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Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits

文献类型： 外文期刊

作者： Zhu, Mengting 1 ; Yang, Yonglin 1 ; Yang, Hua 1 ; Zhao, Zongsheng 2 ; Zhang, Hongmei 3 ; Blair, Hugh T. 4 ; Zheng, Wei 2 ; Wang, Mingyuan 1 ; Fang, Chenhui 2 ; Yu, Qian 1 ; Zhou, Huaqian 2 ; Qi, Hangdong 2 ;

作者机构： 1.Xinjiang Acad Agr & Reclamat Sci, State Key Lab Sheep Genet Improvement & Hlth Prod, Shihezi, Peoples R China

2.Shihezi Univ, Coll Anim Sci & Technol, Shihezi, Xinjiang, Peoples R China

3.Shihezi Univ, Affiliated Hosp 1, Sch Med Coll, Shihezi, Xinjiang, Peoples R China

4.Massey Univ, Inst Vet Anim & Biomed Sci, Palmerston North, New Zealand

关键词： Microevolution; Selection signature; Whole-genome resequencing; GWAS; Reproductive trait; Sheep

期刊名称：BMC GENOMICS （ 2022影响因子：4.4； 五年影响因子：4.7 ）

ISSN： 1471-2164

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

摘要： Background 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. Results We found that these four breeds had a similar expansion experience from similar to 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 FST and.p. 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. Conclusions Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.

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