Population structure, genetic diversity, and trait association analysis in rice (Oryza sativa L.) genotypes for brown spot disease resistance

Brown spot (BS), caused by Bipolaris oryzae, is one of the most important fungal diseases in rice-growing regions of the world. Identification of genomic regions associated with BS-related traits is essential for improving BS resistance in rice. In this study, the population structure and the association mapping between simple sequence repeat (SSR) markers and BS-related traits were assessed in 95 rice genotypes under nursery and field conditions. Genetic analysis indicated that RM3739 and RM7576 had the highest level of diversity indices including number of alleles, number of effective alleles, polymorphic information content value, gene diversity, and Shannon’s information index, which can be useful for other rice breeding programs. A high genetic diversity was found between genotypes, which can be exploited to improve and produce rice cultivars for important traits. Population structure analysis using model-based and distance-based approaches grouped the genotypes into two distinct sub-populations. Association analysis was conducted through the general linear model (GLM) and the mixed linear model (MLM). Using the GLM, 35 and 27 markers were significantly associated after considering Bonferroni correction with BS resistance at the seedling and adult plant stages, respectively, in both 2017 and 2018. Moreover, the significantly associated markers were reduced to 14 and 3 at the seedling and adult plant stages, respectively, by MLM. RM6499 was associated with nursery and field resistance to BS in both GLM and MLM, suggesting that this marker can be used in breeding programs for development of improved BS-resistant rice varieties through marker-assisted selection.