SSR based molecular diversity study in local rice (Oryza sativa L.) genotypes of Bangladesh

Abstract

Genetic diversity is one of the most important factors considered in plant breeding and molecular approaches are well accepted and precise to determine the diversity. This study was conducted to determine the genetic diversity of 28 local rice varieties using Simple Sequence Repeat (SSR) markers. A set of five SSR markers namely RM55, RM259, RM413, RM474 and RM481 were used to study the diversity at molecular level. All of the microsatellite loci were amplified by the polymerase chain reaction (PCR) and found to be 100% polymorphic.  Across 28 varieties, 62 alleles were identified. The highest no. (15) of was identified by RM474. On the other hands RM55, RM259 and RM481 identified the lowest 11 alleles and RM473 observed 14 alleles. Observed heterozygosity for RM55, RM259, RM413, RM474 and RM481 were 0.071, 0.285, 0.107, 0.017 and 0.178, respectively. Genetic differentiation values were found in the range of 0.045 to 0.954 with an average of 0.912.  Variation also observed in allele frequency and diversity index where diversity index ranged from 0.776789 to 0.917101. Over all Nei’s genetic distance value (D) ranged from nil to 2.890 among 178 varietals pairs resulting as a means of permutation combination of 28 rice varieties. The UPGMA dendrogram based on Nei’s genetic distance separated all the varieties among with each other. 28 varieties were identified with at least one and/or combination of 5 primers. The approach of this study will be useful for the development of desirable varieties by selection of parents as well as to protect the varieties through DNA fingerprinting.