Haplotype Variation at Heading Date Loci in Rice Landraces of Kashmir Valley

Rice (Oryza sativa L.) is a staple food of the Kashmir valley where diverse altitudinal gradients necessitate precise heading date regulation for optimal yield and survival. To investigate the genomic basis of adaptative traits, we performed whole genome re-sequencing of 20 prominent traditional rice landraces. Initial screening of major heading date loci Hd1, Hd4 (Ghd7), and Hd5 (Ghd8) was carried out. The haplotype analysis uncovered a complex and fragmented genetic architecture. While Hd4 variation was relatively conserved among the landraces, the Hd1 and Hd5 loci exhibited high diversity with numerous accession-specific haplotypes. The unique genetic signatures suggest an adaptive strategy driven by either distinct evolutionary lineages or the gradual accumulation of minor, fine-tuned mutations. This study highlights the importance of moving beyond known causal variants to uncover the localized genomic adaptations that enable rice to thrivein thespecific microclimates ofthe Kashmir valley.