Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.)
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L.) Susan R. McCouch(1,*), Leonid Teytelman(2), Yunbi Xu(3), Katarzyna B. Lobos(3), Karen Clare(3), Mark Walton(3), Binying Fu(4), Reycel Maghirang(4), Zhikang Li(4), Yongzhong Xing(5), Qifa Zhang(5), Izumi Kono(6), Masahiro Yano(7), Robert Fjellstrom(8), Genevieve DeClerck(9), David Schneider(9), Samuel Cartinhour(9), Doreen Ware(2) and Lincoln Stein(2) 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: 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)