Genomic response to natural selection within alpine cattle breeds

Nina Moravčíková, Mojca Simčič, Gábor Mészáros, Johann Sölkner, Veronika Kukučková, Michal Vlček, Anna Trakovická, Ondrej Kadlečík and Radovan Kasarda
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Nina Moravčíková: Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
Mojca Simčič: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
Gábor Mészáros: Division Livestock Science, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
Johann Sölkner: Division Livestock Science, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
Veronika Kukučková: Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
Michal Vlček: Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
Anna Trakovická: Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
Ondrej Kadlečík: Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia
Radovan Kasarda: Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovakia

Czech Journal of Animal Science, 2018, vol. 63, issue 4, 136-143

Abstract: The aim of this study was to analyse the genomic regions that have been target of natural selection with respect to identifying the loci responsible mainly for fitness traits across six alpine cattle breeds. The genome-wide scan for selection signatures was performed using genotyping data from totally 465 animals. After applying data quality control, overall 35 873 single nucleotide polymorphisms were useable for the subsequent analysis. The detection of genomic regions affected by natural selection was carried out using the approach of principal component analysis. The analysis was based on the assumption that markers extremely related to the population structure are also candidates for local adaptation potential of the population. Based on the expected false discovery rate equal to 10% up to 1138 loci were identified as outliers. The strongest signals of selection were found in genomic regions on BTA 1, 2, 3, 6, 9, 11, 13, and 22. Most genes located in the identified regions have been previously associated with immunity system as well as body growth and muscle formation that mainly reflect the pressure of both natural and artificial selection in respect to adaptation of analysed breeds to the local environmental conditions. The results also signalized that those regions represent a correlated selection response in way to maintain the fitness of analysed breeds.

Keywords: cattle; fitness; footprints of selection; genomics; local adaptation; PCAdapt (search for similar items in EconPapers)
Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:caa:jnlcjs:v:63:y:2018:i:4:id:62-2017-cjas

DOI: 10.17221/62/2017-CJAS

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