Genomic insights into selection signatures and candidate genes for milk production traits in buffalo population

IF 4 2区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Animal Pub Date : 2025-01-21 DOI:10.1016/j.animal.2025.101427

T.X. Deng , X.Y. Ma , A.Q. Duan , X.R. Lu , H. Abdel-Shafy

{"title":"Genomic insights into selection signatures and candidate genes for milk production traits in buffalo population","authors":"T.X. Deng , X.Y. Ma , A.Q. Duan , X.R. Lu , H. Abdel-Shafy","doi":"10.1016/j.animal.2025.101427","DOIUrl":null,"url":null,"abstract":"<div><div>Genetic variability in livestock driven by selection leaves distinct signatures within the genome. However, the comprehensive landscape of the selection responses for milk production traits in the Chinese buffalo population remains elusive. This study employed an integrated haplotype score (iHS) and runs of homozygosity (ROH) analyses of whole-genome sequence data from 100 Chinese buffaloes to decipher selection signatures. Using iHS and ROH, we identified 1 046 and 1 045 significant genomic regions, containing 717 and 263 candidate genes, respectively. The integration of iHS and ROH revealed 258 candidate regions and 108 overlapping genes, representing true selection signatures. Additionally, 94 candidate regions overlapped with 672 previously reported quantitative trait loci associated with key economically important traits. Annotation of the genomic regions highlighted candidate genes linked to milk production traits, including SNORD42, COX18, ANKRD17, ALB, RASSF6, CXCL8, TMEM232, ARHGAP26, and NR3C1. Transcriptome-wide association analysis supported ANKRD17 and CEP41 as potential candidates for affecting milk traits. This study unveils a comprehensive selection signature profile for the Chinese buffalo population by integrating iHS and ROH methods. The findings have broad implications for improving milk production traits in buffalo populations globally, contributing to more sustainable livestock systems. The identified candidate genes shed light on the selection response for milk production traits, offering crucial insights into optimising the breeding strategies for Chinese buffaloes.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"19 4","pages":"Article 101427"},"PeriodicalIF":4.0000,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Animal","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1751731125000102","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}

引用次数: 0

Abstract

Genetic variability in livestock driven by selection leaves distinct signatures within the genome. However, the comprehensive landscape of the selection responses for milk production traits in the Chinese buffalo population remains elusive. This study employed an integrated haplotype score (iHS) and runs of homozygosity (ROH) analyses of whole-genome sequence data from 100 Chinese buffaloes to decipher selection signatures. Using iHS and ROH, we identified 1 046 and 1 045 significant genomic regions, containing 717 and 263 candidate genes, respectively. The integration of iHS and ROH revealed 258 candidate regions and 108 overlapping genes, representing true selection signatures. Additionally, 94 candidate regions overlapped with 672 previously reported quantitative trait loci associated with key economically important traits. Annotation of the genomic regions highlighted candidate genes linked to milk production traits, including SNORD42, COX18, ANKRD17, ALB, RASSF6, CXCL8, TMEM232, ARHGAP26, and NR3C1. Transcriptome-wide association analysis supported ANKRD17 and CEP41 as potential candidates for affecting milk traits. This study unveils a comprehensive selection signature profile for the Chinese buffalo population by integrating iHS and ROH methods. The findings have broad implications for improving milk production traits in buffalo populations globally, contributing to more sustainable livestock systems. The identified candidate genes shed light on the selection response for milk production traits, offering crucial insights into optimising the breeding strategies for Chinese buffaloes.

查看原文本刊更多论文

求助全文

约1分钟内获得全文求助全文

来源期刊

Animal 农林科学-奶制品与动物科学

CiteScore

7.50

自引率

2.80%

发文量

246

审稿时长

3 months

期刊介绍： Editorial board animal attracts the best research in animal biology and animal systems from across the spectrum of the agricultural, biomedical, and environmental sciences. It is the central element in an exciting collaboration between the British Society of Animal Science (BSAS), Institut National de la Recherche Agronomique (INRA) and the European Federation of Animal Science (EAAP) and represents a merging of three scientific journals: Animal Science; Animal Research; Reproduction, Nutrition, Development. animal publishes original cutting-edge research, ''hot'' topics and horizon-scanning reviews on animal-related aspects of the life sciences at the molecular, cellular, organ, whole animal and production system levels. The main subject areas include: breeding and genetics; nutrition; physiology and functional biology of systems; behaviour, health and welfare; farming systems, environmental impact and climate change; product quality, human health and well-being. Animal models and papers dealing with the integration of research between these topics and their impact on the environment and people are particularly welcome.