{"title":"选择特征的基因组扫描揭示了泰国多品种奶牛种群适应和生产性状的候选基因","authors":"Thawee Laodim , Skorn Koonawootrittriron , Mauricio A. Elzo , Thanathip Suwanasopee , Danai Jattawa , Mattaneeya Sarakul","doi":"10.1016/j.livsci.2025.105803","DOIUrl":null,"url":null,"abstract":"<div><div>The genetic improvement of dairy cattle for tropical environments demands a balance between high productivity and adaptability. Although previous studies have explored genomic signatures in various cattle breeds, limited insights exist for the genetically diverse Thai multibreed dairy cattle population developed through crossbreeding of multiple <em>Bos taurus</em> and <em>Bos indicus</em> breeds with Holstein. This study aimed to uncover selection signatures and candidate genes underpinning adaptation and production traits in this population. Using genotype data from 2661 animals (73,762 SNPs), population structure was revealed via Discriminant Analysis of Principal Components (DAPC), identifying four genetically distinct groups. Integrated haplotype score (iHS) analysis identified 376 to 500 genomic regions under selection across groups, harboring 962 to 1657 genes. Seven strong candidate genes – <em>KLF12, MAP2K6, SPATA16, LAMA2, SLC25A28, WNT7A</em>, and <em>HHIPL2</em> – were linked to milk yield, fat synthesis, immune response, and adaptation. Annotation revealed 5036 to 7970 quantitative trait loci (QTLs) per group, with 26.53 % to 28–84 % overlapping with milk traits in groups 1 to 3, and 24.96 % with meat traits in group 4. The QTL enrichment highlighted significant traits such as milk fat yield, immunoglobulin G levels, tick resistance, and coat color, reflecting environmental selection pressures. These findings demonstrate how artificial selection shaped the genomic landscape of Thai dairy cattle, influencing traits critical for productivity, health, and climate resilience. This study provides a foundation for genomic selection strategies tailored to tropical dairy systems and underscores the potential of genetic marker information to enhance dairy cattle efficiency, productivity, and sustainability under region-specific challenges.</div></div>","PeriodicalId":18152,"journal":{"name":"Livestock Science","volume":"301 ","pages":"Article 105803"},"PeriodicalIF":1.9000,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in the Thai multibreed dairy cattle population\",\"authors\":\"Thawee Laodim , Skorn Koonawootrittriron , Mauricio A. Elzo , Thanathip Suwanasopee , Danai Jattawa , Mattaneeya Sarakul\",\"doi\":\"10.1016/j.livsci.2025.105803\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>The genetic improvement of dairy cattle for tropical environments demands a balance between high productivity and adaptability. Although previous studies have explored genomic signatures in various cattle breeds, limited insights exist for the genetically diverse Thai multibreed dairy cattle population developed through crossbreeding of multiple <em>Bos taurus</em> and <em>Bos indicus</em> breeds with Holstein. This study aimed to uncover selection signatures and candidate genes underpinning adaptation and production traits in this population. Using genotype data from 2661 animals (73,762 SNPs), population structure was revealed via Discriminant Analysis of Principal Components (DAPC), identifying four genetically distinct groups. Integrated haplotype score (iHS) analysis identified 376 to 500 genomic regions under selection across groups, harboring 962 to 1657 genes. Seven strong candidate genes – <em>KLF12, MAP2K6, SPATA16, LAMA2, SLC25A28, WNT7A</em>, and <em>HHIPL2</em> – were linked to milk yield, fat synthesis, immune response, and adaptation. Annotation revealed 5036 to 7970 quantitative trait loci (QTLs) per group, with 26.53 % to 28–84 % overlapping with milk traits in groups 1 to 3, and 24.96 % with meat traits in group 4. The QTL enrichment highlighted significant traits such as milk fat yield, immunoglobulin G levels, tick resistance, and coat color, reflecting environmental selection pressures. These findings demonstrate how artificial selection shaped the genomic landscape of Thai dairy cattle, influencing traits critical for productivity, health, and climate resilience. This study provides a foundation for genomic selection strategies tailored to tropical dairy systems and underscores the potential of genetic marker information to enhance dairy cattle efficiency, productivity, and sustainability under region-specific challenges.