Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

PloS One
Natalia A ZinovievaGottfried Brem

Abstract

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses-calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals-were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were ...Continue Reading

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Methods Mentioned

BETA
chips
genotyping
electrophoresis
PCA

Software Mentioned

R package “ pophelper ”
R package ggplot2
fastPHASE
Neighbor
R package “ detectRUNS ”
SNeP
R package qvalue
DCMS
R package “ diveRsity ”
hapFLK

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