A genome-wide scan for signatures of differential artificial selection in ten cattle breeds

BMC Genomics
Sophie RothammerIvica Medugorac

Abstract

Since the times of domestication, cattle have been continually shaped by the influence of humans. Relatively recent history, including breed formation and the still enduring enormous improvement of economically important traits, is expected to have left distinctive footprints of selection within the genome. The purpose of this study was to map genome-wide selection signatures in ten cattle breeds and thus improve the understanding of the genome response to strong artificial selection and support the identification of the underlying genetic variants of favoured phenotypes. We analysed 47,651 single nucleotide polymorphisms (SNP) using Cross Population Extended Haplotype Homozygosity (XP-EHH). We set the significance thresholds using the maximum XP-EHH values of two essentially artificially unselected breeds and found up to 229 selection signatures per breed. Through a confirmation process we verified selection for three distinct phenotypes typical for one breed (polledness in Galloway, double muscling in Blanc-Bleu Belge and red coat colour in Red Holstein cattle). Moreover, we detected six genes strongly associated with known QTL for beef or dairy traits (TG, ABCG2, DGAT1, GH1, GHR and the Casein Cluster) within selection signa...Continue Reading

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Sep 17, 2015·Scientific Reports·Jun Hong XiaGen Hua Yue
Mar 20, 2016·Genetics, Selection, Evolution : GSE·Elisabeth KunzIvica Medugorac
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Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

pcaMethods
- EHH
XP
R
sXPEHH
hierfstat
Haploview
BEAGLE

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