Genomic response to natural selection within alpine cattle breeds

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.