State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China.
Plant Commun. 2022 Sep 12;3(5):100345. doi: 10.1016/j.xplc.2022.100345. Epub 2022 Jun 1.
Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat. Uncovering the landscape of genetic variations in T. urartu will help us understand the evolutionary and polyploid characteristics of wheat. Here, we investigated the population genomics of T. urartu by genome-wide sequencing of 59 representative accessions collected around the world. A total of 42.2 million high-quality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome. The ancient T. urartu population experienced a significant reduction in effective population size (Ne) from ∼3 000 000 to ∼140 000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period. A map of allelic drift paths displayed splits and mixtures between different geographic groups, and a strong genetic drift towards hexaploid wheat was also observed, indicating that the direct donor of the A subgenome originated from northwestern Syria. Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses. A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T. urartu ecotype groups. Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomics-enabled improvements in wheat breeding.
乌拉尔图小麦是四倍体和六倍体小麦 A 亚基因组的祖先。揭示乌拉尔图小麦遗传变异的全景将有助于我们理解小麦的进化和多倍体特征。在这里，我们通过对全球 59 个代表性样本进行全基因组测序，研究了乌拉尔图小麦的群体基因组学。通过将读取内容映射到参考基因组，共获得了 4220 万个高质量的单核苷酸多态性和 300 万个插入和缺失。古代乌拉尔图小麦种群的有效种群数量（Ne）从约 30 万减少到约 14 万，并在新仙女木时期分裂为东地中海沿海和美索不达米亚-外高加索种群。等位基因漂移路径图显示了不同地理群体之间的分裂和混合，同时也观察到了向六倍体小麦的强烈遗传漂移，表明 A 亚基因组的直接供体来自叙利亚西北部。在与植物发育和应激反应相关的基因中，发现了东地中海沿海和美索不达米亚-外高加索种群之间的遗传变化。全基因组关联研究鉴定了 SEMI-DWARF 37 同源物外显子区域的两个单核苷酸多态性，它们与不同的乌拉尔图小麦生态型群体相对应。我们的研究为多倍体小麦 A 亚基因组的起源和遗传遗产提供了新的见解，并为基于基因组的小麦育种改良提供了一个基因库。
