Exploring genomic signatures of selection for adaptation and resilience in nomadic Belahi cattle in the tropical climate.

IF 2.8 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Biology Reports Pub Date : 2025-07-07 DOI:10.1007/s11033-025-10793-9

Shambhuraditya Purushottam Chavan, Kashif Dawood Khan, Ashish Yadav, Rajesh Kumar Gahlyan, Vikas Vohra, Rani Alex, G R Gowane

{"title":"Exploring genomic signatures of selection for adaptation and resilience in nomadic Belahi cattle in the tropical climate.","authors":"Shambhuraditya Purushottam Chavan, Kashif Dawood Khan, Ashish Yadav, Rajesh Kumar Gahlyan, Vikas Vohra, Rani Alex, G R Gowane","doi":"10.1007/s11033-025-10793-9","DOIUrl":null,"url":null,"abstract":"Background: Indigenous cattle in India are known for their resilience to diseases, parasites, and heat stress. Belahi is a newly registered indigenous breed reared by pastoralist communities in the North Himalayan foothills (Shivalik range). It has been naturally selected for adaptability to nomadic grazing, disease resistance, and milk production. This study aimed to identify genomic selection signatures in Belahi cattle.Methods and results: Genome-wide SNP data were analyzed using three intra-population statistics-Tajima's D, Integrated Haplotype Score (iHS), and Nucleotide Diversity-which were combined into De-correlated Composite of Multiple Signals (DCMS). Additionally, Runs of Homozygosity (ROH) were used to detect regions under putative selection. DCMS identified 290 significant SNPs, while ROH revealed 8 overlapping regions. A total of 822 and 339 protein-coding genes were identified from DCMS and ROH, respectively, with 15 genes overlapping. Key genes included IL2 and IL21 (immune response) on BTA 17, and DNAJB13 (stress-related protein-folding) on BTA 15. QTL analysis revealed associations with tick resistance, susceptibility to respiratory and mycobacterial diseases, and pigmentation traits. Significant pathways included interleukin-2 receptor binding, leukocyte-mediated immunity, and peptidyl-tyrosine phosphorylation.Conclusions: The results suggest that Belahi cattle have undergone natural selection for immunity and environmental stress tolerance due to their nomadic lifestyle. These genomic insights support the breed's potential use in improving disease resistance and climate adaptability in cattle breeding programs.","PeriodicalId":18755,"journal":{"name":"Molecular Biology Reports","volume":"52 1","pages":"676"},"PeriodicalIF":2.8000,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Biology Reports","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s11033-025-10793-9","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Background: Indigenous cattle in India are known for their resilience to diseases, parasites, and heat stress. Belahi is a newly registered indigenous breed reared by pastoralist communities in the North Himalayan foothills (Shivalik range). It has been naturally selected for adaptability to nomadic grazing, disease resistance, and milk production. This study aimed to identify genomic selection signatures in Belahi cattle.

Methods and results: Genome-wide SNP data were analyzed using three intra-population statistics-Tajima's D, Integrated Haplotype Score (iHS), and Nucleotide Diversity-which were combined into De-correlated Composite of Multiple Signals (DCMS). Additionally, Runs of Homozygosity (ROH) were used to detect regions under putative selection. DCMS identified 290 significant SNPs, while ROH revealed 8 overlapping regions. A total of 822 and 339 protein-coding genes were identified from DCMS and ROH, respectively, with 15 genes overlapping. Key genes included IL2 and IL21 (immune response) on BTA 17, and DNAJB13 (stress-related protein-folding) on BTA 15. QTL analysis revealed associations with tick resistance, susceptibility to respiratory and mycobacterial diseases, and pigmentation traits. Significant pathways included interleukin-2 receptor binding, leukocyte-mediated immunity, and peptidyl-tyrosine phosphorylation.

Conclusions: The results suggest that Belahi cattle have undergone natural selection for immunity and environmental stress tolerance due to their nomadic lifestyle. These genomic insights support the breed's potential use in improving disease resistance and climate adaptability in cattle breeding programs.

查看原文本刊更多论文

探索热带气候下游牧贝拉希牛适应和恢复能力选择的基因组特征。

背景：印度本土的牛以其对疾病、寄生虫和热应激的抵抗力而闻名。Belahi是一个新注册的本地品种，由北喜马拉雅山麓（Shivalik山脉）的牧民社区饲养。它因适应游牧、抗病和产奶而被自然选择。本研究旨在确定贝拉希牛的基因组选择特征。方法与结果：采用tajima’s D、Integrated Haplotype Score （iHS）和Nucleotide diversity（核苷酸多样性）3种种群内统计方法对全基因组SNP数据进行分析，并将其合并为多重信号去相关复合（DCMS）。此外，纯合子序列（runof Homozygosity， ROH）用于检测假设选择下的区域。DCMS发现290个显著snp，而ROH发现8个重叠区域。从DCMS和ROH中分别鉴定出822个和339个蛋白编码基因，其中15个基因重叠。关键基因包括bta17上的IL2和IL21（免疫应答），bta15上的DNAJB13（应激相关蛋白折叠）。QTL分析显示与蜱的抗性、对呼吸道和分枝杆菌疾病的易感性以及色素沉着性状有关。重要的途径包括白细胞介素-2受体结合、白细胞介导的免疫和肽基酪氨酸磷酸化。结论：游牧生活方式对贝拉希牛的免疫力和环境应激耐受性进行了自然选择。这些基因组的见解支持了该品种在提高牛育种计划中的抗病性和气候适应性方面的潜在用途。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Molecular Biology Reports 生物-生化与分子生物学

CiteScore

5.00

自引率

0.00%

发文量

1048

审稿时长

5.6 months

期刊介绍： Molecular Biology Reports publishes original research papers and review articles that demonstrate novel molecular and cellular findings in both eukaryotes (animals, plants, algae, funghi) and prokaryotes (bacteria and archaea).The journal publishes results of both fundamental and translational research as well as new techniques that advance experimental progress in the field and presents original research papers, short communications and (mini-) reviews.