Genome-wide association analysis for plant type characters and yield using cgSSR markers in rice (Oryza sativa L.)

Plant architecture has a substantial impact on photosynthesis, which leads to increased yield production. Many plant architecture characters are quantitative in inheritance, making bi-parental QTL mapping difficult to discover all the genomic regions underpinning these traits. GWAS approach is the most promising approach to dissect these traits. We developed candidate gene-based SSR (cgSSR) markers and used them in a GWAS study on a panel of diverse rice genotypes evaluated over three seasons for three plant type characters and grain yield. A total of 17 marker-trait associations were detected for four observed traits. Three markers derived from genes OsGID1, OsFBK12 and OsMADS18 showed association with traits that were previously reported to be influenced by these genes. Many novel associations of genes with the traits were detected that had never been reported before. Three markers showed association with two traits each; these markers can be utilized in the simultaneous improvement of both traits. Trait-associated cgSSR markers derived from corresponding or related genes ensure their utility in direct allele selection, while other linked markers aid in allele selection indirectly altering the phenotype of interest. These significantly associated cgSSR markers with plant-type traits can be used in actual plant breeding to accumulate favourable alleles for these traits via marker assisted breeding.