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

Research

Dmitry V. Anshakov¹  Vladimir I. Fisinin²  Olga A. Koshkina³  Anastasia N. Vetokh³  Natalia A. Zinovieva³  Alexandra S. Abdelmanova³  Andrey N. Rodionov³  Elena A. Gladyr³  Arsen V. Dotsev³  Natalia A. Volkova³  Igor V. Gusev³  Michael N. Romanov⁴  Olga I. Stanishevskaya⁵  Darren K. Griffin⁶ 

[1] Breeding and Genetic Centre “Zagorsk Experimental Breeding Farm” – Branch of the Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region, Russia;Federal State Budget Scientific Institution Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region, Russia;L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia;L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia;School of Biosciences, University of Kent, Canterbury, UK;Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, St. Petersburg, Russia;School of Biosciences, University of Kent, Canterbury, UK;

关键词: Acclimation;    Adaptation;    Chicken breeds;    Cold tolerance;    Divergent selection;    Genetic diversity;    Genome-wide scan;    Phenotypic traits;    Selective sweeps;   

DOI  :  10.1186/s40104-022-00813-0

 received in 2022-06-28, accepted in 2022-11-27,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsUsing 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).ConclusionBased 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.

【 授权许可】

CC BY   
© The Author(s) 2023

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