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CROP BREEDING & GENETICS

Microsatellite Markers in and around Rice Genes: Applications in Variety Identification and DUS Testing

^a Crop Science Dep., Federal Univ. of Lavras, Lavras, Minas Gerais, Brazil
^b Plant Research International, P.O. Box 16 6700 AA Wageningen, The Netherlands
^c current address: Brazilian Agricultural Research Corporation, EMBRAPA, Embrapa Wheat, Passo Fundo, Rio Grande do Sul, Brazil

^* Corresponding author (bonow{at}cnpt.embrapa.br).

In Brazil, rice (Oryza sativa L.) varieties adapted to different ecological regions are available on the market. However, these varieties exhibit highly similar morphologies, which makes their identification difficult. In this study we identified microsatellites in and around genes that are useful for the identification of the main rice varieties cultivated in Brazil. Thirteen microsatellites were selected from the region upstream of MADS-box genes and 37 were derived from expressed sequence tags (ESTs). Of the 50 microsatellites selected, 19 were polymorphic, and a small set of five primer pairs was sufficient to discriminate among the 37 rice varieties studied. The polymorphic information content (PIC) value of the 19 microsatellite markers varied between 0.05 and 0.94. Unweighted pair group method with arithmetic mean (UPGMA) analysis showed that these markers group the 37 varieties according to their subspecies, indica or japonica. These results indicate that it is possible to identify informative microsatellites in and around rice genes, and that these markers are capable of discriminating between closely related varieties of rice. Moreover, our findings suggest that microsatellite markers can play an important role as a source of additional information to supplement the morphological descriptors recommended by International Union for the Protection of New Varieties of Plants (UPOV).

Abbreviations: BLAST, Basic Local Alignment Search Tool • EST, expressed sequence tag • DUS, distinctness, uniformity, and stability • NCBI, National Center for Biotechnology Information • PBR, plant breeders' rights • PIC, polymorphic information content • PCR, polymerase chain reaction • UPGMA, unweighted pair group method with arithmetic mean • UPOV, International Union for the Protection of New Varieties of Plants