Genetic diversity analysis and population structure in a rice germplasm collection of different maturity groups

Abstract

Heading date is an important trait influencing the grain yield in rice (Oryza sativa L.) and plays a major role in rice breeding programmes. Molecular diversity among 84 rice genotypes belonging to different maturity groups, including cultivars, wild introgression lines and mutants, was investigated using 57 SSR markers linked to heading date. A total of 99 alleles were identified using 42 polymorphic SSRs, with an average of 2.35 alleles per locus. Cluster analysis grouped 84 genotypes into ten major clusters at a genetic similarity of 0.96. The analysis of the genetic structure in the germplasm collection revealed three levels of stratification and the primary division was between O. sativa cultivars and O.nivara introgression lines, followed by a distinction between cultivars and mutants in the O. sativa group. Intra-specific subgroups were detected within cultivated group representing different maturity groups. Breeding programmes involving these diverse genotypes helps in developing high yielding varieties for different maturity groups.