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, NA; Romanov, MN; Dzhagaev, AY; Larionova, PV; Volkova, LA; Abdelmanova, AS; Vetokh, AN; Griffin, DK; Zinovieva, NA

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 F-2 resource population of chickens (Gallus gallus). Methods: The examined F-2 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 x 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.

Citation

Volkova, N., Romanov, M., Dzhagaev, A., Larionova, P., Volkova, L., Abdelmanova, A., Vetokh, A., Griffin, D., & Zinovieva, N. (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), https://doi.org/10.3390/genes16050583

• Journal Article Type: Article
• Acceptance Date: May 14, 2025
• Online Publication Date: May 15, 2025
• Publication Date: 2025
• Deposit Date: Jun 19, 2025
• Publicly Available Date: Jun 19, 2025
• Print ISSN: 2073-4425
• Electronic ISSN: 2073-4425
• Publisher: MDPI
• Peer Reviewed: Peer Reviewed
• Volume: 16
• Issue: 5
• DOI: https://doi.org/10.3390/genes16050583
• Keywords: chicken (Gallus gallus); genome-wide association study (GWAS); single nucleotide polymorphisms (SNPs); candidate genes; egg performance; GALLUS-GALLUS; 1ST EGG; REPRODUCTIVE TRAITS; FOOD-INTAKE; AGE; QUALITY; GLUCOKINASE; PERFORMANCE; TRANSCRIPTS; LIVESTOCK