SSR Marker-Based Insights into Genetic Diversity and Population Structure of Rice (Oryza sativa L.) Germplasm

Rice, one of the most important cereal crops, serves as a staple food for over half of the global population. Chhattisgarh often referred to as “Rice bowl of India” possesses immense genetic diversity in rice. Genetic diversity represents the heritable variation within and between populations of organisms and is a pre-requisite for improvement of any crop species. Genetic diversity defines all the available variability and desirable alleles in any crop species/ population which may be exploited in crop breeding programs. Hence, the objective of this study was to assess the genetic diversity and population structure of 48 rice accessions using 31 simple sequence repeats (SSR) markers to identify the diverse and useful genotypes for further breeding programmes. The mean polymorphic information content (PIC), major allele frequency and gene diversity were 0.48, 0.56 and 0.54 respectively, suggesting the high polymorphism of the SSR markers used for genotyping of the rice accessions. The population structure revealed two major sub-populations based on their morphological differences. UPGMA algorithm and genetic dissimilarity coefficient based Dendrogram as well as principal component analysis also grouped the rice genotypes into two groups with wide variation among the accessions and strongly supported the outcomes of population structure analysis. Moreover, analysis of molecular variance (AMOVA) detected a significant genetic differentiation between two sub-populations. Total molecular variance was partitioned into two, of which, 6% explained variation among populations and the remaining 94% explained variation within the populations. The study established the existence of considerable genetic diversity among the tested 48 accessions. The selected genetic resources will be useful in further rice breeding activities.