Abstract
Understanding the genetic basis of reproductive stage drought tolerance (RSDT) requires bridging genomic variations with phenotype. This study employed a genome-wide association study (GWAS) using 450 rice accessions for grain yield under reproductive stage drought stress across three locations and two seasons. The results revealed 67 marker-trait associations (MTAs) that corresponded to 23 candidate genes. Superior haplotypes were identified for 10 RSDT-related genes, namely SAP-H22, WRKY109-H6, OsIRO2-H3, OsSOBIR1-H68, OsPGL31-H8, OsDAHPS1-H2, ZCD-H13, OsMC2-H8, Ospdr9-H16, and SDR-H2. These genes are involved in stress-related processes such as transcription regulation, cell wall structure modification, leaf rolling, programmed cell death, redox stress, and secondary metabolite accumulation. Notably, introgressing superior haplotypes from the OsIRO2-H3 gene into an elite rice cultivar led to a yield advantage of 25.0-27.3% over recurrent parents. These findings highlight the potential of these genes as valuable resources for breeding high-yielding, drought-tolerant rice varieties.