Signatures of selection in the genome of Tsarskoye Selo chicken population emerging as an individual breed



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Abstract

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

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About the authors

Yuri Sergeevich Shcherbakov

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

Email: yura.10.08.94.94@mail.ru
ORCID iD: 0000-0001-6434-6287
SPIN-code: 3547-1009
Scopus Author ID: 57221619264
ResearcherId: AAR-5595-2020

PhD in Biology

Researcher 

Laboratory of molecular genetics

Russian Federation, 196601, St. Petersburg, Pushkin, Moskovskoe shosse, 55a

Olga Anatolevna Nikolaeva

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

Author for correspondence.
Email: helgaa.nikolaeva@gmail.com
ORCID iD: 0000-0003-3828-1111
SPIN-code: 7193-6004
Scopus Author ID: 57941963300
ResearcherId: GPK-6027-2022

Junior Researcher 

Laboratory of molecular genetics

Russian Federation, 196601, St. Petersburg, Pushkin, Moskovskoe shosse, 55a

Anatoly Borisovich Vakhrameev

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

Email: ab_poultry@mail.ru
ORCID iD: 0000-0001-5166-979X
SPIN-code: 6810-7339
Scopus Author ID: 56862214400
ResearcherId: AAD-1068-2022

Senior Researcher

laboratory for scientific support of the conservation of poultry genetic resources

 

Russian Federation, 196601, St. Petersburg, Pushkin, Moskovskoe shosse, 55

Anastasia Ivanovna Azovtseva

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

Email: ase4ica15@mail.ru
ORCID iD: 0000-0002-2963-378X
SPIN-code: 5784-2786
Scopus Author ID: 57942391700
ResearcherId: MSZ-1418-2025

Junior Researcher 

Laboratory of molecular genetics

Russian Federation, 196601, St. Petersburg, Pushkin, Moskovskoe shosse, 55a

Natalia Victorovna Dementieva

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

Email: dementevan@mail.ru
ORCID iD: 0000-0003-0210-9344
SPIN-code: 8768-8906
Scopus Author ID: 57189759592
ResearcherId: T-4551-2018

PhD in Biology

Chief Researcher 

Laboratory of Molecular Genetics

196601, St. Petersburg, Pushkin, Moskovskoe shosse, 55a

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