Genome-wide selection signatures in Pinzgau cattle

<table style="height: 589px;" border="0" cellspacing="0" cellpadding="0" width="664" align="left"><tbody><tr><td height="589" align="left" valign="top"><p>The aim of this study was...

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Main Authors: Radovan Kasarda, Nina Moravčíková, Anna Trakovická, Gábor Mészáros, Ondrej Kadlečík
Format: Article
Language:English
Published: HACCP Consulting 2015-08-01
Series:Potravinarstvo
Subjects:
Online Access:http://www.potravinarstvo.com/journal1/index.php/potravinarstvo/article/view/478
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author Radovan Kasarda
Nina Moravčíková
Anna Trakovická
Gábor Mészáros
Ondrej Kadlečík
author_facet Radovan Kasarda
Nina Moravčíková
Anna Trakovická
Gábor Mészáros
Ondrej Kadlečík
author_sort Radovan Kasarda
collection DOAJ
description <table style="height: 589px;" border="0" cellspacing="0" cellpadding="0" width="664" align="left"><tbody><tr><td height="589" align="left" valign="top"><p>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<sub>ST</sub>) 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 &nbsp;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<sub>ST</sub> 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<sub>ST</sub> index was low. Only 24% of F<sub>ST</sub> 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.</p></td></tr></tbody></table> <!--[endif] -->
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spelling doaj.art-19170a19cfff4896b1ed91a495e3ea752022-12-22T02:51:46ZengHACCP ConsultingPotravinarstvo1337-09602015-08-019126827410.5219/478353Genome-wide selection signatures in Pinzgau cattleRadovan Kasarda0Nina Moravčíková1Anna Trakovická2Gábor Mészáros3Ondrej Kadlečík4Slovak University of Agriculture in Nitra, Faculty of Agrobiology and Food Resources, Tr. A. Hlinku 2, 949 76 NitraSlovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 NitraSlovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 NitraUniversity of Natural Resources and Life Sciences, Division of Livestock Sciences, Gregor-Mendel-Straße 33, 1180 WienSlovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra<table style="height: 589px;" border="0" cellspacing="0" cellpadding="0" width="664" align="left"><tbody><tr><td height="589" align="left" valign="top"><p>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<sub>ST</sub>) 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 &nbsp;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<sub>ST</sub> 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<sub>ST</sub> index was low. Only 24% of F<sub>ST</sub> 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.</p></td></tr></tbody></table> <!--[endif] -->http://www.potravinarstvo.com/journal1/index.php/potravinarstvo/article/view/478bovine SNP50 BeadChipFSTiHS scorePinzgau cattleselection sweep
spellingShingle Radovan Kasarda
Nina Moravčíková
Anna Trakovická
Gábor Mészáros
Ondrej Kadlečík
Genome-wide selection signatures in Pinzgau cattle
Potravinarstvo
bovine SNP50 BeadChip
FST
iHS score
Pinzgau cattle
selection sweep
title Genome-wide selection signatures in Pinzgau cattle
title_full Genome-wide selection signatures in Pinzgau cattle
title_fullStr Genome-wide selection signatures in Pinzgau cattle
title_full_unstemmed Genome-wide selection signatures in Pinzgau cattle
title_short Genome-wide selection signatures in Pinzgau cattle
title_sort genome wide selection signatures in pinzgau cattle
topic bovine SNP50 BeadChip
FST
iHS score
Pinzgau cattle
selection sweep
url http://www.potravinarstvo.com/journal1/index.php/potravinarstvo/article/view/478
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AT ninamoravcikova genomewideselectionsignaturesinpinzgaucattle
AT annatrakovicka genomewideselectionsignaturesinpinzgaucattle
AT gabormeszaros genomewideselectionsignaturesinpinzgaucattle
AT ondrejkadlecik genomewideselectionsignaturesinpinzgaucattle