Analysis of the accumulation of homozygosity regions in chickens of the Pushkin breed using data from whole genome genotyping

Abstract

BACKGROUND: The search for genetic factors influencing the formation of the productive qualities of new breeding forms and populations of chickens is an important direction in the study of animal genomes. The knowledge gained can be in demand in projects to create modern domestic highly productive poultry lines. AIM: To conduct a comparative analysis of the localization of homozygous regions on chicken chromosomes in representatives of four breeds from the Genetic Collection of Rare and Endangered Breeds of Chickens to identify traces of selection and search for genes associated with productive traits. MATERIALS AND METHODS: Based on the bioinformatic analysis of 42275 SNP markers identified using the Illumina Chicken 60K SNP iSelect BeadChip microchip, data were obtained on the distribution of homozygous regions of four populations of chickens at the Genetic Collection of Rare and Endangered Breeds of Chickens (VNIIGRZH, St. Petersburg): Pushkinskaya (n = 20), Cornish (n = 22), Black-and-White Australorp (n = 20), Russian White (n = 23). RESULTS AND CONCLUSIONS: In chickens of the Pushkin breed, the observed heterozygosity was 0.372 0.004, which is higher than in other populations. According to the inbreeding index, based on the analysis of homozygous regions, the maximum level was found in Cornish chickens. For the Pushkin breed, the accumulation of homozygous regions on chromosomes 1, 2, 6, 8 was noted. The genes annotated in these loci are evidence of intensive selection.