Historical rice seeds from the 1950s reveal pre-modern genetic structure in indica landraces of mainland Southeast Asia

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ID: 325433
2026
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Abstract
Abstract Understanding crop population history requires genetic material that predates modern breeding. Here, we analyzed historical seeds of rice landraces assembled in Southeast Asia from 1957 to 1958. Target capture resequencing of coding regions yielded high-quality genomic data from 66 historical accessions (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica, and the previously described major regional structure was recovered. Within the historical collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to the traditional growth seasons (fifth- and tenth-month rice). Notably, the fifth-month rice accessions were assigned to the recently reported Vietnam-I5 cluster. Admixture graph, f-statistics, and qpAdm analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage; however, this relationship was not fully explained by sampled indica, japonica, or aus proxies. Together, these results show that major components of the present-day indica regional structure were already present before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice.
Reference Key
openalex_W7203834467 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Koji Numaguchi, Sathya Lim, Chhourn Orn, Yui Higashikubo, Hiroki Saito, Yutaka Sato, Ryo Ishikawa, Rafał M. Gutaker, Takashige Ishii
Journal Journal of experimental botany
Year 2026
DOI
10.1093/jxb/erag411
URL
https://doi.org/10.1093/jxb/erag411
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