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Sent: 15 June 2005 18:04
Subject: 53: Re: Establishing a universal molecular marker data base
This is Kioumars Ghamkhar from Australia, again.Considering messages from Marilyn Warburton (message 42, June 10) and Ted Kisha (message 51, June 14):
In support of Marilyn Warburton's suggestion, I think coordination of using different markers by different labs around the world to characterize a specific germplasm/species by an organisation such as FAO or IPGRI will be a great achievement. These data can be stored and analysed by IPGRI in collaboration with those researchers, after collecting all data. We should not worry about different results from different datasets. What is important is the combined analysis that gives us an almost consensus on all the data.
In terms of using single nucleotide polymorphisms (SNPs), although it is a good idea for wheat or maize it is not a good idea for other not very well-known and newly introduced crops because you will need heaps of sequencing work to have access to SNPs.
Also, supporting, we should not focus only on the protein-coding regions of DNA or markers such as microsatellites that only focus on particular parts of DNA. Because non-coding regions are not necessarily (so-called) junk DNA, we must use techniques such as AFLP and particularly its fluorescent technique which gives us up to 300 bands for each sample (it is a huge source of data). To prove how important the non-coding regions of DNA are, I draw your attention to the fact that coding regions are just "functional needles in a genomic haystack" (Bofkin, L. and S. Whelan. 2004. Functional needles in a genomic haystack. Heredity, 92, 363-364). Also, many "conserved non-genic sequences (CNGs)" have proved to be more conserved between genomes than protein coding sequences, leading to some valuable clues to evolution. More evidence? One study reports that parts of the non-coding DNA may be involved in embryonic development (Peaston A.E. et al. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Developmental Cell, 7. 597 - 606).
Dr Kioumars Ghamkhar
Centre for Legumes in Mediterranean Agriculture (CLIMA)
University of Western Australia
35 Stirling Highway
Crawley WA 6009
Voice: 61 8 6488 7120
Fax: 61 8 6488 1140
E-mail: kioumars (at) cyllene.uwa.edu.au