ARS | Publication request: DEVELOPMENT OF 2,240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA)

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 21, 2002
Publication Date: December 31, 2002
Citation: MCCOUGH, S.R., TEYTELMAN, L., KONO, I., YANO, M., FJELLSTROM, R.G., DECLERCK, G.A., SCHNEIDER, D.J., CARTINHOUR, S.W., WARE, D., STEIN, L. DEVELOPMENT OF 2,240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA). GENOME RESEARCH. 2002.

Interpretive Summary: This study reports the development and release to the public of over 2400 new genetic markers suitable for use in rice breeding. The genetic markers are based on the presence of small repeated regions throughout the rice genome. These regions are abundant, variable, and easily detected using low-cost methods such as PCR (polymerase chain reaction). The total number of PCR based markers is now over 2700, enough to provide nearly complete coverage of all 12 rice chromosomes. It is expected that the markers will be used widely in the generation of new varieties of rice, and they will also be helpful in understanding the relationships between different varieties and their historical origins.

Technical Abstract: A total of 2,417 new di-, tri- and tetra-nucleotide SSR markers, representing 2,243 unique loci have been developed and experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are reported for 7% (174) of the loci. The majority (92%) of primer pairs were developed in regions flanking perfect repeats > 24 bp in length. Using electronic PCR (e-PCR) to align primer pairs against 1,847 publicly sequenced rice BAC and PAC clones (representing about 50% of the total rice genome), 49% of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. Forty SSR markers (1.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy. The largest proportion of SSRs in this dataset correspond to poly(GA) motifs (38%), followed by poly(AT) (15%) and poly(CCG) ( 8%) motifs. AT-rich microsatellites had the longest average 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 2,743 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb (equivalent to approximately 0.55 cM).