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Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

Romanov, Michael N., Abdelmanova, Alexandra S., Fisinin, Vladimir I., Gladyr, Elena A., Volkova, Natalia A., Koshkina, Olga A., Rodionov, Andrey N., Vetokh, Anastasia N., Gusev, Igor V., Anshakov, Dmitry V., and others. (2023) Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds. Journal of Animal Science and Biotechnology, 14 (1). Article Number 35. ISSN 2049-1891. (doi:10.1186/s40104-022-00813-0) (KAR id:100214)


Background: The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. Results: Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). Conclusion: Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

Item Type: Article
DOI/Identification number: 10.1186/s40104-022-00813-0
Uncontrolled keywords: Research, Acclimation, Adaptation, Chicken breeds, Cold tolerance, Divergent selection, Genetic diversity, Genome-wide scan, Phenotypic traits, Selective sweeps
Subjects: 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 > Centre for Interdisciplinary Studies of Reproduction
Divisions > Division of Natural Sciences > Biosciences
Funders: University of Kent (
SWORD Depositor: JISC Publications Router
Depositing User: Mike Romanov
Date Deposited: 24 Feb 2023 16:36 UTC
Last Modified: 08 Sep 2023 09:18 UTC
Resource URI: (The current URI for this page, for reference purposes)

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