UTILIZATION OF SSR PRIMERS TO DISCRIMINATE BETWEEN DIFFERENT SUBSPECIES OF RICE (Oryza sativa, L.)

Abstract

Nine rice (Oryza sativa L.) genotypes of indica and japonica types were used in the present study. Total number of 274 SSR simple sequence repeats primers were used to detect the genetic variation and genetic markers specific for each rice genotype. The results showed that the 219 SSR primers were generate a total 645 amplified alleles, among them 605 alleles were polymorphic. The temperate japonica accessions showed 105 alleles at 50 polymorphic loci. Within three indica accessions, 266 alleles were detected at 122 polymorphic loci. Within the three tropical japonica accessions, 129 alleles were detected at 61 polymorphic loci, respectively. The average number of alleles per locus (A) 2.49, 1.2, 1.55 and 1.25 were observed in total, temperate japonica, indica, and tropical japonica accessions, respectively. Average number of alleles per polymorphic locus (Ap) 2.76, 2.1, 2.18 and 2.11 were observed in total, temperate japonica, indica, and tropical japonica accessions, respectively. The average number of gene diversity (PIC) was 0.51, indicating moderately high variation among the nine accessions. Twelve SSR markers were able to discriminate among the temperate japonica, indica, and tropical japonica rice accessions under the present study.