Abstract

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)FSTbased 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.,TPOandBDNF).

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 thesine qua nonfor 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.

Data Availability

All data generated or analysed during the present study are available from the corresponding author on reasonable request. The datasets supporting the conclusions of this article are included in the main manuscript and supplemental materials.

Abbreviations

  • A R :: Rarefied allelic richness
  • bp:: Base pair
  • FRCARPRTI:: Federal Research Centre “All-Russian Poultry Research and Technological Institute”
  • F ROH :: Genomic inbreeding coefficient inferred from mean ROH lengths
  • F ST :: Fixation index, a measure of genetic differentiation
  • Gb:: Gigabases
  • GGA:: Gallus gallus, Latin name for chicken used to designate chicken chromosomes
  • GRCg6a:: Genome Reference Consortium build 6a for Gallus gallus (chicken)
  • h:: Hour
  • H O :: Observed heterozygosity
  • K:: Number of clusters (ancestral populations)
  • kb:: Kilobases
  • LKEFRCAH:: L. K. Ernst Federal Research Centre for Animal Husbandry
  • M:: Mean value
  • Mb:: Megabases
  • MD:: Marek’s disease
  • OMF:: Orloff Mille Fleur
  • PC:: Principal component
  • PCA:: Principal component analysis
  • PCG:: Prioritized candidate gene
  • PSG:: Positively selected gene
  • QTL:: Quantitative trait locus
  • ROH:: Run of homozygosity
  • RRIFAGB:: Russian Research Institute of Farm Animal Genetics and Breeding
  • RUW:: Russian White
  • SE:: Standard error
  • SNP:: Single nucleotide polymorphism
  • T3 :: Triiodothyronine
  • U F IS :: UHE-based inbreeding coefficient
  • U H E :: Unbiased expected heterozygosity
  • USH:: Ushanka
  • WCR:: White Cornish

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Acknowledgements

The skilled technical assistance of Mrs. Olga M. Romanova in preparing chicken images (Fig. 1 ) is kindly appreciated.

Funding

Genotyping and data analyses were supported by the Russian Science Foundation within the Project No. 21-66-00007. Collecting the samples was performed with the support of the Russian Ministry of Science and Higher Education.

Ethics Declaration

Ethics approval and consent to participate

The study was performed following the LKEFRCAH ethical guidelines (Protocol No. 3/1 approved by the LKEFRCAH Commission on the Ethics of Animal Experiments on 4 December 2019) that comply with relevant international guidelines (Directive 2010/63/EU in Europe). To minimize any possible distress and discomfort to the birds, feather samples were collected from chickens by specially trained lab personnel.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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