Analysis of Extended Homozygous and Heterozygous-Enriched Regions of Chromosomes in Pushkin Breed Chickens

In global practice of chicken breeding, the breeds that are adapted to local climatic conditions were developed. These include the Pushkin breed chicken, which was selected at the Russian Research Institute of Farm Animal Genetics and Breeding and is adapted to the conditions of detention in farms of northern regions. As a result of selection of this breed, the alleles of the genes contributing to a good egg productivity, while preserving the meat qualities of poultry, were selected. In the present study, we aimed to detect traces of selection in the Pushkin breed persisted to the present day. Genotyping of the genomes of this breed chickens was performed using the Illumina 60K SNP chip. As a result, extended homozygous regions of chromosomes (runs of homozygosity, ROHs) and extended heterozygosity-rich regions (HRRs) of chromosomes were identified. It was found that 90% of ROH segments have a length from 0.25 to 2 Mb, while 90% of HRR segments have a length from 0.01 to 0.4 Mb. A preferred localization of short HRR segments of 10–100 kb in short chromosomes and long HRR segments exceeding 100 kb in long chromosomes was detected. In general, the filling of chromosomes with ROH and HRR segments is uneven. ROH islands were identified on GGA1, GGA2, GGA6, and GGA8. HRR islands were found on GGA1, GGA2, GGA11, and GGA18. To confirm the selection of the genes within HRR islands, the Tajima’s D test was used. According to this test, balancing selection is possible within HRR islands on GGA1 (136.0–136.1 Mb) and GGA18 (9.7–9.9 Mb). Summarizing data obtained, it can be argued that the identified ROH and HRR islands can contain traces of selection and the genes located in them, can be candidates for improving the productivity and disease resistance in chickens.