J Exp Bot. 2026 Aug 20:erag411. doi: 10.1093/jxb/erag411. Online ahead of print.
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.
PMID:42623552 | DOI:10.1093/jxb/erag411
