Search for traces of selection for meat productivity in Cornish chicken



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Abstract

BACKGROUND: One of the approaches to identify the “traces” of selection is the search for extended homozygous (ROH) and heterozygous enriched (HRR) regions in the genome of animals. ROH islands are thought to be the result of directional selection, while HRR islands are thought to be the result of balanced selection.AIM: The aim of this study was a genome-wide SNP analysis of the genotype of cross-selected Cornish chicken to identify ROH and HRR islands in the chromosomes of Cornish chicken and annotate the genes within them. MATERIALS AND METHODS: For the purposes of this study, biological materials of Cornish HABBARD cross was obtained from biobank of RRIFAGB institute. The chickens were genotyped with the 60K SNP array.

RESULTS: The HRR segments were an order of magnitude shorter than the ROH segments. Data indicate the removal of monomorphic SNPs from the chicken genome whereas SNPs with minor allele frequency MAF < 0.01 were removed. The localization of the ROH islands was completely altered by the removal of SNPs with a MAF < 0.01, whereas the localization of the HRR islands was only partially altered. Genes in the ROH islands are responsible for the weight of the chickens and their feed consumption while retaining SNPs with a MAF < 0.01. Removal of SNPs with a MAF < 0.01 identified ROH islands containing genes associated with the regulation of intramuscular fat content and number of eggs laid. TheHRRislandsfoundcontaingenesresponsibleforchickenbodyweight,feedintake, andembryonicdevelopment.

CONCLUSIONS: Genes located in ROH islands are responsible for the consumer traits of the Cornish meat breed bred by directional selection, while genes located in HRR islands are most likely not the target of balanced selection.

Key words: single nucleotide polymorphism; runs of homozygosity; heterozygosity rich regions; chickens

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About the authors

Natalia V. Dementieva

Russian Research Institute of Farm Animal Genetics and Breeding — Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Author for correspondence.
Email: dementevan@mail.ru
ORCID iD: 0000-0003-0210-9344
SPIN-code: 8768-8906
Scopus Author ID: 57189759592

Cand. Sci. (Biol.), leading research associate

Russian Federation, St. Petersburg, Tyarlevo settlement, Moskovskoe shosse, 55a

Michael G. Smaragdov

Russian Research Institute of Farm Animal Genetics and Breeding — Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Email: mik7252@yandex.ru
ORCID iD: 0000-0002-5087-6444
Scopus Author ID: 6505918771

Кандидат биологических наук, специалист лаборатории молекулярной генетики

Russian Federation, St. Petersburg, Tyarlevo settlement, Moskovskoe shosse, 55a

Yuri S. Shcherbakov

Russian Research Institute of Farm Animal Genetics and Breeding — Branch of the L.K. Ernst Federal Research Center for Animal Husbandry

Email: yura.10.08.94.94@mail.ru
ORCID iD: 0000-0001-6434-6287
SPIN-code: 3547-1009
Scopus Author ID: 57221619264

Candidate of Biological Sciences, Junior Researcher

Russian Federation, St. Petersburg, Tyarlevo settlement, Moskovskoe shosse, 55a

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