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Deniskova Т.Е., Dotsev А.V., Selionova M.I. Aibazov A.-M.M., Zinovieva N.А. Search for signatures of selection in the genomes of domestic goats (Capra hircus L.) raised in Russia using detec-tion of ROH islands. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2024, Vol. 59, № 4, p. 620-632.
(how to cite this article)

doi: 10.15389/agrobiology.2024.4.620eng

UDC: 636.39:575.174

Acknowledgements:
The equipment of the Center for Biological Resources and Bioengineering of Agricultural Animals (Ernst Federal Research Center for Animal Husbandry) was used.
Funded by the Ministry of Science and Higher Education of the Russian Federation (No. FGGN-2024-0015)

 

SEARCH FOR SIGNATURES OF SELECTION IN THE GENOMES OF DOMESTIC GOATS (Capra hircus L.) RAISED IN RUSSIA USING DETECTION OF ROH ISLANDS

Т.Е. Deniskova1 ✉, А.V. Dotsev1, M.I. Selionova2, A.-M.M. Aibazov3,
N.А. Zinovieva1

1Ernst 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, n_zinovieva@mail.ru;
2Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow, 127434 Russia, e-mail: selionova@rgau-msha.ru;
3All-Russian Research Institute of Sheep and Goat Breeding — Branch of the North Caucasian Agrarian Center, 15, Stavropol, 355017 Russia, e-mail velikii-1@yandex.ru

ORCID:
Deniskova T.E. orcid.org/0000-0002-5809-1262
Aibazov A.-M.M. orcid.org/0000-0002-3704-3210
Dotsev A.V. orcid.org/0000-0003-3418-2511
Zinovieva N.A. orcid.org/0000-0003-4017-6863
Selionova M.I. orcid.org/0000-0002-9501-8080

Final revision received April 04, 2024

Accepted May 15, 2024

 

The genomes of modern populations of farm animals were shaped by long-term selection, signatures of which can be detected using bioinformatics approaches. Thus, runs of homozygosity (ROH) are used to analyze inbreeding in farm animal populations. Moreover, ROH are suitable for identifying signatures of selection through ROH islands. We have previously studied the distribution of runs of homozygosity in the genomes of goat groups bred in Russia. However, no information of signatures of selection in the genome of these goat groups is available. In this work, we performed the first search for signatures of selection in the genomes of goat breeds and populations raised in Russia. Genes within the ROH islands were identified at CHI12, CHI18, CHI25. Among the genes, we found functional candidates associated with wool (IFT88, CUX1) and milk (LATS2) productivity, regulating metabolism (LCAT, PLA2G15, SMPD3), growth (SLC12A4, SH2B2), reproductive (MRPL57, MICU2, SAP18) and immune-adaptive functions (DDX28, IL17D). The research aim is to search for the genes, which underlay selection pressure in the genomes of domestic goats bred in Russia based on identification of ROH islands. The sample of goats (Capra hircus L,) included the following breeds: Altai White Down (n = 20), Altai Mountain (n = 33), Dagestan Downy (n = 34), Dagestan Wool (n = 20), Orenburg (n = 32) and Soviet Mohair (n = 29), as well as a population of Karachaev local goats (n = 36). We conducted earlier genomic studies of Saanen breed populations raised in Russia. Therefore, in this work, SNP profiles of the Saanen breed (n = 33) were used as a comparison group. DNA was extracted from ear notches using the DNA-Extran-2 kit (NPF Sintol LLC, Russia). SNP profiles were generated using the Illumina Goat SNP50 BeadChip DNA chip (Illumina, Inc., USA) in our previous study. The work was carried out at the Ernst Federal Science Center for Animal Husbandry in 2021-2024. The individual Neighbor Net graph was constructed in SplitsTree 4.14.5. A consecutive runs method implemented in the R package “detectRUNS” was used to estimate ROH. The overlapping ROH with the minimal ROH length of 0.3 Mb shared by more than 50 % of the individuals within the group were selected as an indicator of possible ROH islands in the genome. Search for candidate genes located within ROH islands was performed using Genome Data Viewer (NCBI) according to domestic goat genome assembly CHIR_1.0 (GCF_000317765.1). The gene ontology was analyzed using the online resource DAVID (Database for Annotation, Visualization and Integrated Discovery). ROH islands were found on the twelfth chromosome (CHI12) in the Altai Mountain, Soviet Mohair, and Dagestan Downy breeds, and on the eighteenth (CHI18) and twenty-fifth chromosomes (CHI25) in the Altai Mountain and Altai White Downy breeds. Genes were identified and annotated in all ROH islands. The ROH island on CHI12 included thirteen genes, which were common for four breeds, among which the most significant were the genes LATS2 (activation of lactogenesis and potential impact on reproduction), IL17D (immune function), IFT88 (association with cashmere fiber fineness), MRPL57 (regulation of the follicular phase of the estrous cycle), MICU2 and SAP18 (ovarian and embryonic development, spermatogenesis). Sixteen genes regulating lipid metabolism (LCAT, PLA2G15, and SMPD3), involved in the response to hypoxia (DDX28), and associated with muscle fiber development (SLC12A4) were localized within the ROH island on CHI18. The genomic region at CHI25 included the genes PRKRIP, SH2B2, CUX1 and POLR2J. Among them the most promising genes were CUX1, which regulates the development of hair follicles, and SH2B2, which is associated with body size and growth. Thus, our study expands the understanding of the genomic architecture of local goat breeds and populations raised in Russia.

Keywords: SNP, ROH islands, homozygosity, candidate genes, domestic goats, selection signatures, local breeds.

 

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