Integrated GWAS and Transcriptome Analysis Identifies Candidate Genes for Seedling-Stage Drought Tolerance in Indica Rice

Drought stress is a major constraint on rice productivity, especially at the seedling stage. In this study, we evaluated 283 indica rice accessions adapted to the middle and lower Yangtze River region for seedling-stage drought tolerance using four morphological traits: leaf senescence resistance index, leaf wilting score, plant height, and root length. A comprehensive drought tolerance metric (CDTM) was developed to integrate these traits, leading to the identification of ten superior drought-tolerant accessions. Genome-wide association study (GWAS) revealed 128 significantly associated SNPs, mapping to 133 candidate genes for drought-related traits. Transcriptome analysis of drought-tolerant and drought-sensitive cultivars under PEG-induced stress showed distinct expression profiles, with differential expression enriched in pathways related to fatty acid degradation, amino acid metabolism, and hormone signaling. By integrating GWAS and transcriptome analysis, we prioritized 12 core candidate genes repeatedly associated with multiple drought-related traits, six of which were further validated using an independent drought-stress transcriptome dataset from the water-saving and drought-resistant variety Hanyou 73 under drought stress. Alternative splicing analysis revealed a significant skipped exon event in Os03g0700700 under drought stress. Our findings provide valuable genetic resources and candidate genes for molecular breeding amied at enhancing seedling-stage drought tolerance in rice breeding programs.