A. Criscione , S. Ben Jemaa , G. Chessari , S. Riggio , S. Tumino , G. Cammilleri , A. Lastra , F. Carta , M.T. Sardina , B. Portolano , S. Bordonaro , A. Cesarani , S. Mastrangelo
{"title":"Detecting the footprint of selection on the genome of Girgentana goat, a popular ancient breed","authors":"A. Criscione , S. Ben Jemaa , G. Chessari , S. Riggio , S. Tumino , G. Cammilleri , A. Lastra , F. Carta , M.T. Sardina , B. Portolano , S. Bordonaro , A. Cesarani , S. Mastrangelo","doi":"10.1016/j.animal.2025.101466","DOIUrl":null,"url":null,"abstract":"<div><div>Girgentana goats are an ancient breed with distinctive morphological, adaptive, and production traits, making this population an interesting model for studying the genetic architecture underlying these traits. These special features result from natural and human-mediated selection. In this study, we aimed to detect potential signatures of selection in the Girgentana genome by combining the following statistical methods: the integrated haplotype score (<strong>iHS</strong>), the standardised log-ratio of the integrated site-specific extended haplotype homozygosity test between pairs of populations (<strong>Rsb</strong>), the runs of homozygosity (<strong>ROH</strong>) islands and the population differentiation index (<strong>F<sub>ST</sub></strong>). A composite dataset of 206 Girgentana and 334 animals from 13 goat populations across Northern and Southern Italy was analysed. All animals were genotyped using an Illumina Goat medium-density BeadChip. Multidimensional scaling and neighbour-joining analyses revealed a clear separation of the three major clades, coinciding with Girgentana, Northern, and Southern Italian goats. Twelve regions putatively under selection were detected using iHS and Rsb, whereas 16 hotspot regions were identified using F<sub>ST</sub> and ROH. Notably, a candidate region on chromosome 01 was consistently identified in all four tests. This region, along with other candidate regions, includes several genes associated with adaptive immunity, reproduction, and body size traits. The Girgentana breed showed signals of ongoing selection in a region of chromosome 6 encompassing several milk quality genes, such as caseins (<em>CSN2</em>, <em>CSN1S2</em>, and <em>CSN3</em>). Our study provides a glimpse into the genomic regions harbouring genes that presumably affect the desired features of Girgentana. This highlights the importance of ancient breeds in providing essential genetic traits for adapting livestock to increasing climate change challenges.</div></div>","PeriodicalId":50789,"journal":{"name":"Animal","volume":"19 4","pages":"Article 101466"},"PeriodicalIF":4.0000,"publicationDate":"2025-02-17","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/S1751731125000497","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
Girgentana goats are an ancient breed with distinctive morphological, adaptive, and production traits, making this population an interesting model for studying the genetic architecture underlying these traits. These special features result from natural and human-mediated selection. In this study, we aimed to detect potential signatures of selection in the Girgentana genome by combining the following statistical methods: the integrated haplotype score (iHS), the standardised log-ratio of the integrated site-specific extended haplotype homozygosity test between pairs of populations (Rsb), the runs of homozygosity (ROH) islands and the population differentiation index (FST). A composite dataset of 206 Girgentana and 334 animals from 13 goat populations across Northern and Southern Italy was analysed. All animals were genotyped using an Illumina Goat medium-density BeadChip. Multidimensional scaling and neighbour-joining analyses revealed a clear separation of the three major clades, coinciding with Girgentana, Northern, and Southern Italian goats. Twelve regions putatively under selection were detected using iHS and Rsb, whereas 16 hotspot regions were identified using FST and ROH. Notably, a candidate region on chromosome 01 was consistently identified in all four tests. This region, along with other candidate regions, includes several genes associated with adaptive immunity, reproduction, and body size traits. The Girgentana breed showed signals of ongoing selection in a region of chromosome 6 encompassing several milk quality genes, such as caseins (CSN2, CSN1S2, and CSN3). Our study provides a glimpse into the genomic regions harbouring genes that presumably affect the desired features of Girgentana. This highlights the importance of ancient breeds in providing essential genetic traits for adapting livestock to increasing climate change challenges.
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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.