Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains

Abstract Dairy cattle breeds have been exposed to intense artificial selection for milk production traits over the last fifty years. In Italy, where over 80% of milk is processed into cheese, selection has also focused on cheese-making traits. Due to a deep-rooted tradition in cheese-making, current...

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Autores principales:	Michela Ablondi, Massimo Malacarne, Claudio Cipolat-Gotet, Jan-Thijs van Kaam, Alberto Sabbioni, Andrea Summer
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6d03bb73bc2b416c8be6ee5fe304217a
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spelling	oai:doaj.org-article:6d03bb73bc2b416c8be6ee5fe304217a2021-12-02T17:40:47ZGenome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains10.1038/s41598-021-92168-12045-2322https://doaj.org/article/6d03bb73bc2b416c8be6ee5fe304217a2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92168-1https://doaj.org/toc/2045-2322Abstract Dairy cattle breeds have been exposed to intense artificial selection for milk production traits over the last fifty years. In Italy, where over 80% of milk is processed into cheese, selection has also focused on cheese-making traits. Due to a deep-rooted tradition in cheese-making, currently fifty Italian cheeses are marked with the Protected Designation of Origin (PDO) label as they proved traditional land of origin and procedures for milk transformation. This study aimed to explore from a genetic point of view if the presence of such diverse productive contexts in Italy have shaped in a different manner the genome of animals originally belonging to a same breed. We analyzed high density genotype data from 1000 Italian Holstein cows born between 2014 and 2018. Those animals were either farmed in one of four Italian PDO consortia or used for drinkable milk production only. Runs of Homozygosity, Bayesian Information Criterion and Discriminant Analysis of Principal Components were used to evaluate potential signs of genetic divergence within the breed. We showed that the analyzed Italian Holstein cows have genomic inbreeding level above 5% in all subgroups, reflecting the presence of ongoing artificial selection in the breed. Our study provided a comprehensive representation of the genetic structure of the Italian Holstein breed, highlighting the presence of potential genetic subgroups due to divergent dairy farming systems. This study can be used to further investigate genetic variants underlying adaptation traits in these subgroups, which in turn might be used to design more specialized breeding programs.Michela AblondiMassimo MalacarneClaudio Cipolat-GotetJan-Thijs van KaamAlberto SabbioniAndrea SummerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michela Ablondi Massimo Malacarne Claudio Cipolat-Gotet Jan-Thijs van Kaam Alberto Sabbioni Andrea Summer Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains
description	Abstract Dairy cattle breeds have been exposed to intense artificial selection for milk production traits over the last fifty years. In Italy, where over 80% of milk is processed into cheese, selection has also focused on cheese-making traits. Due to a deep-rooted tradition in cheese-making, currently fifty Italian cheeses are marked with the Protected Designation of Origin (PDO) label as they proved traditional land of origin and procedures for milk transformation. This study aimed to explore from a genetic point of view if the presence of such diverse productive contexts in Italy have shaped in a different manner the genome of animals originally belonging to a same breed. We analyzed high density genotype data from 1000 Italian Holstein cows born between 2014 and 2018. Those animals were either farmed in one of four Italian PDO consortia or used for drinkable milk production only. Runs of Homozygosity, Bayesian Information Criterion and Discriminant Analysis of Principal Components were used to evaluate potential signs of genetic divergence within the breed. We showed that the analyzed Italian Holstein cows have genomic inbreeding level above 5% in all subgroups, reflecting the presence of ongoing artificial selection in the breed. Our study provided a comprehensive representation of the genetic structure of the Italian Holstein breed, highlighting the presence of potential genetic subgroups due to divergent dairy farming systems. This study can be used to further investigate genetic variants underlying adaptation traits in these subgroups, which in turn might be used to design more specialized breeding programs.
format	article
author	Michela Ablondi Massimo Malacarne Claudio Cipolat-Gotet Jan-Thijs van Kaam Alberto Sabbioni Andrea Summer
author_facet	Michela Ablondi Massimo Malacarne Claudio Cipolat-Gotet Jan-Thijs van Kaam Alberto Sabbioni Andrea Summer
author_sort	Michela Ablondi
title	Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains
title_short	Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains
title_full	Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains
title_fullStr	Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains
title_full_unstemmed	Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains
title_sort	genome-wide scan reveals genetic divergence in italian holstein cows bred within pdo cheese production chains
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/6d03bb73bc2b416c8be6ee5fe304217a
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Genome-wide scan reveals genetic divergence in Italian Holstein cows bred within PDO cheese production chains

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