Genome-wide selection signatures in Pinzgau cattle

Authors

  • Radovan Kasarda Slovak University of Agriculture in Nitra, Faculty of Agrobiology and Food Resources, Tr. A. Hlinku 2, 949 76 Nitra
  • Nina Moravčí­ková Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra
  • Anna Trakovická Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra
  • Gábor Mészáros University of Natural Resources and Life Sciences, Division of Livestock Sciences, Gregor-Mendel-StraíŸe 33, 1180 Wien
  • Ondrej Kadlečí­k Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra

DOI:

https://doi.org/10.5219/478

Keywords:

bovine SNP50 BeadChip, FST, iHS score, Pinzgau cattle, selection sweep

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.

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Published

2015-07-13

How to Cite

Kasarda, R. ., Moravčí­ková, N. ., Trakovická, A. ., Mészáros, G. ., & Kadlečí­k, O. . (2015). Genome-wide selection signatures in Pinzgau cattle. Potravinarstvo Slovak Journal of Food Sciences, 9(1), 268–274. https://doi.org/10.5219/478