State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China.
BMC Genomics. 2023 Jul 11;24(1):392. doi: 10.1186/s12864-023-09479-y.
Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics.
We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by F and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds.
Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.
绵羊基因组经历了许多基因的丢失、获得和突变，这些变化导致了同一物种的不同品种在经过长时间的自然和人工选择后基因组发生了变异。然而，中国西北地区的本地绵羊的微观进化仍然难以捉摸。我们的目的是比较来自不同气候环境的四个绵羊品种的基因组和相关繁殖特征，揭示该物种所面临的选择挑战，以及绵羊基因组的微观进化差异。在这里，我们对来自中国西北地区的 4 个具有代表性的绵羊品种（包括哈萨克绵羊和多浪羊等本地品种，以及湖羊和萨福克羊等外来品种）进行了基因组重测序。
我们发现这四个品种在大约 10000 到 100 万年前有相似的扩张经历。在过去的 10000 年里，这四个品种的选择强度不一致，导致了繁殖特征的差异。我们通过 F 和 θπ 来探索绵羊的变异性和选择信号。检测到与不同繁殖特征相关的基因的基因组区域，这些基因可能是育种和选择的潜在目标。此外，我们还发现了一组可能的候选基因中的非同义突变，以及在具有不同繁殖特征的品种之间，它们的等位基因频率分布存在显著差异。通过 qPCR、Western blot 和 ELISA 分析，我们确定 PAK1、CYP19A1 和 PER1 是本地绵羊季节性繁殖的可能候选基因。此外，与繁殖相关的 3 个测试基因区域的单倍型频率在四个绵羊品种之间存在显著差异。
我们的研究结果为了解本地绵羊的微观进化提供了新的视角，并为识别与绵羊重要繁殖特征相关的基因提供了有价值的基因组信息。
