Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY Evolutionary Applications Pub Date : 2024-06-21 DOI:10.1111/eva.13697
Fuping Zhao, Rui Xie, Lingzhao Fang, Ruidong Xiang, Zehu Yuan, Yang Liu, Lixian Wang
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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.

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206 个全基因组重测序分析揭示了与胡羊品种特异性相关的选择特征
作为中国绵羊宝贵的种质资源,胡羊以高繁殖力和美丽的波浪形羔羊皮而闻名。它们与众不同的特征是在人工选择和自然选择的共同作用下逐渐形成的。鉴别胡羊的选择特征可以直接了解选择机制,并进一步发现与受选择的品种特异性相关的候选基因。在此,我们对 206 只胡羊个体进行了全基因组重测序,每个个体的覆盖深度约为 6 倍。然后,我们采用了三种互补方法,包括复合似然比、单体型同源性综合评分和同源性运行检测,来检测选择特征。通过多种方法,共同时发现了 10 个显示选择特征的候选基因组区域,跨度为 88.54 Mb。经过注释,这些基因组区域共包含 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 个基因组区域中。其中,两个候选基因脱颖而出:BMPR1B和GNRH2这两个基因都与生育能力有关联,而HOXA基因簇(HOXA1-5、HOXA9、HOXA10、HOXA11和HOXA13)也与生育能力有关。此外,我们还发现了与毛囊发育(LAMTOR3、EEF1A2)、耳朵大小(HOXA1、KCNQ2)、脂肪尾形成(HOXA10、HOXA11)有关的其他基因、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)。我们的研究结果为胡羊品种特异性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。
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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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