Analysis of Identical Runs of Homozygosity in the Genome of Egg-Laying and Ornamental Chicken Breeds

Artificial selection and natural selection have significantly increased the phenotypic and genetic differentiation of chicken breeds. Adaptation to environmental conditions, including acclimatization to harsh climates, has left “traces” of selection in the genome architecture of many breeds. Therefore, monitoring the genetic variability of small chicken breeds is an important part of breeding and conservation programs for poultry populations. Based on the results of genotyping breeds with the Illumina 60K Single Nucleotide Polymorphism (SNP) chip, a bioinformatics analysis was performed for egg-laying and ornamental breeds. Runs of homozygosity (ROH) were analyzed in egg-laying breeds—Czech golden (CZG), Leghorn Light Brown (Italian Partridge) (LLB) and ornamental breeds—Poland White-crested Black (PWC) and Hamburg silver Spangled Dwarf (HSSD). The average number of ROH in the chicken chromosomes varied between 200 ± 6 in PWC and 287 ± 5 in LLB, and the inbreeding coefficient was between 0.29 ± 0.04 in PWC and 0.50 ± 0.013 in HSSD. Among the chicken breeds studied, out of 40 ROH islands identified, 8 identical were found in two or three chicken breeds. These ROH islands were located on GGA1, GGA2, GGA7, GGA11 and GGA25. Genes in the ROH islands were associated with chicken weight, fat metabolism, feed intake, egg yolk weight, feather pecking disorders, and molecular processes mediating DNA replication and mRNA processing. The phenomenon of identical ROH islands in different breeds is discussed in the context of selection.