Identification of Key Candidate Genes in Runs of Homozygosity of the Genome of Two Chicken Breeds, Associated with Cold Adaptation

• Published in: Biology (Basel, Switzerland) Switzerland), 2022-04, Vol.11 (4), p.547
• Main Authors: Fedorova, Elena S, Dementieva, Natalia V, Shcherbakov, Yuri S, Stanishevskaya, Olga I
• Format: Article
• Language: English
• Subjects: Adaptability; Adaptation; Amniotic fluid; Body temperature; candidate genes; Chromosomes; Cold; cold adaptation; Eggs; Environmental conditions; Gene pool; Genes; Genetics; Genomes; Genomic islands; Genomics; Genotyping; Heat; Insulin-like growth factor-binding protein 1; Insulin-like growth factor-binding protein 3; Lipid metabolism; Non-shivering; Physiology; Population; Poultry; respiratory quotient; runs of homozygosity; Ryanodine receptors; selection; Single-nucleotide polymorphism; SNP; Thermogenesis; Thyroid gland; Transient receptor potential proteins
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology11040547

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism ( , , , , ), maintaining body temperature in cold environments ( , , ), non-shivering thermogenesis ( , , ) and muscle development ( ) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work.