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DNA Research 2002 9(6):199-207; doi:10.1093/dnares/9.6.199
© 2002 by Kazusa DNA Research Institute
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Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.)

Susan R. McCouch1,*, Leonid Teytelman2, Yunbi Xu3, Katarzyna B. Lobos3, Karen Clare3, Mark Walton3, Binying Fu4, Reycel Maghirang4, Zhikang Li4, Yongzhong Xing5, Qifa Zhang5, Izumi Kono6, Masahiro Yano7, Robert Fjellstrom8, Genevieve DeClerck9, David Schneider9, Samuel Cartinhour9, Doreen Ware2 and Lincoln Stein2

1Plant Breeding Dept, Cornell University Ithaca, NY 14853-1901, USA
2Cold Spring Harbor Lab P.O. Box 100, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
3RiceTec, Inc. P.O. Box 1305, Alvin, Texas 77512, USA
4International Rice Research Institute P.O. Box 933, Manila 1099, Philippines
5National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University Wuhan 430070, China
6Institute of the Society for Tecno-innovation of Agriculture, Forestry and Fisheries (STAFF) 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
7Applied Genomics Laboratory, Department of Molecular Genetics, National Institute of Agrobiological Sciences 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
8USDA-ARS, Rice Research Unit 1509 Aggie Dr., Beaumont, TX 77713, USA
9USDA Center for Agricultural Bioinformatics, Theory Center, Cornell University Ithaca, NY 14850-1901, USA

* To whom correspondence should be addressed. 240 Emerson Hall, Ithaca, NY 14853-1901. Tel. +1-607-255-0420, Fax. +1-607-255-6683, E-mail: SRM4{at}cornell.edu

A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2240 unique marker 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 3284 publicly sequenced rice BAC and PAC clones (representing about 83% of the total rice genome), 65% 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%) of the newly designed markers along rice chromosomes. Fifty-six SSR markers (2.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy. The largest proportion of SSRs in this data set correspond to poly(GA) motifs (36%), 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 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb.

Key words: simple sequence repeats (SSR); rice (Oryza sativa L.); electronic PCR (e-PCR)


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