Abstract
Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated FST within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing FST values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the FST value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.
Highlights
As for other domestic animals, both natural and artificial selection have resulted over a short period of time in a broad phenotypic variety and in genetic differentiation of numerous different cattle breeds
A spectacular example of success of such genetic improvement programmes is offered by dairy cattle breeds [2]
The goal of this study was to perform a genome scan for SNP differentiation, by considering 42,846 SNPs genotyped in HOL, MON and NOR dairy cattle breeds, to identify the main regions affected by the strong and recent artificial selection they have been subjected to
Summary
As for other domestic animals, both natural and artificial selection have resulted over a short period of time in a broad phenotypic variety and in genetic differentiation of numerous different cattle breeds. This recent history provides a unique opportunity for the identification of loci subjected to adaptive selection. About ,10,000 years ago, early breeders might have imposed a so-called ‘‘unconscious’’ selection ‘‘which results from every one trying to possess and breed from the best individual animals’’ [1]. A spectacular example of success of such genetic improvement programmes is offered by dairy cattle breeds [2]
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