Genomic profiling of selective sweeps through haplotype differentiation unravelled genes associated with production and reproduction traits in Indian goat breeds.

IF 1.7 3区农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE Tropical animal health and production Pub Date : 2024-09-28 DOI:10.1007/s11250-024-04136-2

Marykutty Thomas, Radhika G, R Thirupathy V, Aravindakshan T V

{"title":"Genomic profiling of selective sweeps through haplotype differentiation unravelled genes associated with production and reproduction traits in Indian goat breeds.","authors":"Marykutty Thomas, Radhika G, R Thirupathy V, Aravindakshan T V","doi":"10.1007/s11250-024-04136-2","DOIUrl":null,"url":null,"abstract":"<p><p>A comprehensive genomic scan of selective sweeps was conducted in autochthonous Attappady Black and improved dual-purpose Malabari goat breeds in south India. High-throughput single nucleotide polymorphism (SNP) marker data, obtained through Illumina goat SNP50 BeadChip genotyping of 48 goats (24 each of Attappady Black and Malabari goats), were utilized for the analysis. Selection signature analysis, employing hapFLK analysis based on haplotype differentiation, identified seven significant sweep regions (p < 0.005). Notably, one of these regions encompassed the genomic area housing the casein cluster and quantitative trait loci associated with milk production on chromosome 6. Gene ontology enrichment analysis of 166 putative selective genes associated with these sweep regions revealed 13 significantly over-represented Panther pathways (p ≤ 0.05), including the TGF-beta signalling pathway and GNRHR pathway. The selective sweeps detected in this study contributed significantly to the phenotypic divergence observed between Attappady Black and Malabari goats in south India.</p>","PeriodicalId":23329,"journal":{"name":"Tropical animal health and production","volume":null,"pages":null},"PeriodicalIF":1.7000,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Tropical animal health and production","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s11250-024-04136-2","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

Abstract

A comprehensive genomic scan of selective sweeps was conducted in autochthonous Attappady Black and improved dual-purpose Malabari goat breeds in south India. High-throughput single nucleotide polymorphism (SNP) marker data, obtained through Illumina goat SNP50 BeadChip genotyping of 48 goats (24 each of Attappady Black and Malabari goats), were utilized for the analysis. Selection signature analysis, employing hapFLK analysis based on haplotype differentiation, identified seven significant sweep regions (p < 0.005). Notably, one of these regions encompassed the genomic area housing the casein cluster and quantitative trait loci associated with milk production on chromosome 6. Gene ontology enrichment analysis of 166 putative selective genes associated with these sweep regions revealed 13 significantly over-represented Panther pathways (p ≤ 0.05), including the TGF-beta signalling pathway and GNRHR pathway. The selective sweeps detected in this study contributed significantly to the phenotypic divergence observed between Attappady Black and Malabari goats in south India.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

通过单倍型分化对选择性扫描进行基因组剖析，揭示了与印度山羊品种的生产和繁殖特性相关的基因。

对印度南部自生的 Attappady Black 和改良的 Malabari 两用山羊品种进行了全面的基因组选择性扫描。高通量单核苷酸多态性（SNP）标记数据是通过对 48 只山羊（Attappady Black 和 Malabari 山羊各 24 只）进行 Illumina 山羊 SNP50 BeadChip 基因分型获得的，用于分析。利用基于单倍型分化的 hapFLK 分析进行了选择特征分析，确定了 7 个显著的横扫区域（p

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分钟内获得全文去求助

来源期刊

Tropical animal health and production 农林科学-兽医学

CiteScore

3.40

自引率

11.80%

发文量

361

审稿时长

6-12 weeks

期刊介绍： Tropical Animal Health and Production is an international journal publishing the results of original research in any field of animal health, welfare, and production with the aim of improving health and productivity of livestock, and better utilisation of animal resources, including wildlife in tropical, subtropical and similar agro-ecological environments.