Evaluation of Genetic Diversity in Rice Subspecies Using Microsatellite Markers

Abstract

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. The purpose of this study was to evaluate the genetic diversity within a diverse collection of rice (Oryza sativa L.) accessions, and to determine differences in the patterns of diversity within the two rice subspecies indica and japonica Thirty‐eight rice cultivars of particular interest to U.S. breeding programs and two wild species accessions (O. rufipogon Griffithand O. nivara Sharma et Shastry) were evaluated by means of 111 microsatellite markers distributed over the whole rice genome. A total of 753 alleles were detected, and the number of alleles per marker ranged from 1 to 17, with an average of 6.8. A positive correlation was found between the number of alleles per locus and the maximum number of repeats within a microsatellite marker. Compared to indica cultivars, the japonica group showed significantly higher genetic diversity on chromosomes 6 and 7, and considerably lower diversity on chromosome 2. All rice cultivars and lines could be uniquely distinguished, and the resulting groups corresponded exactly to the indica and japonica subspecies, with japonica divided into temperate and tropical types. With stepwise discrimination, two subsets of approximately 30 markers were identified that produced genetic distance matrices and dendrograms that were the same as those produced by means of all 111 markers. The results suggested that a relatively small number of microsatellite markers could be used for the estimation of genetic diversity and the identification of rice cultivars.