Pan-genome bridges wheat structural variations with habitat and breeding

• 成果类型: Article
• 署名作者: Jiao, Chengzhi; Xie, Xiaoming; Hao, Chenyang; Chen, Liyang; Xie, Yuxin; Garg, Vanika; Zhao, Li; Wang, Zihao; Zhang, Yuqi; Li, Tian; Fu, Junjie; Chitikineni, Annapurna; Hou, Jian; Liu, Hongxia; Dwivedi, Girish; Liu, Xu; Jia, Jizeng; Mao, Long; Wang, Xiue; Appels, Rudi; Varshney, Rajeev K.; Guo, Weilong; Zhang, Xueyong
• 署名单位: Chinese Academy of Agricultural Sciences; Institute of Crop Sciences, CAAS; Nanjing Agricultural University; China Agricultural University; Murdoch University; Harry Perkins Institute of Medical Research; University of Western Australia; South Metropolitan Health Service; Fiona Stanley Fremantle Hospitals Group; Fiona Stanley Hospital; La Trobe University; Department of Economic Development, Jobs, Transport & Resources
• 刊物名称: Nature
• ISSN/ISSBN: 0028-2394
• DOI: 10.1038/s41586-024-08277-0
• 发表日期: 2025-01-09
• 页码: 384-+
• 关键词: bread wheat; gene; alignment; resistance; SEQUENCES; EVOLUTION; collinearity; assemblies; prediction; program

摘要

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 efforts(1,2). 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.