Ecological geneticsEcological geneticsЭкологическая генетика1811-09322411-9202Eco-Vector69122210.17816/ecogen691222CBGPLGGenetic basis of ecosystems evolutionГенетические основы эволюции экосистемResearch ArticleSignatures of selection in the genome of Tsarskoye Selo chicken population emerging as an individual breedАнализ гомозиготных районов царскосельской популяции кур, формирующейся как индивидуальная породаhttps://orcid.org/0000-0001-6434-62873547-1009ShcherbakovYuri S.ЩербаковЮрий Сергеевич
Russian Federation

Cand. Sci. (Biology)

канд. биол. наук

yura.10.08.94.94@mail.ruhttps://orcid.org/0000-0003-3828-11117193-6004NikolaevaOlga A.НиколаеваОльга Анатольевна
Russian Federation
helgaa.nikolaeva@gmail.comhttps://orcid.org/0000-0001-5166-979X6810-7339VakhrameevAnatoly B.ВахрамеевАнатолий Борисович
Russian Federation
ab_poultry@mail.ruhttps://orcid.org/0000-0002-2963-378X5784-2786AzovtsevaAnastasiia I.АзовцеваАнастасия Ивановна
Russian Federation
ase4ica15@mail.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. Эрнста27112025090220262343393502409202519112025Copyright ©; 2025, Eco-VectorCopyright ©; 2025, Эко-Вектор2025Eco-VectorЭко-Векторhttps://creativecommons.org/licenses/by-nc-nd/4.0/https://journals.eco-vector.com/ecolgenet/article/view/691222

BACKGROUND: Tsarskoye Selo is a large population with a 30-year history, derived by crossbreeding Cornish, White Plymouth Rock, New Hampshire and Poltava Clay chicken breeds. Over the course of classical selection and the application of genetic methods, homozygous regions—Islands of runs of homozygosity (ROH islands) have formed in the genome of this population as a result of artificial selection. Through ROH analysis we can assess the inbreeding intensity within the population and to identify genes associated with traits that have been under sustained selective pressure for several decades. The current investigation provides one of the molecular genetic bases supporting the recognition of the Tsarskoye Selo as a distinct autosexing dual-purpose (meat and egg) breed. Previously, authors performed a genome wide association analysis, then assessed genotype-based divergence, and conducted an extensive evaluation of the exterior and interior profiles of Tsarskoye Selo chickens. However, homozygous regions have not been searched in this population.

AIM: This study aims to search for traces of selection and to establish the role of genes in the ROHs islands we found on productive, adaptive and aspects related to quality characteristics.

METHODS: We searched for homozygous regions using the detectRUNS R dataset of previously sequenced samples on the NovaSeq 6000 Illumina instrument and found two short homozygous regions indicative of traces of selection.

RESULTS: Analysis of detected ROH showed a gene pool related to chicken productivity, whereas other ROH included genes responsible for adaptive traits.

CONCLUSION: The formation history and the search of selection traces are demonstrate an influence of artificial selection and subsequent changes in genome of Tsarskoye Selo population, which is an example of selection achievement in the present day, and actually has evolved into an individual breed.

Обоснование. Царскосельские куры представляют собой многочисленную популяцию с 30-летней историей, происходящие от таких пород как корниш, белый плимутрок, нью гемпшир и полтавская глинистая, скрещенных между собой. За время ведения классической селекции и применения генетических методов в формировании царскосельской линии в геноме данной популяции сформировались гомозиготные районы (островки ROH) как результат искусственного отбора. Анализ гомозиготных районов позволит оценить степень инбридинга в популяции и идентифицировать гены, связанные с признаками, которые несколько десятилетий находились под селекционным давлением. Данное исследование является одним из молекулярно-генетических обоснований для признания царскосельской популяции кур индивидуальной аутосексной породой мясо-яичного направления. Ранее авторы выполняли полногеномный поиск ассоциаций, оценивали дивергенцию на основе генотипов и проводили обширную оценку экстерьерного и интерьерного профилей царскосельской породы кур. Однако поиск гомозиготных районов в этой популяции не проводился.

Цель исследования. Поиск следов селекции и установление роли генов в обнаруженных ROH островков по продуктивным, адаптивным и аспектам, связанным с качественными характеристиками.

Методы. Поиск гомозиготных районов проведен с помощью R-пакета данных detectRUNS ранее секвенированных образцов на приборе NovaSeq 6000 Illumina, обнаружены два коротких гомозиготных района, свидетельствующих о следах селекции.

Результаты. Анализ выявленных ROH показал пул генов, связанных с продуктивностью кур, другой ROH содержал гены, ответственные за адаптивные свойства.

Заключение. История селекции кур царскосельской породы и поиск следов селекции в данном исследовании демонстрируют влияние искусственного отбора на геном этой популяции, которая на сегодняшний день является примером селекционного достижения и фактически сформирована в отдельную породу.

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