Variety identification and genetic diversity analysis in rice (Oryza sativa L.) using STMS markers

Abstract

In the present study, 14 rice specific sequence tagged microsatellite site markers (STMS) were used to develop
fingerprints and to determine the genetic relatedness among 48 rice genotypes/cultivars. Ten of the 14 SSR primer
pairs were found to be polymorphic, generating a total of 39 distinct reproducible alleles with an average of 2.79
alleles per primer pair and 22 (56.41%) of the 39 bands amplified emerged as polymorphic. The number of alleles per
primer ranged from one to six. The polymorphic information content (PIC) value ranged from 0.03 to 0.7 with an
average of 0.35. Cluster analysis based on Jaccard’s similarity coefficient using unweighted pair group methods for
arithmetic mean (UPGMA) grouped the 48 rice cultivars into five major clusters with an average similarity index of
0.87. A diagrammatic representation of DNA fingerprints of the rice cultivars based on 10 informative SSR markers
was developed for ready reference, which are expected to be key in varietal identification as well as provide IPR to
halt biopiracy.