Comparative Genetic Diversity Assessment and Marker–Trait Association Using Two DNA Marker Systems in Rice (Oryza sativa L.)

In this paper, the genetic diversities of 12 rice genotypes (Oryza sativa L.), representing Indica, Japonica, and Indica–Japonica varieties, were assessed using twelve ISSR five SSR markers. addition, evaluated for 11 agro-morphological traits in a two-year trial. Association mapping was performed to detect any association between DNA markers traits. An analysis conducted considering relative kinship among accounting population structure unified mixed-model approach avoid possible false-positive associations. Seventy-three alleles collectively produced by ISSRs SSRs, with an average 6.3 2.8 per locus, respectively. Both marker systems informative, polymorphism information content (PIC) 0.222 0.352 The expected heterozygosity (Hexp) 0.264 compared 0.457 SSRs. After false discovery rate (FDR) method, revealed total significant marker–trait associations six traits, including no. unfiled grains panicle−1, panicle length, weight, panicles plant−1, tillers 1000-grain weight. showed seven markers, while SSRs three phenotypic variance (R2) explained each ranged 29.2% HB11 (associated weight) 49.3% HB8 plant−1). identified reported herein may improve gain future molecular-based rice-breeding programs, particularly those designed improving grain-related or harvest-related