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Oct 01, 2025;26 (1): 327.

Phylogenomics provides comprehensive insights into the evolutionary relationships among cultivated buckwheat species.

Yaliang Shi, Bo Li, Yuanfen Gao, Xiaohan Wang, Yang Liu, Xiang Lu, Hao Lin, Wei Li, Dili Lai, Ming Hao, Jia Gao, Kaixuan Zhang, Dengcai Liu, Sun-Hee Woo, Muriel Quinet, Alisdair R Fernie, Xu Liu, Yuqi He, Meiliang Zhou
Author Information
  1. Yaliang Shi: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  2. Bo Li: Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
  3. Yuanfen Gao: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  4. Xiaohan Wang: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  5. Yang Liu: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  6. Xiang Lu: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  7. Hao Lin: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  8. Wei Li: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  9. Dili Lai: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  10. Ming Hao: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 610000, China.
  11. Jia Gao: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  12. Kaixuan Zhang: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  13. Dengcai Liu: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 610000, China.
  14. Sun-Hee Woo: Department of Crop Science, Chungbuk National University, Cheong-ju, 28644, Republic of Korea.
  15. Muriel Quinet: Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université Catholique de Louvain, Croix du Sud 45, Boîte L7.07.13, B-1348, Louvain-La-Neuve, Belgium.
  16. Alisdair R Fernie: Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, 14476, Germany.
  17. Xu Liu: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. liuxu03@caas.cn.
  18. Yuqi He: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. heyuqi@caas.cn.
  19. Meiliang Zhou: National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs. P. R. China, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. zhoumeiliang@caas.cn.
PMID: 41035109 DOI: 10.1186/s13059-025-03793-2

Abstract

BACKGROUND: Buckwheat belongs to the family Polygonaceae and genus Fagopyrum, which is characterized by high flavonoid content, short growth period, and strong environmental adaptability. Buckwheat has three cultivated species, including the annual food crops common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum), and the perennial traditional herbal medicine golden buckwheat (Fagopyrum cymosum). However, the unclear phylogenetic relationships among these three species based on genomic data limit buckwheat interspecific hybridization and genetic improvement.
RESULTS: Despite their enormous differences in morphology and genome, we confirm the closet relationship between Fagopyrum cymosum and Fagopyrum tataricum, but not Fagopyrum esculentum. The results are also verified through collecting and sequencing an extensive sampling of cultivated/wild populations across all environmentally distinct regions in which these species are found. The changes in flowering time and style morphology controlled by the AP1 and S-ELF3 loci significantly contribute to the buckwheat speciation. The introgression from Fagopyrum cymosum into wild Fagopyrum tataricum explains why wild Fagopyrum tataricum exhibits seed morphology similar to Fagopyrum cymosum. Furthermore, the convergent traits of leaf morphology and higher flavonoid content between Fagopyrum cymosum and wild Fagopyrum esculentum are linked to high-altitude adaptation. Fagopyrum cymosum is more closely related to wild Fagopyrum tataricum, a fact that is confirmed by interspecific hybridization.
CONCLUSIONS: Our work provides a valuable example of how phylogenomics can be efficiently utilized for phylogenetic relationship analysis between crops and their wild species relatives, as well as elucidating the plant speciation from the perspectives of genomic evolution and adaptive mechanisms.

Keywords

Buckwheat Gene flow Phylogenetic relationship Population genetics Speciation

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Grants

  1. 32360054/National Natural Science Foundation of China
  2. 32161143005/National Natural Science Foundation of China
  3. 2023YFF1002500/National Key R&D Program of China

MeSH Term

Fagopyrum
Phylogeny
Genome, Plant
Evolution, Molecular
Genomics
Journal Article

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