</div></div>\",\"PeriodicalId\":18152,\"journal\":{\"name\":\"Livestock Science\",\"volume\":\"301 \",\"pages\":\"Article 105803\"},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2025-08-15\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Livestock Science\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1871141325001647\",\"RegionNum\":3,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"AGRICULTURE, DAIRY & ANIMAL SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Livestock Science","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1871141325001647","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}
引用次数: 0
摘要
热带环境下奶牛的遗传改良需要在高产和适应性之间取得平衡。虽然以前的研究已经探索了各种牛品种的基因组特征,但通过将多个牛品种和牛品种与荷斯坦杂交而形成的遗传多样性泰国多品种奶牛种群的见解有限。本研究旨在揭示该种群适应和生产性状的选择特征和候选基因。利用2661只动物(73762个snp)的基因型数据,通过主成分判别分析(Discriminant Analysis of Principal Components, DAPC)揭示了种群结构,确定了4个遗传上不同的群体。综合单倍型评分(iHS)分析确定了376至500个基因组区域,其中包含962至1657个基因。七个强有力的候选基因——KLF12、MAP2K6、SPATA16、LAMA2、SLC25A28、WNT7A和HHIPL2——与产奶量、脂肪合成、免疫反应和适应有关。每组共有5036 ~ 7970个qtl,其中1 ~ 3组与乳性状重叠率为26.53% ~ 28 ~ 84%,4组与肉性状重叠率为24.96%。QTL富集突出了乳脂产量、免疫球蛋白G水平、蜱虫抗性和毛色等显著性状,反映了环境选择压力。这些发现证明了人工选择如何塑造了泰国奶牛的基因组景观,影响了对生产力、健康和气候适应能力至关重要的性状。该研究为针对热带奶牛系统的基因组选择策略提供了基础,并强调了遗传标记信息在提高奶牛效率、生产力和区域特定挑战下的可持续性方面的潜力。
Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in the Thai multibreed dairy cattle population
The genetic improvement of dairy cattle for tropical environments demands a balance between high productivity and adaptability. Although previous studies have explored genomic signatures in various cattle breeds, limited insights exist for the genetically diverse Thai multibreed dairy cattle population developed through crossbreeding of multiple Bos taurus and Bos indicus breeds with Holstein. This study aimed to uncover selection signatures and candidate genes underpinning adaptation and production traits in this population. Using genotype data from 2661 animals (73,762 SNPs), population structure was revealed via Discriminant Analysis of Principal Components (DAPC), identifying four genetically distinct groups. Integrated haplotype score (iHS) analysis identified 376 to 500 genomic regions under selection across groups, harboring 962 to 1657 genes. Seven strong candidate genes – KLF12, MAP2K6, SPATA16, LAMA2, SLC25A28, WNT7A, and HHIPL2 – were linked to milk yield, fat synthesis, immune response, and adaptation. Annotation revealed 5036 to 7970 quantitative trait loci (QTLs) per group, with 26.53 % to 28–84 % overlapping with milk traits in groups 1 to 3, and 24.96 % with meat traits in group 4. The QTL enrichment highlighted significant traits such as milk fat yield, immunoglobulin G levels, tick resistance, and coat color, reflecting environmental selection pressures. These findings demonstrate how artificial selection shaped the genomic landscape of Thai dairy cattle, influencing traits critical for productivity, health, and climate resilience. This study provides a foundation for genomic selection strategies tailored to tropical dairy systems and underscores the potential of genetic marker information to enhance dairy cattle efficiency, productivity, and sustainability under region-specific challenges.
期刊介绍:
Livestock Science promotes the sound development of the livestock sector by publishing original, peer-reviewed research and review articles covering all aspects of this broad field. The journal welcomes submissions on the avant-garde areas of animal genetics, breeding, growth, reproduction, nutrition, physiology, and behaviour in addition to genetic resources, welfare, ethics, health, management and production systems. The high-quality content of this journal reflects the truly international nature of this broad area of research.