BACKGROUND: Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. RESULTS: Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. CONCLUSIONS: This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.

Agricultural Institute of Slovenia Hacquetova ulica 17 SI 1000 Ljubljana Slovenia

Biological Sciences University of Southampton Life Sciences Building 85 Highfield Campus Southampton SO17 1BJ UK

Biotechnical Faculty University of Ljubljana Jamnikarjeva 101 SI 1000 Ljubljana Slovenia

Department of Crop Science Chungbuk National University Cheong ju Republic of Korea

Department of Molecular Physiology Max Planck Institute of Molecular Plant Physiology 14476 Potsdam Germany

Gene Bank Crop Research Institute Drnovská 507 Prague 6 Czech Republic

Groupe de Recherche en Physiologie Végétale Université catholique de Louvain Croix du Sud 45 boîte L7 07 13 B 1348 Louvain la Neuve Belgium

Nutrition Institute Koprska Ulica 98 SI 1000 Ljubljana Slovenia

Research Center of Buckwheat Industry Technology Guizhou Normal University Guiyang 550001 China

State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 China

Tibet Key Experiments of Crop Cultivation and Farming College of Plant Science Tibet Agriculture and Animal Husbandry University Linzhi 860000 China

Xichang Institute of Agricultural Science Liangshan Yi People Autonomous Prefecture Liangshan Sichuan 615000 China

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Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat