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 > or = 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.

Development of core collections is an effective tool to extensively characterize large germplasm collections, and the use of a mini-core subsampling strategy further increases the effectiveness of genetic diversity analysis at detailed phenotype and molecular levels. We report the formation of a mini-core subset containing 217 entries derived from 1794 core entries representing the genetic diversity found in more than 18,000 accessions of the USDA-ARS rice (Oryza sativa L.) germplasm collection. The mini-core was developed with PowerCore software on the basis of 26 phenotypic traits and 70 molecular markers. The 217 entries in the mini-core had a similar distribution over 15 geographical regions, with 1794 entries in the original core collection. The resultant mini-core had 6.3% of mean difference (MD%), 16.5% of variance difference (VD%), 102.7% of variable rate (VR%), and 97.5% of coincidence rate (CR%) with the core collection, which brought about full coverage of 26 traits. All 962 alleles identifi ed by the 70 markers in the core collection were captured in the mini-core, which maximized allelic richness up to 100% and resulted in an average genetic diversity (Nei index) of 0.76, ranging from 0.37 to 0.97 among the markers. In conclusion, the mini-core presented in this study is a highly suitable and representative subset of the USDA rice core collection as well as the entire USDA-ARS rice germplasm holdings.

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A valuable core collection that is a subset of a whole germplasm collection should capture most of the variation present in the whole collection, while allowing for more efficient evaluation and management due to smaller size. The United States Department of Agriculture (USDA) rice (Oryza sativa L.) core subset (RCS), assembled by stratified random sampling, consists of 1790 entries from 114 countries and represents approximately 10% of the 18412 accessions in the rice whole collection (RWC). Data for this study were obtained from the USDA germplasm system at http://www.ars-grin.gov for the RWC and from an evaluation conducted in 2002 for the RCS. Comparative analysis for frequency distributions of 14 descriptors demonstrated that the RCS was highly correlated with the RWC (r = 0.94, P < 0.0001). Thus, information drawn from the RCS could be effectively used to assess the RWC with 88% certainty. Correlation coefficients between the RCS and the RWC for eight descriptors were ≥ 0.9, indicating that the RCS was highly representative of the RWC. Correlation coefficients for the other six descriptors were lower (0.65–0.88), but still significant.