Genetic variation, population structure, and cluster analysis of rice (Oryza sativa L.) genotypes using morphological characteristics and molecular markers

Indigenous landraces are heterogeneous and exhibit greater gene diversity, and are therefore an excellent source of variation and material for crop improvement. However, they are very prone to genetic erosion, therefore exploration of genetic variability in landraces is essential step for crop breeding. Discovery of the genetics of a character in rice, that cope adverse condition, is important for maintaining world-food supply. In this study, fifty rice genotypes were assessed for the phenotypic and genetic diversity and their relatedness using morpho-physiological traits of the genotypes. Further clustering and population structure analysis were performed using phenotypic and simple sequence repeat (SSR) markers data through unweighted pair group method with arithmetic mean (UPGMA) and STRUCTURE analysis. Significant variation among yield components were identified. Phenotypic and genotypic coefficients of variability were higher for filled grains, whereas heritability was highest for plant height. Panicle number and 100-grain weight displayed significant relationship with yield. Phylogenetic clustering of the agromorphological traits divided the genotypes into eight clusters, whereas SSR markers yielded ten clusters. SSR markers produced a total of 138 alleles varying from two to nine with 77.53% polymorphic allele having 3.69 alleles per locus (average). The polymorphic information content indices and observed number of alleles varied among markers with an average of 0.649, exhibiting RM336, RM316, and RM287 have the greatest potentiality in exploring genetic diversity among genotypes. Among the genotypes, Dolkochu, Jolduba, BRRI Dhan-32, and Mokbul displayed significant variability, suggesting their suitability as potential parents in hybridization programs. Population structure study demonstrated that the genotypes were structurally diverse that grouped the accessions into two subpopulations (K = 2). Therefore, this research aimed to identify potential genotypes and suitable traits of rice germplasms for breeding programs.