Genome-wide association mapping for rapid and uniform germination traits associated with direct-seeded adaptation in rice

The genetic basis of rapid and uniform seed germination and its associated traits is crucial for improving seed vigour and seedling establishment for higher productivity in direct-seeded rice (DSR) systems. This study investigates the phenotypic diversity and genetic architecture of germination traits in 163 rice genotypes, using a genome-wide association studies (GWAS). An association panel of 163 diverse rice genotypes, including varieties, germplasm and breeding lines, was evaluated for seed germination traits over 2 years (2022 and 2023). The panel was genotyped using 295 simple sequence repeat (SSR) markers, including 80 random SSRs and 215 candidate gene SSRs linked to seed traits and morphological attributes. The genotyping of 163 lines with 295 markers revealed a range of genetic diversity, with polymorphic information content values between 0.04 and 0.93. Population structure analysis indicated the presence of two groups and four sub-groups. GWAS identified 80 significant marker-trait associations (MTAs) across 12 chromosomes at P ≤ 0.05, which narrow down to 18 MTAs at P ≤ 0.01. Twelve candidate genes are identified which were related with multiple traits, linked to important functions, such as seed-size regulation, nutrient mobilization and plant growth. Candidate gene-based SSR (cgSSR) markers such as M169 (OsMIK), M57 (THIS1), M66 (GW2), and M18 (OsBAK1), displayed pleiotropy including rapid and uniform germination (germination index, germination rate index and mean germination time) traits. The newly identified candidate gene markers associated with seed rapid and uniform germination traits can be leveraged in marker-assisted breeding programs to introduce diverse alleles for enhanced seed vigour and crop establishment. Markers closely linked to multiple traits hold significant potential for the simultaneous improvement of several traits.