Genetic Diversity of Indigenous Rice Varieties Cultivated by Mon-Khmer-Speaking Ethnic Communities in Thailand

Abstract Rice (Oryza sativa L.) has been a vital staple crop in East and Southeast Asia for thousands of years, playing a key role in the development of human civilizations. Over time, different ethnic groups in these regions have selected rice varieties that suit their tastes and local growing conditions. As people migrated, they often brought their preferred rice varieties with them, contributing to the greater diversity of rice across regions. The Mon-Khmer-speaking peoples are believed to be the first settlers to introduce rice cultivation from southern China to northern Thailand during the Neolithic period. There are currently various indigenous rice varieties still being cultivated in Mon-Khmer communities of northern Thailand, but little is known about the genetic diversity of these rice varieties. This study examines 100 rice samples collected from 11 villages representing the Khmuic and Palaungic language branches of the Mon-Khmer group. Morphological analysis revealed differences in pericarp coloration, with Khmuic rice predominantly exhibiting off-white, brown, and black colors, while Palaungic rice tended to be lighter, including light and red shades. Genome-wide analysis identified two primary genetic clusters corresponding to these ethnolinguistic groups. Khmuic rice displayed high genetic homogeneity and characteristics of Subtropical Japonica rice, suggesting a stable lineage with limited seed exchange. In contrast, Palaungic rice exhibited greater genetic diversity, composed of both Japonica and Indica rice, likely due to extensive seed-sharing networks. Our findings provide insights into the relationship between ethnolinguistic groups and rice diversity, highlighting the importance of preserving indigenous rice varieties. This research also contributes to identifying novel genetic resources that may be useful for future rice breeding and improvement programs.