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Vetokh A.N., Volkova N.A., Larionova P.V., Abdelmanova A.S., Volkova L.A., Zinovieva N.A. Genome-wide associations of meat productivity traits in cockerels based on whole genome sequencing data. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2025, Vol. 60, № 6, p. 1044-1054.
(how to cite this article)

doi: 10.15389/agrobiology.2025.6.1044eng

UDC: 636.52/.58:577.2

Acknowledgements:
Supported by the Ministry of Science and Higher Education of the Russian Federation within theme № FGGN-2023-0002

 

GENOME-WIDE ASSOCIATIONS OF MEAT PRODUCTIVITY TRAITS IN COCKERELS BASED ON WHOLE GENOME SEQUENCING DATA

A.N. Vetokh✉, N.A. Volkova, P.V. Larionova, A.S. Abdelmanova, L.A. Volkova, N.A. Zinovieva

Ernst Federal Research Center for Animal Husbandry, 60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia, e-mail anastezuya@mail.ru (✉ corresponding author) natavolkova@inbox.ru, volpolina@mail.ru, abdelmanova@vij.ru, ludavolkova@inbox.ru, zinovieva@mail.ru

ORCID:
Vetokh A.N. orcid.org/0000-0002-2865-5960
Abdelmanova A.S. orcid.org/0000-0003-4752-0727
Volkova N.A. orcid.org/0000-0001-7191-3550
Volkova L.A. orcid.org/0000-0002-9407-3686
Larionova P.V. orcid.org/0000-0001-5047-1888
Zinovieva N.A. orcid.org/0000-0003-4017-6863

Final revision received August 28, 2025
Accepted October 13, 2025

The search and identification of genetic markers associated with formation of promising phenotypes and the assessment of productive potential form the basis for marker-assisted and genomic selection in poultry breeding. This includes efforts aimed at creating and improving high-yielding meat breeds and crosses of chickens. In this study the first identification of novel significant SNPs and candidate genes linked to productivity traits in meat-type cockerels. The detected SNPs can be further investigated as genetic markers to enhance meat productivity in meat-type chicken breeds and crosses through breeding. The aim of this study was to identify single nucleotide polymorphisms (SNPs), and candidate genes associated with growth intensity, slaughter yield, and the weight parameters of the carcass and its individual parts in cockerels. The research was carried out in 2023-2025 at the L.K. Ernst Federal Research Center for Animal Husbandry. The study subjects were F2 generation cockerels from a resource chicken population (Gallus gallus), created by crossing two breeds contrasting in growth intensity: the White Cornish meat breed, characterized by a high growth rate and used to produce high-performance meat crosses, and the Russian White breed of egg-laying direction (paternal line), distinguished by a moderate growth rate. The F2 generation chicks were reared in several stages under different housing systems: brooding and floor rearing. For the genome-wide association study (GWAS), 40 cockerels with high (n = 20) and low (n = 20) live body weight at 63 days of age were selected from the general F2 population. These individuals were characterized by growth and meat productivity indicators: live body weight, average daily gain, slaughter yield, carcass weight, and weights of breast, thigh, drumstick, and wings. For DNA extraction and subsequent identification of SNPs and genes associated with growth traits, feather pulp samples were collected. Genomic DNA was extracted using the DNA-Extran-2 kit (LLC "Syntol", Moscow, Russia). Genotyping of the resource population chickens was performed using whole-genome sequencing. A GWAS was performed using PLINK 1.9 software (https://www.cog-genomics.org/plink/) to identify statistically significant associations between SNPs and the studied growth and meat productivity traits. Gene annotation for the identified SNPs was conducted using the resource https://www.ncbi.nlm.nih.gov/datasets/genome/. The analysis revealed 59 significant SNPs, and 12 genes located at these SNP positions, including 51 SNPs and 10 genes associated with live body weight and average daily gain, and 13 SNPs and 4 genes linked to weight parameters of the carcass and its parts in the studied cockerel population. The identified SNPs and genes were localized to 5 out of the 28 assessed chromosomes: GGA2 (1 SNP, 1 gene), GGA4 (55 SNPs, 8 genes), GGA6 (2 SNPs, 2 genes), GGA9 (19 SNPs, 1 gene), and GGA23 (2 SNPs). Furthermore, 12 SNPs (rs16451696, rs734169095, rs734922454, rs739717793, rs733453394, rs317394303, rs733563521, rs312391845, rs314257889, rs318214875, rs312310372, rs318006749) were common to the group of studied traits, and 5 genes (ATRN, CTN2, DAF9, GFRA4, DLG1) were identified in the regions containing from 2 to 7 of the significant SNPs. The maximum number of significant associations with the studied traits (n = 5) was found for SNP rs318006749, located in the DLG1 gene. Analysis of allelic variants of the DLG1 gene at this locus revealed a significant association (p < 0.001) of the CC genotype with high live body weight, average daily gain, and weights of carcass, breast, thigh, drumstick, and wings in the studied cockerel population. These results can be valuable for marker-assisted and genomic selection programs in meat-type chicken breeds and crosses, aimed at enhancing growth rate and improving meat productivity traits.

Keywords: Gallus gallus, GWAS, SNP, candidate genes, meat productivity traits.

 

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