Genome-wide selection signatures in Pinzgau cattle

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 (F ST ) 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 F ST 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 F ST index was low. Only 24% of F ST 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.

Genome-Wide Survey of Selection Signatures in Pakistani Cattle Breeds

“…Secondly, we used population differentiation (Fst) approach to identify the selection signatures in different breeds. Moreover, samples were also pruned for high LD SNPs using PLINK software version 1.9 (Purcell et al, 2007) and remaining 250,469 SNPs were used for selection signatures identification using population differentiation (Fst) method (Akey et al, 2002;Kasarda et al, 2015). To reduce the heterozygosity level in the data set of all the breeds, we used LD pruning as reported in some European and African zebu cattle breeds (Malkina et al, 2015).…”

“…A selection signature is considered as an important genetic based approach in farm animals, especially in cattle (Tang et al, 2007). It provides a wide picture of evolutionary processes as well as complex functional information in the genome (Kasarda et al, 2015). This information helps in identification of effective loci for breeding programs and also for functional genomics annotation (Ismael et al, 2016).…”

Evaluating signatures of selection through variation in linkage disequilibrium among different cattle breeds

“…In addition, they observed MSTN and FTO gene which are connected with beef production and thus were not preserved in our study with dairy and dual-purpose cattle. Kasarda et al (2015) found only 2 SNPs close to gene FTO using the integrated Haplotype Score (iHS) in Slovak and Austrian cattle. The highest peak (0.01%) between Slovak and Austrian on chromosome 23, between Slovak Pinzgau and Simmental on chromosome 4 and between Slovak Pinzgau and Holstein on chromosomes 1, 7 and 20 was observed.…”

“…The same approach was utilized in this study to detect signatures of selection in common and different across populations. Kasarda et al (2015) identified the evidence of recent selection based on estimation of the iHS, F ST and characterized affected regions near QTL associated with traits under strong selection in Pinzgau cattle. Recent investigations of the structural variation in cattle genome suggest that selective forces, in addition to the genotypic and haplotypic patterns, operate on the copy number variation (CNV) in candidate genes and can be helpful to characterize the effects of domestication, breed formation and artificial selection (Perez O´Brian et al, 2014).…”

Detection of Selection Signatures Based on the Integrated Haplotype Score in Chinese Jinnan Cattle

“…The iHS tests for Pinzgau cattle, which is a local breed of domestic cattle from the Pinzgau region of the federal state of Salzburg in Austria, showed that only seven regions had an iHS of >1.7 (Kasarda et al, 2015). This suggests that these commercial breeds have undergone stronger and more intensive selection pressure than Chinese Jinnan breed.…”