Genetic diversity, allelic variation and marker trait associations in gamma irradiated mutants of rice (Oryza sativa L.)

Abstract

Purpose Rice is a prime staple crop for more than half of the world population. Improved White Ponni (IWP) is a premium quality grain rice variety that is fetching a good price and is increasingly popular among the consumers of Tamil Nadu. Tall plant stature of IWP makes them susceptible to lodging and medium duration are two undesirable traits in the variety increases yield losses in the field and also productivity. In this context, we aimed to generate a large mutant population of IWP irradiated with various doses of gamma irradiation to recover putative mutants for semi-dwarfism and earliness. Materials and methods Totally, 34 putative mutants (22 early, 11 semi-dwarf and early and 1 Narrow-leaf dwarf mutant) were phenotyped for nine morphological traits and genotyped using 34 microsatellite markers linked to a trait of interest of earliness and semi-dwarfism. Trait variability, allelic variations, genetic structure and marker-trait associations in gamma-irradiated putative mutants of Improved White Ponni (IWP) rice were investigated in this study. Results The hierarchical clustering of morphological data produced five clusters with a dissimilarity coefficient of 1.39. A minimum dissimilarity coefficient of 0.23 was observed between the mutants IWPM9 and IWPM20 and a maximum dissimilarity coefficient of 2.55 was observed between IWPM1 and IWPM25. In cluster analysis with molecular marker data, five clusters with a similarity coefficient of 0.67 were observed. The mutant IWPM29 exhibited the most divergence from the wild type at the genotype level. The first principal component explained 50.99% of the total variability and the majority of the traits were contributed positively. The single-marker analysis revealed the strong association of SSR marker RM3912 with the traits plant height, panicle length and number of grains per panicle with an R2 value of 0.235, 0.235 and 0.250 respectively. Conclusions The study identified semi-dwarf and short-duration rice mutants of IWP that can be utilized as potential breeding stocks. The trait-linked SSR markers can improve selection cycles in advanced breeding programs.