Genome Sequencing of Rice Landraces from the Yuanyang Terraces Uncovers Ancient and Diverse Lineages of Indica Rice

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High-yielding elite rice cultivars exhibit limited genetic variability, raising concerns about our capacity to sustain productivity amid changing biotic and abiotic threats. Meeting the challenges that lie ahead largely depends on our ability to leverage novel sources of genetic variation and re-engineer agrosystems. We report on the evolutionary history and population genetic structure of 353 accessions representing 90 landraces from China’s centuries-old Yuanyang terraces (YYT) of rice paddies. We found that the indica YYT landraces are genetically distinct from other indica groups, forming a unique lineage with high standing variation. YYT landraces experienced a demographic bottleneck 500 – 1,000 years ago, coinciding with the emergence of YYT. Among the 90 sampled seed bags, most contained mixed-ancestry genotypes or genotypes from different genetic clusters, suggesting high genotype heterogeneity in paddy fields. Analysis of natural selection reveals that innate immunity genes exhibit marked differences in coevolutionary dynamics between modern and traditional rice, with directional selection exerting a stronger influence in modern varieties. The high genetic diversity observed in indica YYT landraces is characterized by a substantial proportion of exclusive polymorphisms and haplotypes at immunity genes, alongside older, shared alleles maintained by rare-allele advantage at NLR receptors. Our study highlights the necessity of preserving landraces within their native agrosystems, and opens new avenues for targeted efforts to harness their genetic diversity and population structure for future crop improvement and sustainable disease management.