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Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity

Dementieva, Natalia V., Kudinov, Andrei A., Larkina, Tatiana A., Mitrofanova, Olga V., Dysin, Artyom P., Terletsky, Valeriy P., Tyshchenko, Valentina I., Griffin, Darren K., Romanov, Michael N. (2020) Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity. Animals, 10 (10). Article Number 1887. ISSN 2076-2615. (doi:10.3390/ani10101887) (KAR id:83858)

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Official URL
https://dx.doi.org/10.3390/ani10101887

Abstract

Simple Summary

To maintain the uniqueness of conserved chicken populations of local and imported breeds is of great importance. In this study, we genotyped small populations belonging to 14 breeds and 7 crossbreds using an Illumina Chicken 60K SNP (Single Nucleotide Polymorphisms) BeadChip and looked for appropriate methods to characterize their purity/variability. It was not straightforward to identify crossbred individuals, and the best approach was based on calculating the length and number of homozygous regions, or runs of homozygosity (ROH), in the populations studied. The latter enabled most accurate identification of crossbreds and can be served as an effective tool in testing genome-wide purity of chicken breeds.

Abstract

Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity.

Item Type: Article
DOI/Identification number: 10.3390/ani10101887
Uncontrolled keywords: chicken breeds; germplasm conservation; SNPs; runs of homozygosity; linkage disequilibrium
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 > School of Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 02 Nov 2020 14:38 UTC
Last Modified: 19 Jul 2021 18:09 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/83858 (The current URI for this page, for reference purposes)
Dementieva, Natalia V.: https://orcid.org/0000-0003-0210-9344
Kudinov, Andrei A.: https://orcid.org/0000-0002-7811-576X
Larkina, Tatiana A.: https://orcid.org/0000-0002-7764-1338
Mitrofanova, Olga V.: https://orcid.org/0000-0003-4702-2736
Dysin, Artyom P.: https://orcid.org/0000-0002-4468-0365
Terletsky, Valeriy P.: https://orcid.org/0000-0003-4043-3823
Tyshchenko, Valentina I.: https://orcid.org/0000-0003-4964-9938
Griffin, Darren K.: https://orcid.org/0000-0001-7595-3226
Romanov, Michael N.: https://orcid.org/0000-0003-3584-4644
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