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Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations

Dementieva, Natalia V., Mitrofanova, Olga V., Dysin, Artyom P., Kudinov, Andrei A., Stanishevskaya, Olga I., Larkina, Tatiana A., Plemyashov, Kirill V., Griffin, Darren K., Romanov, Michael N., Smaragdov, M.G. and others. (2021) Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations. Animal, 15 (3). Article Number 100171. ISSN 1751-7311. E-ISSN 1751-732X. (doi:10.1016/j.animal.2021.100171) (KAR id:89167)

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https://doi.org/10.1016/j.animal.2021.100171

Abstract

Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60 K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (FST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD < 0.5 and LD < 0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the RussianWhite RG population, pruningwas substantial for Dataset I, and FST valueswere only positivewhen LD< 0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the RussianWhite RG populationwith the smallest r2 values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates.

Item Type: Article
DOI/Identification number: 10.1016/j.animal.2021.100171
Uncontrolled keywords: Single nucleotide polymorphisms; Fixation index; Heterozygosity; Linkage disequilibrium pruning; Poultry
Subjects: Q Science > QH Natural history > QH324.2 Computational biology
Q Science > QH Natural history > QH426 Genetics
Q Science > QH Natural history > QH75 Conservation (Biology)
S Agriculture > SF Animal culture
Divisions: Divisions > Division of Natural Sciences > Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 12 Jul 2021 05:43 UTC
Last Modified: 24 Sep 2021 14:13 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/89167 (The current URI for this page, for reference purposes)
Dementieva, Natalia V.: https://orcid.org/0000-0003-0210-9344
Mitrofanova, Olga V.: https://orcid.org/0000-0003-4702-2736
Dysin, Artyom P.: https://orcid.org/0000-0002-4468-0365
Kudinov, Andrei A.: https://orcid.org/0000-0002-7811-576X
Stanishevskaya, Olga I.: https://orcid.org/0000-0001-9504-3916
Larkina, Tatiana A.: https://orcid.org/0000-0002-7764-1338
Plemyashov, Kirill V.: https://orcid.org/0000-0002-3658-5886
Griffin, Darren K.: https://orcid.org/0000-0001-7595-3226
Romanov, Michael N.: https://orcid.org/0000-0003-3584-4644
Smaragdov, M.G.: https://orcid.org/0000-0002-5087-6444
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