Genome-wide association study for carcass traits in Tsarskoye Selo chicken breed



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Abstract

Background. The efficiency of modern selection programs in poultry breeding largely depends on animal genotyping. The availability of genotyping data allows to perform genome-wide association studies (GWAS), a genotype array analysis that identifies relationships between phenotypic traits and genome. Establishing local poultry breeds for meat production, a crucial protein source for human nutrition, is a significant priority within the national poultry sector. Achieving this goal requires examination of available genetic resources and identification of genomic regions responsible for manifestation of meat productivity. The aim of the present research was to perform a GWAS for carcass traits in Tsarskoye Selo chicken breed to establish the genetic determinants of meat productivity.

 Materials and methods. Tsarskoye Selo chicken breed (n=96) was used as material for the study. Genotyping data were obtained using the Illumina Chicken 60K SNP iSelectBeadChip, and GWAS analysis was performed using EMMAX with Bonferroni correction. Genome-wide significance was assessed using the simple method in R, the calculation of the effective number of independent tests was performed using the Meff program. Gene annotation was performed via ENSEMBL genome browser, using GRCg6a genome assembly.

 Results. For 8 out of 12 traits, 11 suggestive SNPs (2,31E-05) were obtained on chromosomes 1,3,11,12,15,22,23 and 27. The highest number of SNPs was detected for the thigh muscles (TM) - 3 SNPs, and for breast muscles (BM) - 2 SNPs. For the remaining traits, 1 SNP each was detected. A total of 16 genes associated with immunity (SKAP1, DCAF1, ISCU, TRAFD1), metabolism (GPATCH1, CMKLR1, TBC1D15, RAB21), osteogenesis (GPM6B, RAB9A, TRAPPC2), protein synthesis (RPL6), serotonin biosynthesis and eating behavior (TPH2), myogenesis (AGO3), morphogenesis (UNC5D), and DNA damage response (CLSPN) were identified.

Conclusion. The results obtained can be successfully used in selection programs of Tsarskoye Selo chicken breed, and can be recommended for approbation in other breeds.

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About the authors

Anastasiia I. Azovtseva

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

Author for correspondence.
Email: ase4ica15@mail.ru
ORCID iD: 0000-0002-2963-378X
SPIN-code: 5784-2786

Junior Researcher, Laboratory of Molecular Genetics

Russian Federation, Saint-Petersburg, Tyarlevo settlement, Moskovskoe shosse, 55a

Anna E. Ryabova

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

Email: aniuta.riabova2016@yandex.ru
ORCID iD: 0000-0003-2362-2892
SPIN-code: 4336-0310

Junior Researcher, Laboratory of Molecular Genetics

Russian Federation, Saint-Petersburg, Tyarlevo settlement, Moskovskoe shosse, 55a

Natalia V. Dementieva

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

Email: dementevan@mail.ru
ORCID iD: 0000-0003-0210-9344
SPIN-code: 8768-8906

Head of the Laboratory of Molecular Genetics, Leading Researcher, Cand. Biol. Sci.

Russian Federation, Saint-Petersburg, Tyarlevo settlement, Moskovskoe shosse, 55a

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