National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
Nat Genet. 2017 Apr;49(4):579-587. doi: 10.1038/ng.3807. Epub 2017 Mar 6.
Comparative population genomics offers an excellent opportunity for unraveling the genetic history of crop domestication. Upland cotton (Gossypium hirsutum) has long been an important economic crop, but a genome-wide and evolutionary understanding of the effects of human selection is lacking. Here, we describe a variation map for 352 wild and domesticated cotton accessions. We scanned 93 domestication sweeps occupying 74 Mb of the A subgenome and 104 Mb of the D subgenome, and identified 19 candidate loci for fiber-quality-related traits through a genome-wide association study. We provide evidence showing asymmetric subgenome domestication for directional selection of long fibers. Global analyses of DNase I-hypersensitive sites and 3D genome architecture, linking functional variants to gene transcription, demonstrate the effects of domestication on cis-regulatory divergence. This study provides new insights into the evolution of gene organization, regulation and adaptation in a major crop, and should serve as a rich resource for genome-based cotton improvement.
比较群体基因组学为揭示作物驯化的遗传历史提供了极好的机会。陆地棉（Gossypium hirsutum）长期以来一直是一种重要的经济作物，但对人类选择影响的全基因组和进化理解还很缺乏。在这里，我们描述了 352 个野生和驯化棉花品系的变异图谱。我们扫描了 93 个驯化 sweeps，占据了 A 亚基因组的 74 Mb 和 D 亚基因组的 104 Mb，通过全基因组关联研究鉴定了 19 个与纤维质量相关性状的候选基因座。我们提供的证据表明，长纤维的定向选择导致了亚基因组的不对称驯化。DNase I 超敏位点和 3D 基因组结构的全局分析，将功能变体与基因转录联系起来，证明了驯化对顺式调控分化的影响。这项研究为主要作物的基因组织、调控和适应进化提供了新的见解，应该成为基于基因组的棉花改良的丰富资源。
