Lineage-specific variation and molecular evolution in the rice landrace Thavalakannan: an in silico framework for...

This genomic atlas identifies unique Sub1 allelic diversity and 2,557 wild-derived non-reference genes in Thavalakannan, providing a molecular framework and SSR toolkit to accelerate precision breeding for flood resilient rice. Rice (Oryza sativa L.) landraces harbour untapped genetic diversity essential for climate-adaptive breeding. Thavalakannan, an endemic South Indian indica landrace, is traditionally associated with flood resilience, yet its molecular architecture remains undocumented. We established the first high-resolution genomic atlas for Thavalakannan, identifying 3,670,532 SNPs, 602,474 InDels, and 56,395 structural variants (SVs). Benchmarking against the 3000 Rice Genomes (3KRG) panel revealed 279,422 unique SNPs and significant lineage-specific divergence. Specifically, 43 novel variants were localised within the Sub1 gene cluster on Chromosome 9, including a start-lost mutation and an in-frame deletion in SUB1A, and frameshift mutations in SUB1B, SKL3-2, and SKL4-1. These findings indicate potential divergence in the regulation of quiescence and escape-associated pathways. Pathway enrichment analysis evidenced a potential metabolic adaptation of starch metabolism, hormone signal transduction, and ROS scavenging. Integration with the Q-TARO database confirmed variant enrichment within key stress-responsive QTLs (Sub1, qLEI3, qTIL12). Furthermore, de novo assembly of unmapped reads uncovered 2,557 putative non-reference genes with high homology to wild Oryza species, representing a "hidden" reservoir of adaptive alleles. Finally, we developed an extensive toolkit of 126,937 simple sequence repeats (SSRs) spanning both conserved and lineage-specific segments. Collectively, this study defines the evolutionary framework of Thavalakannan and provides a foundational resource for targeted allele mining and the precision breeding of flood-resilient rice cultivars.