MOLECULAR CHARACTERIZATION AND GENETIC DIVERSITY ANALYSIS OF BORO RICE GERMPLASM USING SSR MARKERS

Abstract

An experiment was carried out with twenty four Boro rice germplasm at the laboratory of Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, during the period of November 2017 to March 2018 to investigate molecular characterization and genetic diversity analysis. Rice genome specific twelve well known SSR primers were selected and synthesized for molecular diversity analysis. All of the twelve primers were able to produce polymorphic bands. The highest (8) number of bands was observed in SSR primers RM206. Fifty four alleles, ranged from 1 to 8 alleles per locus and an average of 4.5 were detected. Forty five polymorphic alleles were also identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice germplasms. Six primers showed high diversity, three primers showed moderate diversity and three primers showed low diversity on the basis of PIC value. The value of pair-wise comparisons of Nei’s genetic distance (D) among 24 rice genotypes was computed from combined data for the 12 primers, ranged from 0.1667 to 0.9167 with an average of 0.5417. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. This result can be conveniently used for molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.