Re‐sequencing 142 rice genomes reveals the fine‐scale population structure and phylogenetic affinities of landraces of Kashmir Valley: Evidence from domestication and adaptive signatures

Abstract

The emergence of rice ( Oryza sativa ) as a cultivated crop has represented a landmark in the history of agriculture in Kashmir Valley. Unlike winter cereals, such as wheat and barley, which exhibit clear West‐Asian origins, rice attained a different domestication trajectory linked to East‐Asian Neolithic cultures. However, evidence of such origins and adaptive history of Kashmir's rice landraces have relied on limited archaeo‐botanical data, tool typologies, and information pertaining regional cultural exchange. We present the first comprehensive genomics‐resource for the region produced through whole genome re‐sequencing of 142 rice germplasm lines. By leveraging on the 3000 Rice Genomes Project (3K RGP) database, we analyzed fine‐scale population structures and evolutionary relationships. Our findings reveal that local landraces possess temperate japonica ( Tej ) genetic signatures with the origins having been traced to North‐East Asia, while the modern bred varieties in the region often align with indica (derivative) lineages from subtropical India. The sequence data were generated with a mean depth of 13.6x, and 3.94 million high‐confidence single nucleotide polymorphisms (SNPs) after stringent filtering. Populations resolved into a bipartite genetic structure ( K  = 2) comprising two major sub‐populations with an admixed group, with the help of high‐polymorphism information content SNP panels. Genome‐wide diversity analyses revealed the positive Tajima's D values, indicating extensive population structure and balancing selection, with localized signatures of directional selection. The allelic characterization explained the rich diversity at the functionally polymorphic loci linked to domestication, quality, and adaptive traits, particularly those associated with cold tolerance. The gene repository shall provide for development of better quality and climate resilient cultivars.