Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F2 Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White

Volkova, Natalia A.; Romanov, Michael N.; Dzhagaev, Alan Yu.; Larionova, Polina V.; Volkova, Ludmila A.; Abdelmanova, Alexandra S.; Vetokh, Anastasia N.; Griffin, Darren K.; Zinovieva, Natalia A.

doi:10.3390/genes16050583

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Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F₂ Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White

by

Natalia A. Volkova

^1,†

,

Michael N. Romanov

^1,2,3,*,†

,

Alan Yu. Dzhagaev

¹

,

Polina V. Larionova

¹

,

Ludmila A. Volkova

¹,

Alexandra S. Abdelmanova

¹,

Anastasia N. Vetokh

¹

,

Darren K. Griffin

^2,3,4

and

Natalia A. Zinovieva

^1,*

¹

L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia

²

School of Natural Sciences, University of Kent, Kent, Canterbury CT2 7NJ, UK

³

Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand

⁴

Royal Veterinary School, University of London, London NW1 0TU, UK

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Genes 2025, 16(5), 583; https://doi.org/10.3390/genes16050583

Submission received: 23 April 2025 / Revised: 13 May 2025 / Accepted: 14 May 2025 / Published: 15 May 2025

(This article belongs to the Special Issue Genetic Breeding of Poultry)

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Abstract

Background/Objectives: Finding single nucleotide polymorphisms (SNPs) and candidate genes that influence the expression of key traits is essential for genomic selection and helps improve the efficiency of poultry production. Here, we aimed to conduct a genome-wide association study (GWAS) for egg production traits in an F₂ resource population of chickens (Gallus gallus). Methods: The examined F₂ population was produced by crossing two divergently selected breeds with contrasting phenotypes for egg performance traits, namely Russian White (of higher egg production) and Cornish White (of lower egg production). Sampled birds (n = 142) were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. Results: In the course of the GWAS analysis, we were able to clarify significant associations with phenotypic traits of interest and economic value by using 47,432 SNPs after the genotype dataset was filtered. At the threshold p < 1.06 × 10⁻⁶, we found 23 prioritized candidate genes (PCGs) associated with egg weight at the age of 42–52 weeks (FGF14, GCK), duration of egg laying (CNTN4), egg laying cycle (SAMD12) and egg laying interval (PHF5A, AKR1B1, CALD1, ATP7B, PIK3R4, PTK2, PRKCE, FAT1, PCM1, CC2D2A, BMS1, SEMA6D, CDH13, SLIT3, ATP10B, ISCU, LRRC75A, LETM2, ANKRD24). Moreover, two SNPs were co-localized within the FGF14 gene. Conclusions: Based on our GWAS findings, the revealed SNPs and candidate genes can be used as genetic markers for egg weight and other performance characteristics in chickens to attain genetic enhancement in production and for further genomic selection.

Keywords: chicken (Gallus gallus); genome-wide association study (GWAS); single nucleotide polymorphisms (SNPs); candidate genes; egg performance

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MDPI and ACS Style

Volkova, N.A.; Romanov, M.N.; Dzhagaev, A.Y.; Larionova, P.V.; Volkova, L.A.; Abdelmanova, A.S.; Vetokh, A.N.; Griffin, D.K.; Zinovieva, N.A. Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F₂ Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White. Genes 2025, 16, 583. https://doi.org/10.3390/genes16050583

AMA Style

Volkova NA, Romanov MN, Dzhagaev AY, Larionova PV, Volkova LA, Abdelmanova AS, Vetokh AN, Griffin DK, Zinovieva NA. Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F₂ Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White. Genes. 2025; 16(5):583. https://doi.org/10.3390/genes16050583

Chicago/Turabian Style

Volkova, Natalia A., Michael N. Romanov, Alan Yu. Dzhagaev, Polina V. Larionova, Ludmila A. Volkova, Alexandra S. Abdelmanova, Anastasia N. Vetokh, Darren K. Griffin, and Natalia A. Zinovieva. 2025. "Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F₂ Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White" Genes 16, no. 5: 583. https://doi.org/10.3390/genes16050583

APA Style

Volkova, N. A., Romanov, M. N., Dzhagaev, A. Y., Larionova, P. V., Volkova, L. A., Abdelmanova, A. S., Vetokh, A. N., Griffin, D. K., & Zinovieva, N. A. (2025). Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F₂ Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White. Genes, 16(5), 583. https://doi.org/10.3390/genes16050583

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Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F₂ Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White

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