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He M, He Y, Zhang K, Lu X, Zhang X, Gao B, Fan Y, Zhao H, Jha R, Huda MN, Tang Y, Wang J, Yang W, Yan M, Cheng J, Ruan J, Dulloo E, Zhang Z, Georgiev MI, Chapman MA, Zhou M. Comparison of buckwheat genomes reveals the genetic basis of metabolomic divergence and ecotype differentiation. New Phytol 2022; 235:1927-1943. [PMID: 35701896 DOI: 10.1111/nph.18306] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/22/2022] [Indexed: 05/09/2023]
Abstract
Golden buckwheat (Fagopyrum dibotrys or Fagopyrum cymosum) and Tartary buckwheat (Fagopyrum tataricum) belong to the Polygonaceae and the Fagopyrum genus is rich in flavonoids. Golden buckwheat is a wild relative of Tartary buckwheat, yet golden buckwheat is a traditional Chinese herbal medicine and Tartary buckwheat is a food crop. The genetic basis of adaptive divergence between these two buckwheats is poorly understood. Here, we assembled a high-quality chromosome-level genome of golden buckwheat and found a one-to-one syntenic relationship with the chromosomes of Tartary buckwheat. Two large inversions were identified that differentiate golden buckwheat and Tartary buckwheat. Metabolomic and genetic comparisons of golden buckwheat and Tartary buckwheat indicate an amplified copy number of FdCHI, FdF3H, FdDFR, and FdLAR gene families in golden buckwheat, and a parallel increase in medicinal flavonoid content. Resequencing of 34 wild golden buckwheat accessions across the two morphologically distinct ecotypes identified candidate genes, including FdMYB44 and FdCRF4, putatively involved in flavonoid accumulation and differentiation of plant architecture, respectively. Our comparative genomic study provides abundant genomic resources of genomic divergent variation to improve buckwheat with excellent nutritional and medicinal value.
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Affiliation(s)
- Ming He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Xiang Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Bin Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Rintu Jha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Md Nurul Huda
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Junzhen Wang
- Research Station of Alpine Crop, Xichang Institute of Agricultural Sciences, Liangshan, 616150, Sichuan, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Ehsan Dulloo
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Zongwen Zhang
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Milen I Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4002, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, 4002, Plovdiv, Bulgaria
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
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