Search for traces of selection for meat productivity in Cornish chickens

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Abstract

BACKGROUND: One approach to identify the “traces” of selection is to search for extended homozygous (ROH) and heterozygous-enriched (HRR) regions in the animal genome. ROH islands are thought to result from directional selection, while HRR islands are thought to result from balanced selection.

AIM: This study aimed to perfrom a genome-wide SNP analysis of the genotype of cross-selected Cornish chickens to identify ROH and HRR islands on their chromosomes and to annotate the genes within them.

METHODS: For this study, biological materials of the Cornish Hubbard cross were obtained from the biobank of the RRIFAGB institute. The chickens were genotyped with a 60K SNP array.

RESULTS: The HRR segments were an order of magnitude shorter than the ROH segments. The data indicate the removal of monomorphic SNPs from the chicken genome, since SNPs with a 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 identified while retaining SNPs with a MAF < 0.01 are responsible for chicken weight and their feed consumption. Removal of SNPs with a MAF < 0.01 identified ROH islands containing genes associated with the regulation of intramuscular fat content and the number of eggs laid. The HRR islands that were found contain genes responsible for chicken body weight, feed intake, and embryonic development.

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 targets of balanced selection.

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About the authors

Michael G. Smaragdov

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

Email: mik7252@yandex.ru
ORCID iD: 0000-0002-5087-6444
SPIN-code: 9897-0884

Cand. Sci. (Biology)

Russian Federation, Pushkin, Saint Petersburg

Natalia V. Dementieva

Research Institute of Farm Animal Genetics and Breeding—Branch of the Academician 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

Cand. Sci. (Biology)

Russian Federation, Pushkin, Saint Petersburg

Yuri S. Shcherbakov

Research Institute of Farm Animal Genetics and Breeding—Branch of the Academician 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

Cand. Sci. (Biology)

Russian Federation, Pushkin, Saint Petersburg

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Supplementary files

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2. Fig. 1. Dependence of the total length of ROH segments on the number of ROH segments in the genome of Cornish chickens (SNPs with all MAFs were retained).

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3. Fig. 2. Dependence of the total length of ROH segments on the number of ROH segments in the genome of Cornish chickens (SNPs with MAFs < 0.01 were removed).

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4. Fig. 3. Dependence of the total length of HRR segments on the number of HRR segments in the genome of Cornish chickens (SNPs with all MAFs were retained).

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5. Fig. 4. Dependence of the total length of HRR segments on the number of HRR segments in the genome of Cornish chickens (SNPs with MAFs < 0.01 were removed).

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