Genomic and Transcriptomic Insights into Stage-Specific Drought Resilience in Diverse Myanmar Rice Germplasm

Drought stress remains a critical constraint to rice productivity, particularly during the early vegetative stages in rainfed environments. To elucidate the genetic and molecular mechanisms underpinning drought tolerance in rice, we conducted an integrated genome-wide association study (GWAS) and transcriptomic analysis on 236 genetically diverse Myanmar landraces, a region renowned for its unique and locally adapted rice germplasm. Phenotypic evaluation under simulated drought conditions revealed substantial variation in germination and seedling survival, with approximately 18% of accessions exhibiting high tolerance and 22% displaying susceptibility. Notably, contrasting responses between germination and seedling stages in some landraces suggest stage-specific genetic regulation of drought resilience. Population structure analyses demonstrated distinct clustering aligned with geographic origin, reflecting local adaptation and a complex evolutionary history distinct from other major rice populations. GWAS identified twelve significant QTLs across chromosomes 2, 4, 5, 7, 8, 9, 10, and 11, containing 546 candidate genes involved in ABA signaling, osmotic regulation, and stress-responsive pathways. Haplotype analysis at key loci, particularly on chromosome 7, revealed allelic variants strongly associated with enhanced drought tolerance, exemplified by favorable haplotypes linked to higher germination rates under stress. Complementary RNA-seq profiling of a superior drought-tolerant genotype (V5) and a highly sensitive one (V3) uncovered 3,476 and 2,590 differentially expressed genes, respectively. Tolerant landraces exhibited downregulation of photosynthesis-related genes and upregulation of osmotic adjustment and detoxification pathways. Integration of GWAS and transcriptomic data pinpointed 103 candidate genes within QTL regions, with Os07g0513000 (ATP synthase gamma chain) and Os07g0691200 (D-alanine ligase) emerging as prime candidates due to their strong upregulation in tolerant lines and linkage disequilibrium with major QTLs. Validation via qRT-PCR confirmed their potential roles in drought adaptation. These findings highlight the unique genetic architecture of Myanmar landraces, offering valuable alleles and regulatory networks for molecular breeding aimed at enhancing drought resilience in rice, and underscore the importance of conserving regional landraces as vital resources for climate-smart agriculture.