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Koshkina O.A., Deniskova Т.Е., Romanov M.N., Zinovieva N.А. Genomic studies in domestic goats (Capra hircus L.): current advances and prospects (review). Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2024, Vol. 59, № 4, p. 587-604.
(how to cite this article)

doi: 10.15389/agrobiology.2024.4.587eng

UDC: 636.38:636.082:577.21

Acknowledgements:
Funded by the Russian Science Foundation, grant No. 24-46-02012, https://rscf.ru/project/24-46-02012/.

 

GENOMIC STUDIES IN DOMESTIC GOATS (Capra hircus L.): CURRENT ADVANCES AND PROSPECTS (review)

O.A. Koshkina1, Т.Е. Deniskova1, 2 ✉, M.N. Romanov1, 3, 4,
N.А. Zinovieva1

1Ernst Federal Research Center for Animal Husbandry,60, pos. Dubrovitsy, Podolsk District, Moscow Province, 142132 Russia, e-mail olechka1808@list.ru, horarka@yandex.ru (✉ corresponding author), m.romanov@kent.ac.uk, n_zinovieva@mail.ru;
2Basic Department of Genetic Technologies in livestock Farming, Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23, ul. Akademika Skryabina, Moscow, 109472 Russia;
3School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NZ, UK;
4Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

ORCID:
Koshkina O.A. orcid.org/0000-0003-4830-6626
Romanov M.N. orcid.org/0000-0003-3584-4644
Deniskova T.E. orcid.org/0000-0002-5809-1262
Zinovieva N.A. orcid.org/0000-0003-4017-6863

Final revision received October 5, 2023  
Accepted November 3, 2023

 

The domestic goat (Capra hircus) is a versatile small ruminant species spread on all continents, whose genomic features are becoming the subject of study by research teams from all over the world (A.M.A.M. Zonaed Siddiki et al., 2020; M.I. Selionova et al., 2021). The goal of this review is to elucidate the results of recent genomic studies on domestic goats using DNA chips and whole genome sequencing (WGS) analysis, and to compile a list of WGS-identified candidate genes associated with economically significant and adaption traits. This review summarizes and analyzes the results of WGS studies from 2020 to 2024. A list of candidate genes identified using WGS and associated with economically important and adaptive traits in goats is presented. An analysis of the methodological and bioinformatic approaches used to study WGS of domestic goats is executed. Using DNA chips, genetic relationships between different goat breeds and populations were established (T.E. Deniskova et al., 2021; V. Mukhina et al., 2022; A. Manunza et al., 2023), their genetic diversity was assessed (B.A. Vlaic et al., 2024; G. Chessari et al., 2024), and introgression from wild species of the genus Capra was studied (H. Asadollahpour Nanaei et al., 2023; N. Pogorevc et al., 2024). The decline in the WGS costs (B. Gu et al., 2022) has boosted an increase in the number of WGSs generated in goats (S. Belay et al., 2024). Genes under convergent selection pressure in sheep and goats have been identified, including DGKB, FAM155A, GRM5 (J. Yang et al., 2024) and CHST11 (L. Tao et al., 2021). An increase in the copy number of the GBP1 gene has been shown to be associated with immune resistance and prolificacy (R.Q. Zhang et al., 2019; R. Di Gerlando et al., 2020; M. Arslan, 2023). A large group of genes has been identified that affect milk productivity — ANPEP (J. Ni et al., 2024), ERBB4 (Z. Liu et al., 2024), NCAM2 (Z. Amiri Ghanatsaman et al., 2023) and GLYCAM1 (J. Xiong et al., 2023; H.B. Gebreselase et al., 2024), carcass quality — ACOX1, PGM1 (Z.X. An et al., 2024), ZNF385B and MYOT (H.B. Gebreselase et al., 2024), growth — HMGA2 and GJA3 (C. Li et al., 2024), live weight — STIM1 and ADM (R. Saif et al., 2021), and wool performance — CCNA2 (Y. Rong et al., 2024) and FGF5 (Q. Zhao et al., 2024). The TSHR and STC1 genes associated with domestication were discovered in Swiss breeds (H. Signer-Hasler et al., 2022). Genes involved in the formation of protective responses of the body to diseases and unfavorable climatic factors have been identified, including PIGR, TNFAIP2 (Q. Chen et al., 2021, 2022), KHDRBS2 (X. Sun et al., 2022), PPP2R3C (R. HuangFu et al., 2024), GNG2 (Z.X. An et al., 2024), HOXC12 and MAPK8IP2 (O. Sheriff et al., 2024). Genome-wide association studies (GWAS) based on WGS identified candidate genes associated with body size, including FNTB, CHURC1 (R. Yang et al., 2024), PSTPIP2 and SIPA1L (B. Gu et al., 2022), and milk production (H. Wu et al., 2023). To date, candidate genes have been identified on 21 of the 29 autosomes, with the largest number on CHI5 (9 genes), CHI18 (8 genes), CHI1, CHI3, CHI57 and CHI23 (7 genes on each chromosome). Thus, the compiled list of target candidate genes may be used in marker-assisted selection programs.

Keywords: Capra hircus, SNPs, DNA chips, whole genome sequences, candidate genes, GWAS, signatures of selection, copy number variation (CNV).

 

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