Exploring the Italian equine gene pool via high-throughput genotyping
Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene p...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1099896/full |
| _version_ | 1797945418773954560 |
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| author | Stefano Capomaccio Stefano Capomaccio Michela Ablondi Daniele Colombi Daniele Colombi Cristina Sartori Andrea Giontella Andrea Giontella Katia Cappelli Katia Cappelli Enrico Mancin Vittoria Asti Roberto Mantovani Alberto Sabbioni Maurizio Silvestrelli Maurizio Silvestrelli |
| author_facet | Stefano Capomaccio Stefano Capomaccio Michela Ablondi Daniele Colombi Daniele Colombi Cristina Sartori Andrea Giontella Andrea Giontella Katia Cappelli Katia Cappelli Enrico Mancin Vittoria Asti Roberto Mantovani Alberto Sabbioni Maurizio Silvestrelli Maurizio Silvestrelli |
| author_sort | Stefano Capomaccio |
| collection | DOAJ |
| description | Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent “colonization”. In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool.Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed.Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness. |
| first_indexed | 2024-04-10T20:54:50Z |
| format | Article |
| id | doaj.art-a00b48d632194276849648d2a7fd3f40 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T20:54:50Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-a00b48d632194276849648d2a7fd3f402023-01-23T06:54:22ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011410.3389/fgene.2023.10998961099896Exploring the Italian equine gene pool via high-throughput genotypingStefano Capomaccio0Stefano Capomaccio1Michela Ablondi2Daniele Colombi3Daniele Colombi4Cristina Sartori5Andrea Giontella6Andrea Giontella7Katia Cappelli8Katia Cappelli9Enrico Mancin10Vittoria Asti11Roberto Mantovani12Alberto Sabbioni13Maurizio Silvestrelli14Maurizio Silvestrelli15Department of Veterinary Medicine, University of Perugia, Perugia, ItalySport Horse Research Centre (CRCS), University of Perugia, Perugia, ItalyDepartment of Veterinary Science, University of Parma, Parma, ItalyDepartment of Veterinary Medicine, University of Perugia, Perugia, ItalyDepartment of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, ItalyDepartment of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, ItalyDepartment of Veterinary Medicine, University of Perugia, Perugia, ItalySport Horse Research Centre (CRCS), University of Perugia, Perugia, ItalyDepartment of Veterinary Medicine, University of Perugia, Perugia, ItalySport Horse Research Centre (CRCS), University of Perugia, Perugia, ItalyDepartment of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, ItalyDepartment of Veterinary Science, University of Parma, Parma, ItalyDepartment of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, ItalyDepartment of Veterinary Science, University of Parma, Parma, ItalyDepartment of Veterinary Medicine, University of Perugia, Perugia, ItalySport Horse Research Centre (CRCS), University of Perugia, Perugia, ItalyIntroduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent “colonization”. In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool.Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed.Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.https://www.frontiersin.org/articles/10.3389/fgene.2023.1099896/fullbiodiversitylocal breedsgenomic dataSNPhorse |
| spellingShingle | Stefano Capomaccio Stefano Capomaccio Michela Ablondi Daniele Colombi Daniele Colombi Cristina Sartori Andrea Giontella Andrea Giontella Katia Cappelli Katia Cappelli Enrico Mancin Vittoria Asti Roberto Mantovani Alberto Sabbioni Maurizio Silvestrelli Maurizio Silvestrelli Exploring the Italian equine gene pool via high-throughput genotyping Frontiers in Genetics biodiversity local breeds genomic data SNP horse |
| title | Exploring the Italian equine gene pool via high-throughput genotyping |
| title_full | Exploring the Italian equine gene pool via high-throughput genotyping |
| title_fullStr | Exploring the Italian equine gene pool via high-throughput genotyping |
| title_full_unstemmed | Exploring the Italian equine gene pool via high-throughput genotyping |
| title_short | Exploring the Italian equine gene pool via high-throughput genotyping |
| title_sort | exploring the italian equine gene pool via high throughput genotyping |
| topic | biodiversity local breeds genomic data SNP horse |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1099896/full |
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