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

Michela Ablondi,Andrea Summer,Alberto Sabbioni,Massimo Malacarne,Jan-Thijs Van Kaam,Claudio Cipolat-Gotet

doi:10.1038/s41598-021-92168-1

Michela Ablondi, Andrea Summer + Show 4 more

Open Access

https://doi.org/10.1038/s41598-021-92168-1

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Journal: Scientific Reports	Publication Date: Jun 15, 2021
Citations: 8	License type: open-access

Affiliation: University of Parma

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.

Highlights

Dairy cattle breeds have been exposed to intense artificial selection for milk production traits over the last fifty years
Nearly half of the Italian cheeses are marked with the Protected Designation of Origin (PDO) label according to the CE Regulation 1151/2012 (EU 2012)[9]
In this study we aimed to evaluate detectable signs of divergence in the genome of Italian Holstein cows bred in five different contexts, from drinkable milk production to PDO cheese consortia

Summary

Introduction

Dairy cattle breeds have been exposed to intense artificial selection for milk production traits over the last fifty years. The production covers 34 provinces in five Italian regions in the North of Italy mainly located across the Po Valley lowland Such provinces are regulated by the same disciplinary, it is still possible to identify differences in the dairy farming systems and cheese-making technology among specific geographical areas. Strict rules on animal feeding and cheese making procedures are defined in the Parmigiano Reggiano disciplinary Another example of a deep-rooted tradition of cheese production is the Asiago consortium. As a matter of fact, the Italian Holstein association counts more than 1,000,000 alive animals and 9896 breeders, with in 2018 an average of 10,136 kg of milk produced per cow per year[14,16] The milk of this breed has been used over time for a multitude of purposes, from drinkable milk to highly specialized consortia for PDO cheese production

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