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Deniskova Т.Е., Dotsev A.V., Koshkina O.A., Churbakova N.A., Yakovleva O.S., Vladimirov M.A., Solovyeva A.D., Zinovieva N.A. Genomic assessment of two local goat (Capra hircus) breeds in comparison with foreign breeds. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2025, Vol. 60, № 6, p. 1019-1032.
(how to cite this article)

doi: 10.15389/agrobiology.2025.6.1019eng

UDC: 636.39:636.082:577.21

Acknowledgements:
Funded by RSF, project number 24-46-02012, https://rscf.ru/project/24-46-02012/

 

GENOMIC ASSESSMENT OF TWO LOCAL GOAT (Capra hircus) BREEDS IN COMPARISON WITH FOREIGN BREEDS

Т.Е. Deniskova ✉, A.V. Dotsev, O.A. Koshkina, N.A. Churbakova,
O.S. Yakovleva, M.A. Vladimirov, A.D. Solovyeva, N.A. Zinovieva

Ernst Federal Research Center for Animal Husbandry, 60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia, e-mail horarka@yandex.ru (✉ corresponding author) asnd@mail.ru, olechka1808@list.ru,
nadushik95@mail.ru, olya111011@gmail.com, maksim-taranov@rambler.ru, anastastasiya93@mail.ru, n_zinovieva@mail.ru

ORCID:
Deniskova T.E. orcid.org/0000-0002-5809-1262
Yakovleva O.S. orcid.org/0009-0001-1928-6569
Dotsev A.V. orcid.org/0000-0003-3418-2511
Vladimirov M.A. orcid.org/0009-0008-9489-6173
Koshkina O.A. orcid.org/0000-0003-4830-6626
Solovyova A.D.orcid.org/0000-0003-2628-9554
Churbakova N.A. orcid.org/0009-0006-1061-2715
Zinovieva N.A. orcid.org/0000-0003-4017-6863

Final revision received September 18, 2025
Accepted October 29, 2025

The study of the genomic architecture underlying economically significant and adaptive traits of goats is important for identifying candidates for using in marker-assisted selection. In this regard, search for signatures of selection in local goat breeds in comparison with foreign breeds is very promising. In this work, for the first time we identified the genes that underlie pressure of selection in the Orenburg and Karachay breeds in a comparison with foreign breeds. We found that the Orenburg and Karachay breeds are characterized by high allelic and genetic diversity. It was established that the Orenburg and Karachay breeds formed their own independent branches within the cluster formed by down breeds that may indicate on their genetic uniqueness. The goal of this work is to assess the genetic diversity and identify candidate genes that underly pressure of selection and are associated with adaptive and economically significant traits of the Orenburg and Karachay goat breeds in comparison with foreign breeds. The study was conducted at the Ernst Federal Research Center for Animal Husbandry in 2024-2025. Samples of Orenburg and Karachay goat breeds (Capra hircus) were used as materials for this study. We used whole-genome data of Orenburg (n = 81, of which 19 were extracted from complete genomes) and Karachay (n = 34, of which 20 were extracted from complete genomes) goats. As comparison groups, we used whole-genome SNP genotypes of 15 foreign breeds (n = 550) that included dairy (Alpine, Saanen, Murciano Granadina, Nubian, Toggenburg) and meat (Barbari, Boer, Djallonke, Caninde, Chappar), down (Angora, Ankara, Cashmere, Kil, Kilis) breeds. The search for loci that underlie selection pressure was carried out by calculating pairwise FSTvalues based on the analysis of 48155 SNP. Unbiased expected (HE) and observed (HO) heterozygosity, unbiased coefficient of inbreeding (UFIS), rarefied allelic diversity (AR), pairwise fixation index (FST) values were calculated using the R package “diveRsity”. The Neighbor Net graph based on matrix of pairwise FST values was visualized in the SplitsTree 4.14.5 program. The values of genetic and allelic diversity in local breeds were comparable with those estimated in foreign ones: HO = 0.401 and 0.385 and AR = 1.971 and 1.953 in Orenburg and Karachay versus HO = 0.31-0.401 and AR = 1.902 -1.972. Based on comparative analysis of the Orenburg breed and foreign breeds we identified candidate genes that underly the pressure of selection and regulate reproduction (SPATA16, GSE1) and metabolic processes (PCSK1, HOXC8). The genes that contribute to adaptation to temperature stress (C16orf74, GSG1L, SBK1, HOXC4, HOXC6, and HOXC9) were found. Comparing the Karachay breed with foreign breeds, we identified genes that regulate reproductive functions (CCDC14, SNORA70, ROPN1, SLC8A3, E2F1, TEX14, RAD51C), growth and development (TEX14, RAD51, MYLK), immunity (IL26, IL22, and IL26) and coat color (RALY). The genes associated with immunity (C1QA, C1QC, HTR4, and HSPA8), climate adaptation (HTR4, HSPA8), growth and development (HTR4, GREB1), were shared by both local goat breeds in comparison with foreign breeds. Based on the obtained results, a more detailed study of the polymorphism of the identified genes is recommended.

Keywords: Capra hircus, local breeds, candidate genes, signatures of selection, genetic diversity. 

 

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