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

Abstract

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