Fuping Zhao, Rui Xie, Lingzhao Fang, Ruidong Xiang, Zehu Yuan, Yang Liu, Lixian Wang
{"title":"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","authors":"Fuping Zhao, Rui Xie, Lingzhao Fang, Ruidong Xiang, Zehu Yuan, Yang Liu, Lixian Wang","doi":"10.1111/eva.13697","DOIUrl":null,"url":null,"abstract":"<p>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: <i>BMPR1B</i> and <i>GNRH2</i>, both of which have documented associations with fertility, and a HOXA gene cluster (<i>HOXA1</i>-<i>5</i>, <i>HOXA9</i>, <i>HOXA10</i>, <i>HOXA11</i> and <i>HOXA13</i>) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (<i>LAMTOR3</i>, <i>EEF1A2</i>), ear size (<i>HOXA1</i>, <i>KCNQ2</i>), fat tail formation (<i>HOXA10</i>, <i>HOXA11</i>), growth and development (<i>FAF1</i>, <i>CCNDBP1</i>, <i>GJB2</i>, <i>GJA3</i>), fat deposition (<i>ACOXL</i>, <i>JAZF1</i>, <i>HOXA3</i>, <i>HOXA4</i>, <i>HOXA5</i>, <i>EBF4</i>), immune (<i>UBR1</i>, <i>FASTKD5</i>) and feed intake (<i>DAPP1</i>, <i>RNF17</i>, <i>NPBWR2</i>). 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.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13697","citationCount":"0","resultStr":"{\"title\":\"Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep\",\"authors\":\"Fuping Zhao, Rui Xie, Lingzhao Fang, Ruidong Xiang, Zehu Yuan, Yang Liu, Lixian Wang\",\"doi\":\"10.1111/eva.13697\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>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: <i>BMPR1B</i> and <i>GNRH2</i>, both of which have documented associations with fertility, and a HOXA gene cluster (<i>HOXA1</i>-<i>5</i>, <i>HOXA9</i>, <i>HOXA10</i>, <i>HOXA11</i> and <i>HOXA13</i>) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (<i>LAMTOR3</i>, <i>EEF1A2</i>), ear size (<i>HOXA1</i>, <i>KCNQ2</i>), fat tail formation (<i>HOXA10</i>, <i>HOXA11</i>), growth and development (<i>FAF1</i>, <i>CCNDBP1</i>, <i>GJB2</i>, <i>GJA3</i>), fat deposition (<i>ACOXL</i>, <i>JAZF1</i>, <i>HOXA3</i>, <i>HOXA4</i>, <i>HOXA5</i>, <i>EBF4</i>), immune (<i>UBR1</i>, <i>FASTKD5</i>) and feed intake (<i>DAPP1</i>, <i>RNF17</i>, <i>NPBWR2</i>). 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.</p>\",\"PeriodicalId\":168,\"journal\":{\"name\":\"Evolutionary Applications\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-06-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13697\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Evolutionary Applications\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/eva.13697\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Evolutionary Applications","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/eva.13697","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}
Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep
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.
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.