|Schneider, David - Dave|
Submitted to: DNA Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/26/2002
Publication Date: 1/26/2003
Citation: MCCOUCH, S.R., TEYTELMAN, L., XU, Y., LOBOS, K.B., CLARE, K., WALTON, M., FU, B., MAGHIRANG, R., LI, Z., XING, Y., ZHANG, Q., KONO, I., YANO, M., FJELLSTROM, R.G., DECLERCK, G.A., CARTINHOUR, S.W., SCHNEIDER, D.J., WARE, D., STEIN, L. DEVELOPMENT AND MAPPING OF 2240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA L.). DNA Research 9:199-207. 2002. Interpretive Summary: DNA markers are used to map important traits in the rice genome and can be used in marker-aided selection of these traits. Simple-sequence repeat (SSR) markers (also known as microsatellite markers) are particularly useful for gene mapping and marker-based selection since these markers are amenable to high-throughput analysis and are informative in many types of genetic crosses. The utility of SSR markers is especially valuable in US rice breeding research since many of the varieties used in breeding programs arise from a genetically narrow gene pool. This research paper presents the development of 2,240 new SSR markers for rice, a vast increase over the 500 previously available SSR markers. This development was made possible by the joint contributions of nine international research groups, two of which are from the USDA Agricultural Research Service, known as the International Rice Microsatellite Research Initiative, organized by Dr. Susan McCouch at Cornell University. This initiative was motivated by the public release of 6,655 SSR-containing DNA sequences by Monsanto Corporation in 2001. The IRMI goal was to systematically develop at least 1,000 SSR markers from this sequence information and to make these markers available to the international rice research community. This research paper reports the successful achievement of this goal.
Technical Abstract: A total of 2,414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2,240 unique marker loci have been developed and experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are reported for 7 percent (174) of the loci. The majority (92 percent) of primer pairs were developed in regions flanking perfect repeats greater than 24 bp in length. Using electronic PCR (e-PCR) to align primer pairs against 3,284 publicly sequenced rice BAC and PAC clones (representing about 83 percent of the total rice genome), 65 percent of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. Additional information based on genetic mapping and 'nearest marker' information provided the basis for locating a total of 1825 (81 percent) of the newly designed markers along rice chromosomes. Fifty-six SSR markers (2.8 percent) hit BAC clones on two or more different chromosomes and appeared to be multiple copies. The largest proportion of SSRs in this dataset correspond to poly(GA) motifs (38 percent), followed by poly(AT) (15 percent) repeat tracts, while GC-rich motifs were the shortest. In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2,740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb.