Studying the structure of a gene pool population of the Russian White chicken breed by genome-wide SNP scan

Dementeva, Natalia V. and Romanov, Michael N and Kudinov, Andrei A and Mitrofanova, Olga V and Stanishevskaya, Olga I and Terletsky, Valeriy P and Fedorova, Elena S and Nikitkina, E V and Plemyashov, Kirill V (2017) Studying the structure of a gene pool population of the Russian White chicken breed by genome-wide SNP scan. Sel’skokhozyaistvennaya Biologiya [Agricultural Biology], 52 (6). pp. 1166-1174. ISSN 0131-6397. E-ISSN 2412-0324. (doi:https://doi.org/10.15389/agrobiology.2017.6.1166eng) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)

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Official URL
http://dx.doi.org/10.15389/agrobiology.2017.6.1166...

Abstract

A population of the Russian White chickens, bred at the gene pool farm of ARRIFAGB for 25 generations using individual selection, is characterized by resistance to a lowered temperature in the early postnatal period and white colour of the embryonic down. In 2002-2012, breeding was carried out by panmixia, and by now a new population of the Russian White chickens has been formed on the basis of the surviving stock. Comparison of the genetic variability of this population and the archival DNA of representatives of the 2001 population using microarray screening technology will help to assess the population structure and the preservation of the unique characteristics of its genome. The material for the study was DNA extracted from 162 chicken blood samples. Two groups of the Russian White breed were studied, the 2001 population and the current population. Genome-wide analysis using single nucleotide markers (SNP) included screening by means of the Illumina Chicken 60K SNP iSelect BeadChip microarray. Quality control of genotyping, determination of the population genetic structure by multidimensional scaling (MDS), calculation of linkage disequilibrium (LD) and allele frequency in the groups were carried out using PLINK 1.9 software program. The construction of a cluster delimitation model based on SNP genotypes was carried out using the ADMIXTURE program. According to the MDS analysis results, the current population can be divided into four MDS groups, which, when compared to the data of the pedigree, adequately reflect the origin of the studied individuals. The representatives of the ancestral population were genetically similar to the MDS3 group of the current population. Using the F-statistic of the two-way analysis of variance, a significant effect of the group, chromosome, chromosome in the group, and the distance between SNP markers on LD (r2) values was observed. In the 2001 group, the maximum r2 and the high incidence of LD equal to 1 were observed for all chromosomes, with a distance between SNP markers being 500-1000 Kb. There was also the greatest number of monomorphic alleles in this group. Based on the SNP analysis, we may conclude that the current Russian White chicken population is characterized by the disintegration of long LD regions of the ancestral population. Modelling clusters using the ADMIXTURE program revealed differences between the current population groups determined by MDS analysis. The groups composed of individuals included in MDS1 and MDS2 had a homogeneous structure and differed from each other at K = 4 and K = 5. The MDS4 group formed a genetically heterogeneous cluster different from the MDS1 and MDS2 groups at K of 2-5. The MDS3 group was phylogenetically close to the 2001 population (at K of 2-5). In general, the analysis of the current gene pool population of the Russian White chickens showed its heterogeneity while one of its groups (MDS3) was similar to the ancestral population of 2001, which in turn is characterized by a large number of monomorphic alleles and a high frequency of long LD regions. Thus, SNP scanning allowed evaluating the genetic similarity of individuals and the population structure of the Russian White chicken breed. Understanding the genetic structure is an important point in the panmictic breeding and tracking of historical changes in the molecular organization of the genome of a gene pool population with a limited number of animals.

Item Type: Article
Projects: [UNSPECIFIED] Development of the Methodology of Genomic Selection for the Conservation and Effective Use of the Potential of Genetic Resources, and Creation of Highly Productive Strains in the Poultry Industry of Russia
Uncontrolled keywords: population structure, genetic diversity, SNP genotyping, Russian White breed of chickens
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: Faculties > Sciences > School of Biosciences > Biomedical Research Group
Depositing User: M. Romanov
Date Deposited: 20 Feb 2018 12:34 UTC
Last Modified: 20 May 2019 15:19 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/65981 (The current URI for this page, for reference purposes)
Dementeva, Natalia V.: https://orcid.org/0000-0003-0210-9344
Romanov, Michael N: https://orcid.org/0000-0003-3584-4644
Kudinov, Andrei A: https://orcid.org/0000-0002-7811-576X
Mitrofanova, Olga V: https://orcid.org/0000-0003-4702-2736
Stanishevskaya, Olga I: https://orcid.org/0000-0001-9504-3916
Terletsky, Valeriy P: https://orcid.org/0000-0003-4043-3823
Fedorova, Elena S: https://orcid.org/0000-0002-1618-6271
Nikitkina, E V: https://orcid.org/0000-0002-8496-5277
Plemyashov, Kirill V: https://orcid.org/0000-0002-3658-5886
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