Pan-genome bridges wheat structural variations with habitat and breeding

Chengzhi Jiao, Xiaoming Xie, Chenyang Hao, Liyang Chen, Yuxin Xie, Vanika Garg, Li Zhao, Zihao Wang, Yuqi Zhang, Tian Li, Junjie Fu, Annapurna Chitikineni, Jian Hou, Hongxia Liu, Girish Dwivedi, Xu Liu, Jizeng Jia, Long Mao, Xiue Wang, Rudi Appels, Rajeev K. Varshney (), Weilong Guo () and Xueyong Zhang ()
Additional contact information
Chengzhi Jiao: Chinese Academy of Agricultural Sciences
Xiaoming Xie: China Agricultural University
Chenyang Hao: Chinese Academy of Agricultural Sciences
Liyang Chen: Smartgenomics Technology Institute
Yuxin Xie: Chinese Academy of Agricultural Sciences
Vanika Garg: Murdoch University
Li Zhao: Chinese Academy of Agricultural Sciences
Zihao Wang: China Agricultural University
Yuqi Zhang: China Agricultural University
Tian Li: Chinese Academy of Agricultural Sciences
Junjie Fu: Chinese Academy of Agricultural Sciences
Annapurna Chitikineni: Murdoch University
Jian Hou: Chinese Academy of Agricultural Sciences
Hongxia Liu: Chinese Academy of Agricultural Sciences
Girish Dwivedi: the University of Western Australia
Xu Liu: Chinese Academy of Agricultural Sciences
Jizeng Jia: Chinese Academy of Agricultural Sciences
Long Mao: Chinese Academy of Agricultural Sciences
Xiue Wang: Nanjing Agricultural University
Rudi Appels: Murdoch University
Rajeev K. Varshney: Murdoch University
Weilong Guo: China Agricultural University
Xueyong Zhang: Chinese Academy of Agricultural Sciences

Nature, 2025, vol. 637, issue 8045, 384-393

Abstract: Abstract Wheat is the second largest food crop with a very good breeding system and pedigree record in China. Investigating the genomic footprints of wheat cultivars will unveil potential avenues for future breeding efforts1,2. Here we report chromosome-level genome assemblies of 17 wheat cultivars that chronicle the breeding history of China. Comparative genomic analysis uncovered a wealth of structural rearrangements, identifying 249,976 structural variations with 49.03% (122,567) longer than 5 kb. Cultivars developed in 1980s displayed significant accumulations of structural variations, a pattern linked to the extensive incorporation of European and American varieties into breeding programmes of that era. We further proved that structural variations in the centromere-proximal regions are associated with a reduction of crossover events. We showed that common wheat evolved from spring to winter types via mutations and duplications of the VRN-A1 gene as an adaptation strategy to a changing environment. We confirmed shifts in wheat cultivars linked to dietary preferences, migration and cultural integration in Northwest China. We identified large presence or absence variations of pSc200 tandem repeats on the 1RS terminal, suggesting its own rapid evolution in the wheat genome. The high-quality genome assemblies of 17 representatives developed and their good complementarity to the 10+ pan-genomes offer a robust platform for future genomics-assisted breeding in wheat.

Date: 2025
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DOI: 10.1038/s41586-024-08277-0

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