Genetic diversity of rice cultivars by microsatellite markers tightly linked to cooking and eating quality

Abstract Improving cooking and eating quality of rice is one of the important objectives of many breeding programs. The study of genetic diversity in specific regions of rice genome using molecular markers is an important index that can be used for the application of marker assisted selection (MAS) in rice breeding programs. In this study, 48 rice genotypes were grouped using 7 microsatellite (SSR) markers tightly linked to major QTLs controlling three major components of rice cooking and eating quality (i.e. amylose content, gelatinization temperature and gel consistency). The number of polymorphic alleles produced by each microsatellite marker ranged from 3 alleles at RM314 locus to 10 alleles at RM276 locus. The total number of polymorphic alleles was 41 alleles with the average of 5.86 alleles per SSR locus. Effective number of alleles varied from 2.68 to 5.25 alleles at RM314 and RM276, respectively, with an average of 3.74 alleles per locus. The average heterozygosity based on Nei's gene diversity was 0.72 indicating high genetic variation among the studied varieties. Cluster analysis with UPGMA method based on simple matching (SM) similarity coefficient divided the genotypes into four groups and separated the landrace cultivars with good cooking and eating quality (based on Iranian taste) from others. Cophenetic correlation coefficient between similarity matrix and cophentic matrix was 0.93 indicating that the used similarity coefficient and cluster analysis method were suitable to use the information derived from markers to group rice genotypes. Results of this research indicated that microsatellite markers linked to genes or QTLs controlling grain cooking and eating properties are suitable tools for marker assisted selection (MAS) to identify rice grain quality