PDF(Pubmed)
Abstract：
As an invaluable Chinese sheep germplasm resource, Hu sheep are renowned for their high fertility and beautiful wavy lambskins. Their distinctive characteristics have evolved over time through a combination of artificial and natural selection. Identifying selection signatures in Hu sheep can provide a straightforward insight into the mechanism of selection and further uncover the candidate genes associated with breed-specific traits subject to selection. Here, we conducted whole-genome resequencing on 206 Hu sheep individuals, each with an approximate 6-fold depth of coverage. And then we employed three complementary approaches, including composite likelihood ratio, integrated haplotype homozygosity score and the detection of runs of homozygosity, to detect selection signatures. In total, 10 candidate genomic regions displaying selection signatures were simultaneously identified by multiple methods, spanning 88.54 Mb. After annotating, these genomic regions harbored collectively 92 unique genes. Interestingly, 32 candidate genes associated with reproduction were distributed in nine genomic regions detected. Out of them, two stood out as star candidates: BMPR1B and GNRH2, both of which have documented associations with fertility, and a HOXA gene cluster (HOXA1-5, HOXA9, HOXA10, HOXA11 and HOXA13) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (LAMTOR3, EEF1A2), ear size (HOXA1, KCNQ2), fat tail formation (HOXA10, HOXA11), growth and development (FAF1, CCNDBP1, GJB2, GJA3), fat deposition (ACOXL, JAZF1, HOXA3, HOXA4, HOXA5, EBF4), immune (UBR1, FASTKD5) and feed intake (DAPP1, RNF17, NPBWR2). Our results offer novel insights into the genetic mechanisms underlying the selection of breed-specific traits in Hu sheep and provide a reference for sheep genetic improvement programs.
摘要：
作为我国宝贵的绵羊种质资源,湖羊以其高生育力和美丽的波浪状羊皮而闻名。它们的独特特征随着时间的推移通过人工和自然选择的结合而演变。识别湖羊的选择特征可以提供对选择机制的直接了解，并进一步发现与受选择的品种特异性性状相关的候选基因。这里,我们对206只湖羊进行了全基因组重测序，每个都有大约6倍的覆盖深度。然后我们采用了三种互补的方法，包括复合似然比，整合单倍型纯合性评分和纯合性运行的检测，以检测选择签名。总的来说,通过多种方法同时鉴定了10个显示选择特征的候选基因组区域。跨越88.54Mb。注释后，这些基因组区域共有92个独特的基因。有趣的是,32个与繁殖相关的候选基因分布在检测到的9个基因组区域。在他们当中,其中两个是明星候选人：BMPR1B和GNRH2，两者都与生育率有关联，HOXA基因簇（HOXA1-5，HOXA9，HOXA10，HOXA11和HOXA13）也与生育力有关。此外,我们确定了与毛囊发育相关的其他基因（LAMTOR3，EEF1A2），耳朵大小（HOXA1，KCNQ2），脂肪尾巴形成（HOXA10，HOXA11），生长发育（FAF1，CCNDBP1，GJB2，GJA3），脂肪沉积(ACOXL，JAZF1,HOXA3,HOXA4,HOXA5,EBF4),免疫（UBR1，FASTKD5）和采食量（DAPP1，RNF17，NPBWR2）。我们的研究结果为湖羊品种特异性性状选择的遗传机制提供了新的见解，并为绵羊遗传改良计划提供了参考。
