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

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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.

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About the authors

Natalia V. Dementieva

All-Russian Research Institute of Genetics and Breeding of Farm Animals – Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Email: dementevan@mail.ru
ORCID iD: 0000-0003-0210-9344
SPIN-code: 8768-8906
Scopus Author ID: 57189759592
ResearcherId: Т-4551-2018

Cand. Sci. (Biol.), Main Researcher

Russian Federation, Pushkin, Saint Petersburg

Yuri S. Shcherbakov

All-Russian Research Institute of Genetics and Breeding of Farm Animals – Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Email: yura.10.08.94.94@mail.ru
ORCID iD: 0000-0001-6434-6287
SPIN-code: 3547-1009
Scopus Author ID: 57221619264
ResearcherId: AAR-5595-2020

Junior Researcher

Russian Federation, Pushkin, Saint Petersburg

Olga V. Mitrofanova

All-Russian Research Institute of Genetics and Breeding of Farm Animals – Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Email: mo1969@mail.ru
ORCID iD: 0000-0003-4702-2736
SPIN-code: 4378-9500
Scopus Author ID: 57188701229
ResearcherId: S-5336-2018

Cand. Sci. (Biol.), Scientific Secretary

Russian Federation, Pushkin, Saint Petersburg

Anatoly B. Vakhrameev

All-Russian Research Institute of Genetics and Breeding of Farm Animals – Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Author for correspondence.
Email: ab_poultry@mail.ru
ORCID iD: 0000-0001-5166-979X
SPIN-code: 6810-7339
Scopus Author ID: 56862214400
ResearcherId: AAD-1068-2022

Senior Researcher

Russian Federation, Pushkin, Saint Petersburg

Vadim K. Khlestkin

All-Russian Research Institute of Genetics and Breeding of Farm Animals – Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Email: khlestkin@bionet.nsc.ru
ORCID iD: 0000-0001-9605-8028
SPIN-code: 6367-2970
Scopus Author ID: 56368129500
ResearcherId: D-5493-2018

Cand. Sci. (Chem.), Director

Russian Federation, Pushkin, Saint Petersburg

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Supplementary files

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2. Figure 1. Inbreeding index calculated on the basis of ROH parameters for hens of four populations. ABS - black-and-white Australorp, Сor - Cornish, Pu - Pushkin, RW - Russian White

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3. Figure 2. Population affiliation of 85 chickens, performed using the Admixture program based on the analysis of 42275 SNP markers, for the number of clusters k = 2 (A), k = 3 (B), k = 4 (C). ABS - black-and-white Australorp, Сor - Cornish, Pu - Pushkin, RW - Russian White

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