The impact of artificial selection on runs of homozygosity in Slovak Spotted and Pinzgau cattle

Abstract

The aim of this study was to analyse the distribution of runs of homozygosity (ROH) across the genomes of Slovak Spotted and Slovak Pinzgau cattle and to describe the autozygosity islands resulting from the selective breeding for traits of interest during the development of these breeds. The genome-wide data for a total of 236 animals were obtained by using two platforms: Illumina BovineSNP50v2 BeadChip and ICBF International Dairy and Beef v3. After quality control, the database of genotyping data consisted of 39,261 common SNPs across both breeds that covered overall length 2,497,077 kb of the genome with average distance between adjacent SNPs 63.67 kb. The ROH segments were defined as genomic regions with 15 or more consecutive homozygous calls with maximum gap between SNPs of 1 Mb and minimum density of one SNPs on every 100 kb. The distribution of ROH was analysed for five length categories (> 1 Mb, > 2 Mb, > 4 Mb, > 8 Mb, and > 16 Mb). The results showed that the ROH segments were present across the genome of all animals, with the average number of 54.59 ± 18.58 segments and the average length of 130.33 ± 58.40 Mb. The short segments (> 1 Mb) were the most frequent through the genomes and accounted for 70.26 % (Slovak Spotted) or 65.99 % (Slovak Pinzgau) of all segments detected. Thus, our results indicated that on average 6.11 % (Slovak Spotted) and 4.72 % (Slovak Pinzgau) of the genomes are autozygous. Moreover, the proportion of ROH > 16 Mb revealed that on average 0.45 % of the Slovak Spotted and 0.88 % of the Slovak Pinzgau genomes could be affected by recent inbreeding. Despite the fact that the distribution of ROH differentiated between breeds, the major fraction of chromosome residing in ROH was observed on BTA6 (13.49 % resp. 14.26 % of autosomal length in ROH). In this region we identified various QTLs and genes responsible for milk production (CSN1S1, CSN1S2, CSN2, CSN3), and coat colour patterns (KIT). Generally, our results confirmed that the regions displaying autozygosity in Slovak Spotted and Slovak Pinzgau cattle are linked mostly to milk production and muscle development thus ensuring selection for dual-purpose performance.