Ecological geneticsEcological geneticsЭкологическая генетика1811-09322411-9202Eco-Vector68541610.17816/ecogen685416JYOJBSGenetic basis of ecosystems evolutionГенетические основы эволюции экосистемResearch ArticleGenome-wide association study for carcass traits in Tsarskoye Selo chicken breedПолногеномный поиск ассоциаций с показателями тушки у царскосельской породы курhttps://orcid.org/0000-0002-2963-378X5784-2786AzovtsevaAnastasiia I.АзовцеваАнастасия Ивановна
Russian Federation
ase4ica15@mail.ruhttps://orcid.org/0000-0003-2362-28924336-0310RyabovaAnna E.РябоваАнна Евгеньевна
Russian Federation

Cand. Sci. (Biology)

канд. биол. наук

aniuta.riabova2016@yandex.ruhttps://orcid.org/0000-0003-0210-93448768-8906DementievaNatalia V.ДементьеваНаталия Викторовна
Russian Federation

Cand. Sci. (Biology)

канд. биол. наук

dementevan@mail.ruRussian Research Institute of Farm Animal Genetics and Breeding—Branch of the Academician L.K. Ernst Federal Research Center for Animal HusbandryВсероссийский научно-исследовательский институт генетики и разведения сельскохозяйственных животных — филиал Федерального исследовательского центра животноводства — ВИЖ им. акад. Л.К. Эрнста16102025090220262343293382006202515102025Copyright ©; 2025, Eco-VectorCopyright ©; 2025, Эко-Вектор2025Eco-VectorЭко-Векторhttps://eco-vector.com/for_authors.php#07https://journals.eco-vector.com/ecolgenet/article/view/685416

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.

AIM: the present research aimed to perform a GWAS for carcass traits in Tsarskoye Selo chicken breed to establish the genetic determinants of meat productivity.

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 (Illumina Inc., USA), and GWAS 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 obtained results can be successfully used in selection programs of Tsarskoye Selo chicken breed, and can be recommended for approbation in other breeds.

Обоснование. Эффективность современных селекционных программ в птицеводстве во многом зависит от генотипирования животных. На основании данных генотипирования можно проводить полногеномный поиск ассоциаций (GWAS) — анализ массива генотипов, который выявляет взаимосвязь между фенотипическими признаками и геномом. В отечественном птицеводстве актуальной задачей остается развитие локальной племенной базы для производства мяса птицы — важного источника белка в питании человека. Для достижения этой цели необходимо генотипировать имеющиеся генетические ресурсы и установить регионы в геноме, ответственные за проявление мясной продуктивности.

Цель исследования. Проведение полногеномного поиска ассоциаций с показателями тушки у царскосельской породы кур для установления генетических детерминант мясной продуктивности.

Методы. Материалом для исследования стала царскосельская порода кур (96 голов). Данные генотипирования получены при помощи чипа Illumina Chicken 60K SNP iSelectBeadChip (Illumina Inc., США), а GWAS — при помощи EMMAX с применением поправки Бонферрони. Общегеномная значимость оценена при помощи метода simple в R, расчет эффективного числа независимых тестов — с помощью программы Meff. Для аннотирования генов использовали геномный браузер ENSEMBL, сборка генома GRCg6a.

Результаты. Для 8 из 12 признаков получено 11 предположительно значимых SNP (2,31E-05) на хромосомах 1,3,11,12,15,22,23 и 27. Наибольшее число SNP обнаружено для показателя массы мышц бедра (МБ) — 3 SNP, а также для массы мышц груди (МГр) — 2 SNP. Для оставшихся показателей получено по 1 SNP. Всего идентифицировано 16 генов, ассоциированных с иммунитетом (SKAP1, DCAF1, ISCU, TRAFD1), метаболизмом (GPATCH1, CMKLR1, TBC1D15, RAB21), остеогенезом (GPM6B, RAB9A, TRAPPC2), синтезом белка (RPL6), биосинтезом серотонина и пищевым поведением (TPH2), миогенезом (AGO3), морфогенезом (UNC5D) и реакцией на повреждение ДНК (CLSPN).

Заключение. Полученные результаты могут быть использованы в селекции царскосельской породы и рекомендованы к апробации в других породах кур.

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