Functional role of genes in ROH sites in <i>Czech Golden</i> chickens

Abstract

Modern technologies make it possible to identify homozygous chromosome regions that have arisen as a result of animal selection. The article presents the results obtained in the genotyping of chickens using the Illumina Chicken 60KSNP iSelect Bead Chip. For the first time, a genome-wide analysis of the extended homozygous SNP sequences (ROH) was performed in the genome of Czech Golden hens. The average number of ROH segments in the chicken genome was 143 ± 8. ROH segments are usually randomly distributed in chicken chromosomes. It has been proposed to prohibit the use of heterozygous SNPs in ROH segments to prevent overestimation of ROH data. The average inbreeding coefficient in chickens calculated from ROH data was 0.34 ± 0.03. ROH islands were found on chromosomes 2, 3, 9 and 22.They contain genesassociatedwithimmunity, degradation of neurons, Fabricius bursa weight, obesity, feather pigmentation, and regulation of hit-shock genes. In the Czech Golden chicken breed, selection and the associated inbreeding have therefore influenced the genes involved in several biological processes.