Genomic insights into the medieval cultivation history of influential high-yielding Asian rice

High-yielding rice landraces that contributed substantially to historical population expansions were widely cultivated across Asia. These landraces are generally believed to have been Champa rice, which originated in present-day Vietnam. Historical records indicate that Champa rice was disseminated to southern China in the eleventh century and subsequently transmitted to medieval western Japan. Contrary to the recent view that Champa rice was derived from the Aus group, our extensive molecular phylogenetic and population genomic analyses indicate that currently available Vietnamese and Japanese Champa rice candidates are associated with the Indica group. Furthermore, although the Japanese landraces were expected to be phylogenetically closer to Vietnamese Indica landraces, they are distinct from the Southeast Asian Indica subpopulation and instead cluster within the Chinese Indica subpopulation. In addition, although the examined Vietnamese landraces show evidence of hybridization between Indica and Japonica, their Indica-derived components appear to be more closely related to Southeast Asian Indica. These findings suggest that historically influential high-yielding rice in Asia did not originate from a single source; rather, a broader diversity of landraces than previously recognized contributed to improvements in rice productivity through complex dissemination processes.