Population Structure and Genetic Differentiation Analyses Reveal High Level of Diversity and Allelic Richness in Crop Wild Relatives of AA-Genome Species of Rice (Oryza sativa L.) in India

Abstract

Abstract With a view to explore genetic diversity in crop wild relatives of AA-genome species of rice (Oryza sativa L.) in India, we analyzed 96 accessions of 10 Oryza species for 17 quantitative traits with 45 microsatellite markers. The morpho-quantitative traits revealed high extent of phenotypic variation within and between species. Shannon-Weiner's diversity index (H′) also confirmed the presence of high level of genetic variation for both within species, in O. nivara (H′=1.09) and O. rufipogon (H′=1.12), and between species (H′=1.31). Principal component (PC) analysis explained 79.22% variance with five PCs. Among the traits related to phenology, morphology and yield, days to heading showed strong positive association with days to 50% flowering (r = 0.99). However, filled grains per panicle revealed positive association with spikelet fertility (0.71) but negative with awn length (-0.58) and panicle bearing tillers (-0.39). Cluster analysis grouped all the accessions into three major clusters. Microsatellite analysis revealed 676 alleles with mean of 15.02 alleles per locus and 0.83 mean polymorphism information content. UPGMA dendrogram separated wild rice accessions at 0.10 similarity value and delineated 96 accessions into four major clusters. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while third subpopulation included both O. nivara and O. rufipogon accessions. Molecular variance among the populations was 11.0%, whereas it was 70.0% among genotypes and 19.0% within genotypes. The high level of molecular and morphological variability detected in the germplasm of crop wild relatives could be utilized for genetic improvement of cultivated rice.