Abstract
The aim of this study was to identify the evidence of recent selection based on estimation of the integrated Haplotype Score (iHS), population differentiation index (FST) and characterize affected regions near QTL associated with traits under strong selection in Pinzgau cattle. In total 21 Austrian and 19 Slovak purebreed bulls genotyped with Illumina bovineHD and bovineSNP50 BeadChip were used to identify genomic regions under selection. Only autosomal loci with call rate higher than 90%, minor allele frequency higher than 0.01 and Hardy-Weinberg equlibrium limit of 0.001 were included in the subsequent analyses of selection sweeps presence. The final dataset was consisted from 30538 SNPs with 81.86 kb average adjacent SNPs spacing. The iHS score were averaged into non-overlapping 500 kb segments across the genome. The FST values were also plotted against genome position based on sliding windows approach and averaged over 8 consecutive SNPs. Based on integrated Haplotype Score evaluation only 7 regions with iHS score higher than 1.7 was found. The average iHS score observed for each adjacent syntenic regions indicated slight effect of recent selection in analysed group of Pinzgau bulls. The level of genetic differentiation between Austrian and Slovak bulls estimated based on FST index was low. Only 24% of FST values calculated for each SNP was greather than 0.01. By using sliding windows approach was found that 5% of analysed windows had higher value than 0.01. Our results indicated use of similar selection scheme in breeding programs of Slovak and Austrian Pinzgau bulls. The evidence for genome-wide association between signatures of selection and regions affecting complex traits such as milk production was insignificant, because the loci in segments identified as affected by selection were very distant from each other. Identification of genomic regions that may be under pressure of selection for phenotypic traits to better understanding of the relationship between genotype and phenotype is one of the challenges for livestock genetics.
Highlights
Genome-wide screening of single nucleotide polymorphisms (SNPs) can improve the understanding of the connection between genotype and phenotype changes resulting from the formation of modern livestock breeds
The dataset consisting of the total 30538 autosomal SNPs that passed the filtering criteria have been used to identify genomic regions in Pinzgau bulls that may be influenced by recent selection
The integrated Haplotype Score (iHS) statistic was applied on dataset to detect selection sweeps
Summary
Genome-wide screening of single nucleotide polymorphisms (SNPs) can improve the understanding of the connection between genotype and phenotype changes resulting from the formation of modern livestock breeds. The explanation and identification of selection signatures can provide basic knowledge about evolutionary changes which shaped the genome and can be very perspective for identifying domestication-related loci that may help to further genetically improve of economically important traits (De Simoni Gouveia et al, 2014; Qanbari et al, 2014). If the mutation was recent and the selection is strong all alleles under positive selection will increase in frequency by producting selective sweep or selection signature. For neutral mutation, this will take many generations until the mutated allele has reached a high population frequency through drift. Where the loci selection is slight or the mutation is old little evidence of this selection may be left in the genome (Qanbari et al, 2010a; Kemper et al, 2014)
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