State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Genome Biol. 2024 Jun 6;25(1):148. doi: 10.1186/s13059-024-03288-6.
Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.
We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats.
Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
绵羊和山羊经历了驯化和改良，产生了相似的表型，这些表型受到结构变异（SVs）的极大影响。在这里，我们报告了亚洲盘羊的高质量染色体水平参考基因组，并对来自世界各地的野生和家养绵羊和山羊种群的 897 个基因组中的 SV 进行了全面分析，以揭示趋同进化的遗传特征。
我们从遗传多样性、染色体分布以及它们与基因、QTL 和转座元件的关系等方面描述了 SV 景观，并研究了它们对调控元件的影响。我们鉴定了几个新的 SV，并注释了与重要生产性状相关的相应基因（例如 BMPR1B、BMPR2、RALYL、COL21A1 和 LRP1B），如繁殖力、肉奶产量和羊毛/毛发细度。我们检测到了选择的迹象，涉及到驯化、局部环境适应和改良过程中同源 SV 相关基因的平行进化。特别是，我们发现产仔数性状经历了针对 BMPR1B 基因的趋同选择，DEL00067921 缺失解释了山羊中观察到的表型变异的约 10.4%。
我们的研究结果为 SV 的趋同进化提供了新的见解，并为未来绵羊、山羊和相关家畜的改良提供了丰富的资源。
