MOLECULAR CHARACTERIZATION AND GENETIC DIVERSITY ANALYSIS OF T. AMAN RICE GERMPLASM BY USING SSR MARKERS

Abstract

A total of Twelve (12) Simple Sequence Repeats (SSRs) were used to covered the entire twelve (12) rice chromosomes over twenty-five (25) T. aman rice germplasms to characterize the genotypes, analyze the genetic diversity and also to establish the sovereignty of Bangladesh rice gene pool. A total fifty (50) alleles were detected across the 12 loci obtained in the study. The number of alleles per locus ranged from 2 (RM411) to 7 (RM252), with an average of 4.16. The frequency of the most common allele at each locus ranged from 48% (RM252) to 92% (RM320) with an average of 69%. The gene diversity was observed and ranged from 0.15 (RM320) to 7.0 (RM252) with an average of 0.47 which compliance with PIC values. The polymorphism information content (PIC) value ranged from 0.14 (RM320) to 0.67 (RM252) with an average of 0.43, were identified in all loci. The PIC values revealed that RM252 and RM206 were the most suitable markers for identification and diversity estimation of twenty-five (25) T. aman rice genotypes. The pairwise genetic dissimilarity coefficient ranged from 0.00 to 0.92 (0% to 92%) with an average of 0.45 (45%). Principal component analysis and clustering system based on UPGMA and Unrooted-neighbors joining tree analysis from the population structure method showed the tested germplasms as intermediate diverse in structure and clustered the twenty-five germplasms into six major clusters namely I, II, III, IV, V and VI. Among the clusters, cluster IV, V and VI were divided in to further clusters. In conclusion, it is suggested that markers RM252 and RM206 were most suitable in the detection of polymorphism over the entire twenty-five transplant aman rice genotypes studied and should be utilize in further study. Therefore, hybridization could be made between the two distant populations with highest genetic dissimilarities such as, genotypes Bohi × Ranga, Bohi × Purple Rice-2, Bohi × Purple Rice-3 which serve as parents to produce new varieties by plant breeders or geneticist for the benefit of the farmers.