Du Mengrui, Zhang Fan, Wang Xu, Zhang Tianhao, Yang Xuanwen, Liu Yuting, Zhang Yingchun, Hou Ting, Hang Guizhou, Fang Xinyue, Li Jiacui, Xue Hui, Zhou Yongfeng, Wang Jiagang
Special Orphan Crops Research Center of the Loess Plateau, Ministry of Agriculture and Rural Affairs, College of Agriculture, Shanxi Agricultural University, Taigu 030801, China.
National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
iScience. 2025 Aug 6;28(9):113295. doi: 10.1016/j.isci.2025.113295. eCollection 2025 Sep 19.
Crop domestication typically accumulates structural and deleterious variants through genetic bottlenecks and selection hitchhiking. However, the structural and deleterious variant burden has not been investigated in the foxtail millet (). Integrating comparative genomics, pangenomics, population genetics, and quantitative genetics, we identified 6,713 gene gains and 2,802 losses during domestication, affecting flowering time and developmental processes. Population genetics of 333 wild and cultivated accessions revealed 25.76% and 40.40% reductions in structural and deleterious variant burdens in cultivars, potentially reflecting a dramatic loss of genetic diversity of the wild progenitor. Quantitative genetics detected genetic association of yield traits, and essential roles of deleterious and structural variants in the formation of yield traits. In general, this study highlights significant impacts of structural and deleterious variants on yield traits and provides valuable guidelines for molecular breeding of foxtail millet.
作物驯化通常会通过遗传瓶颈和选择搭便车积累结构变异和有害变异。然而，尚未对谷子中的结构变异和有害变异负担进行研究。整合比较基因组学、泛基因组学、群体遗传学和数量遗传学，我们在驯化过程中鉴定出6713个基因获得和2802个基因丢失，这些变化影响了开花时间和发育过程。对333份野生和栽培种质的群体遗传学研究表明，栽培品种的结构变异和有害变异负担分别降低了25.76%和40.40%，这可能反映了野生祖先遗传多样性的显著丧失。数量遗传学检测到产量性状的遗传关联，以及有害变异和结构变异在产量性状形成中的重要作用。总体而言，本研究突出了结构变异和有害变异对产量性状的重大影响，并为谷子分子育种提供了有价值的指导。
