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

• Published in: Journal of applied genetics 2023-12, Vol.64 (4), p.645-666
• Main Authors: Mahendran, Aswin, Yadav, Mahesh C., Tiwari, Shailesh, Bairwa, Rakesh Kumar, Krishnan, S. Gopala, Rana, Mukesh Kumar, Singh, Rakesh, Mondal, Tapan Kumar
• Format: Article
• Language: English
• Subjects: Alleles; Analysis; Animal Genetics and Genomics; Biological diversity; Biomedical and Life Sciences; Cluster analysis; Cultivation; Differentiation; Fertility; Flowering; Gene flow; Gene polymorphism; Genetic analysis; Genetic diversity; Genetic markers; Genetic variability; Genomes; Genomics; Genotypes; Germplasm; Grain cultivation; Human Genetics; Life Sciences; Microbial Genetics and Genomics; Microsatellites; Morphology; Oryza sativa; Phenotypic variations; Plant Genetics and Genomics; Plant Genetics • Original Paper; Polymorphism; Population (statistical); Population genetics; Population statistics; Population structure; Rice; Statistical analysis; Structural analysis; Subpopulations; Variance; Wild type
• ISSN: 1234-1983; 2190-3883
• DOI: 10.1007/s13353-023-00787-3

  Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice ( Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H′) revealed a high level of within-species variability in O. nivara (H′ = 1.09) and O. rufipogon (H′ = 1.12). 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 15.02 alleles per locus. High polymorphism information content (PIC = 0.83) and Shannon’s information index (I = 2.31) indicated a high level of genetic variation in the CWRs. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while the third subpopulation included both O. nivara and O. rufipogon accessions. Population statistics revealed a moderate level of genetic differentiation ( F ST  = 0.14), high gene diversity ( H E  = 0.87), and high gene flow ( N m = 1.53) among the subpopulations. We found a high level of molecular variance among the genotypes (70%) and low among populations (11%) and within genotypes (19%). The high level of molecular and morphological variability detected in the germplasm of CWRs could be utilized for the improvement of cultivated rice.