Yilin Wen , Junxi Huang , Yunyun Zhang , JiaHui Li , Lei Xu , Qiuming Chen , Yang Guo , Juan Geng
{"title":"全基因组分析揭示了四个新疆牛品种的选择信号","authors":"Yilin Wen , Junxi Huang , Yunyun Zhang , JiaHui Li , Lei Xu , Qiuming Chen , Yang Guo , Juan Geng","doi":"10.1016/j.genrep.2024.102000","DOIUrl":null,"url":null,"abstract":"<div><p>Xinjiang is home to three indigenous cattle breeds (Xinjiang Mongolian, Altay white-headed, and Kazakh cattle) and one crossbreed (Xinjiang Brown cattle), each possessing distinct and remarkable characteristics. In this study, we conducted comprehensive genome analyses of these four breeds in comparison with eight representative cattle breeds from around the world. Despite being predominantly <em>Bos taurus</em>, the proportion of <em>Bos indicus</em> ancestry in these indigenous breeds decreases with increasing latitude. This mixed genomic composition contributes to higher nucleotide diversity, lower linkage disequilibrium, and larger effective population sizes. Notably, Xinjiang Brown cattle exhibited higher LD at short distances, faster LD decay, and the largest effective population size, indicative of hybrid characteristics. Furthermore, we identified selective signals for lipids dynamics and coat colour in Altay white-headed cattle, immune resistance to local pathogens in Kazakh cattle, hydro-electrolyte balance and immune response in Xinjiang Mongolian cattle, and rapid growth and large body size in Xinjiang Brown cattle, as well as substance metabolism in three indigenous cattle. Our findings not only deepen the understanding of breed origins and diversity but also provide a foundation for exploring the genetic mechanisms underlying breed characteristics and facilitating further breed improvement.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0000,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Whole-genome analyses reveal selective signals in four Xinjiang cattle breeds\",\"authors\":\"Yilin Wen , Junxi Huang , Yunyun Zhang , JiaHui Li , Lei Xu , Qiuming Chen , Yang Guo , Juan Geng\",\"doi\":\"10.1016/j.genrep.2024.102000\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Xinjiang is home to three indigenous cattle breeds (Xinjiang Mongolian, Altay white-headed, and Kazakh cattle) and one crossbreed (Xinjiang Brown cattle), each possessing distinct and remarkable characteristics. In this study, we conducted comprehensive genome analyses of these four breeds in comparison with eight representative cattle breeds from around the world. Despite being predominantly <em>Bos taurus</em>, the proportion of <em>Bos indicus</em> ancestry in these indigenous breeds decreases with increasing latitude. This mixed genomic composition contributes to higher nucleotide diversity, lower linkage disequilibrium, and larger effective population sizes. Notably, Xinjiang Brown cattle exhibited higher LD at short distances, faster LD decay, and the largest effective population size, indicative of hybrid characteristics. Furthermore, we identified selective signals for lipids dynamics and coat colour in Altay white-headed cattle, immune resistance to local pathogens in Kazakh cattle, hydro-electrolyte balance and immune response in Xinjiang Mongolian cattle, and rapid growth and large body size in Xinjiang Brown cattle, as well as substance metabolism in three indigenous cattle. Our findings not only deepen the understanding of breed origins and diversity but also provide a foundation for exploring the genetic mechanisms underlying breed characteristics and facilitating further breed improvement.</p></div>\",\"PeriodicalId\":12673,\"journal\":{\"name\":\"Gene Reports\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.0000,\"publicationDate\":\"2024-08-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Gene Reports\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2452014424001237\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Gene Reports","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2452014424001237","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Whole-genome analyses reveal selective signals in four Xinjiang cattle breeds
Xinjiang is home to three indigenous cattle breeds (Xinjiang Mongolian, Altay white-headed, and Kazakh cattle) and one crossbreed (Xinjiang Brown cattle), each possessing distinct and remarkable characteristics. In this study, we conducted comprehensive genome analyses of these four breeds in comparison with eight representative cattle breeds from around the world. Despite being predominantly Bos taurus, the proportion of Bos indicus ancestry in these indigenous breeds decreases with increasing latitude. This mixed genomic composition contributes to higher nucleotide diversity, lower linkage disequilibrium, and larger effective population sizes. Notably, Xinjiang Brown cattle exhibited higher LD at short distances, faster LD decay, and the largest effective population size, indicative of hybrid characteristics. Furthermore, we identified selective signals for lipids dynamics and coat colour in Altay white-headed cattle, immune resistance to local pathogens in Kazakh cattle, hydro-electrolyte balance and immune response in Xinjiang Mongolian cattle, and rapid growth and large body size in Xinjiang Brown cattle, as well as substance metabolism in three indigenous cattle. Our findings not only deepen the understanding of breed origins and diversity but also provide a foundation for exploring the genetic mechanisms underlying breed characteristics and facilitating further breed improvement.
Gene ReportsBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
3.30
自引率
7.70%
发文量
246
审稿时长
49 days
期刊介绍:
Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.