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
State Key Laboratory of Crop Gene Resources and Breeding/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China.
Nature. 2025 Jan;637(8045):384-393. doi: 10.1038/s41586-024-08277-0. Epub 2024 Nov 27.
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. 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.
小麦是中国第二大粮食作物，拥有良好的育种体系和系谱记录。研究小麦品种的基因组印记将为未来的育种工作揭示潜在途径。在此，我们报告了17个小麦品种的染色体水平基因组组装，这些组装记录了中国的育种历史。比较基因组分析发现了大量的结构重排，鉴定出249,976个结构变异，其中49.03%（122,567个）长度超过5 kb。20世纪80年代培育的品种显示出结构变异的显著积累，这种模式与当时欧美品种广泛纳入育种计划有关。我们进一步证明，着丝粒近端区域的结构变异与交叉事件的减少有关。我们表明，普通小麦通过VRN-A1基因的突变和重复从春性类型进化为冬性类型，作为对不断变化的环境的适应策略。我们证实了小麦品种的变化与中国西北地区的饮食偏好、移民和文化融合有关。我们在1RS末端鉴定出pSc200串联重复序列的大量存在或缺失变异，表明其在小麦基因组中自身的快速进化。17个代表性品种的高质量基因组组装及其与10多个泛基因组的良好互补性为未来小麦基因组辅助育种提供了一个强大的平台。
