor countries such as Brazil, for example. So, ideally we could use countries like Brazil (and others, of course) to help with MAS development in other developing countries. This refers to the concept of "South-South collaborations".
b) Nobody (as far as I know) has talked about bioinformatics. How do you analyze your markers? In a recent IAEA meeting (DNA-based techonologies), it was proposed to the plenary to help with the establishment of a working group in bioinformatics. As you know, bioinformatics is one of the disciplines that can be developed with success in developing countries. The World Health Organization (WHO) has recognized its importance and created 3 centers for "Bioinformatics and applied genomics": http://www.who.int/tdr/grants/awards/bioinformatics-10-01.htm. [The meeting referred to is the international symposium on "Applications of gene-based technologies for improving animal production and health in developing countries", held on 6-10 October 2003 in in Vienna, Austria, jointly organized by the International Atomic Energy Agency (IAEA) and FAO. The book of extended synopses from the meeting is available at http://www.iaea.org/programmes/nafa/d3/mtc/synopses.pdf or contact h.makkar (at) iaea.org for more details...Moderator].
I have not seen anything similar in the livestock research field, especially for developing countries.
So, my suggestion is to promote the establishment of the working group on bioinformatics (in developing countries) for livestock research having, as the main goal, the development of that discipline in developing countries.
Alberto M. R. Davila, PhD
Kinetoplastid Biology and Disease (Biomed Central)
DBBM / Instituto Oswaldo Cruz / FIOCRUZ
Av. Brasil 4365
Rio de Janeiro, RJ, Brasil
Email: davila (at) fiocruz.br amrdavila (at) yahoo.com
Phone: 55-21-3865-8229 / 3865-8206
Centralized Trypanosome Resources: http://www.trypanosome.com