Genetic variation, population structure, and marker-trait association of rice (Oryza sativa L.) cultivars using morphological characteristics and molecular markers

Abstract

Abstract Indigenous germplasms are the excellent sources of diversity, however, they are prone to genetic erosion, therefore exploration of genetic variability in indigenous germplasm is an essential step for future breeding programs. Discovery of genetic mechanisms of the characters in landraces that could cope adverse situations is important for maintaining world-food supply. Here rice landraces were assessed for their genetic diversity and relatedness using morpho-physiological data and SSR markers and found significant variation among yield attributing features. Phenotypic and genotypic coefficients of variability were higher for filled grains, whereas high heritability was found for plant height. Panicle number and 100-grain weight displayed significant relationships with yield. Phylogenetic clustering of the agro-morphological traits divided the germplasms into 8 clusters, whereas SSR marker yielded 10 clusters. Markers produced 138 alleles varying from 2 to 9 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 0.649 (average), exhibiting RM336, RM316, and RM287 have the greatest potentiality in exploring genetic diversity among genotypes. The genotypes Dolkochu, Jolduba, BRRI Dhan-32, and Mokbul were present in a single cluster and showed wider variability, indicating their potentiality to be parents in hybridization programs in crop breeding. Population structure study demonstrated that the genotypes were structurally diverse that grouped the accessions into two sub-populations (K = 2). Twenty-one marker-trait associations (p < 0.05) for 8 characteristics were identified. These diverse germplasms and polymorphic trait-linked markers might be suitable for molecular breeding.