Genetic relatedness of Portuguese rice accessions from diverse origins as assessed by microsatellite markers

Simple sequence repeat (SSR) markers detect a significantly high degree of polymorphism in rice (Oryza sativa L.) and are particularly suitable for evaluating genetic diversity among closely related cultivars. A total of 176 rice accessions originating from 19 countries in the Portuguese working germplasm collection and two standard rice varieties (IR36-indica and Nipponbare-japonica) were analyzed for DNA profile using 24 SSR loci covering two loci per chromosome. A total of 184 alleles were detected. The number of alleles per locus ranged from 3 to 16, with an average of 7.7, and the PIC value ranged from 0.179 to 0.894 with an average of 0.667. All the loci were polymorphic among the accessions and clearly distinguished the indica and japonica subspecies. At 20% similarity, cluster analysis of the 178 accessions revealed three major groups, japonica, basmati, and indica (Groups 1, 11, and 111, respectively). The japonica group contained 87% of the accessions and showed a wide range of similarity values (0.21-0.92), revealing a high degree of diversity among the accessions. Many of the accessions included in this study are morphologically similar and lack pedigree information. Hence, identification of genetic distances among the accessions should improve their use in breeding programs. As a result of this study, genetically diverse parents can be identified, increasing the usefulness of germplasm collections by broadening the genetic base of rice varieties.