Deniskova TE, Abdelmanova AS, Koshkina OA, Dotsev AV, Zinovieva NA.

Animal Husbandry and Fodder Production. 2026. Vol. 109. No. 3. Р. 95-112.

doi: 10.33284/2658-3135-109-3-95

Original article

A study of the genomic characteristics of goats of the Altai Mountain and Soviet Mоhair breeds based on differentiating SNPs

 

Tatyana E Deniskova1, Alexandra S Abdelmanova2, Olga A Koshkina3, Arsen V Dotsev4,

Natalia A Zinovieva5

1,2,3,4,5Federal Research Center for Animal Husbandry named after Academy Member LK Ernst, Dubrovitsy, Russia

1horarka@yandex.ru, https://orcid.org/0000-0002-5809-1262

2abdelmanova@vij.ru, https://orcid.org/0000-0003-4752-0727

3olechka1808@list.ru, https://orcid.org/0000-0003-4830-6626

4asnd@mail.ru, https://orcid.org/0000-0003-3418-2511

5n_zinovieva@mail.ru, https://orcid.org/0000-0003-4017-6863

Abstract. This study aimed to identify the most differentiating single-nucleotide polymorphisms (SNPs) in the Altai Mountain and Soviet Mohair goat breeds. For this purpose, whole-genome sequencing was performed with an average coverage depth of 20×. A comparative analysis of the genomes of the two goat breeds was conducted in two stages. In the first stage, regions with the highest mean FST value in each window were identified using a sliding FST window. Next, SNPs with the highest FST values were selected within these regions. Allele and genotype frequencies were calculated at the identified loci for each breed. Fixed SNPs were identified: two (6_13558772 and 19_2003492) in the Altai Mountain breed and one (21_55792542) in the Soviet Mohair breed. Comparative analysis revealed both known candidates and genes that were poorly studied or previously uncharacterized in goats (AP1AR, FICD, and TRPC4AP). Among the candidates we found genes, which were associated with milk production and lipid metabolism (ACSS2, TOM1L2), immunity (ALPK1, TIFA, and CCDC88C), reproductive functions (ALKBH5, MAD1L1, and DRC3), growth and development (MYH7B), and stress resistance (ATPAF2). Additionally, we identified 14 SNPs that significantly differed between the studied goat breeds. Our results pave the way for further studies of the genetic mechanisms underlying adaptation and economically important traits in goat breeds raised in Russia.

Keywords: domestic goats, SNPs, whole genome sequencing data, candidate genes, signatures of selection, genotypes

Acknowledgments: the work was supported by the Russian Science Foundation, Project      No. 24-46-02012.

For citation: Deniskova TE, Abdelmanova AS, Koshkina OA, Dotsev AV, Zinovieva NA. A study of the genomic characteristics of goats of the Altai Mountain and Soviet Mohair breeds based on differentiating SNPs. Animal Husbandry and Fodder Production. 2026;109(3):95-112. (In Russ.)].           https://doi.org/10.33284/2658-3135-109-3-95

References

  1. Kargachakova TB, Chikalev AI, Yuldashbaev YuA, Demin VA. Biological and some economic features of Mountain Altai downy goats. Sheep, goats, wool business. 2024;3:21- doi: 10.26897/2074-0840-2024-3-21-24
  2. Beketov SV, Piskunov AK, Voronkova VN, Petrov SN, Kharzinova VR, Dotsev AV, Zinovieva NA, Selionova MI, Stolpovsky YuA. Genetic diversity and philogeny of fleece-bearing goats of Central and Middle Asia. Russian Journal of Genetics. 2021;57(7):810-819. doi: 10.31857/S0016675821070031
  3. Deniskova TE, Abdelmanova AS. Identification of selective sweeps in the Romanov sheep breed based on haplotype analysis. Animal Husbandry and Fodder Production. 2026;109(1):99-111. doi: 10.33284/2658-3135-109-1-99
  4. Mongush BM, Ondar GK. Assessment of the exterior and seasonal dynamics of the live weight of Soviet Mohair goats bred in the conditions of the ESPC "Zhivotnovod" TuvSU (Conference proceedings) Tuva State University: 30 years on the way to sustainable development of the region through science, education and culture: materials of the International Scientific and practical conference, (Kyzyl, October 30, 2025). Kyzyl: TuvSU Publishing House. 2025:251-255.
  5. Novopashina SI, Sannikov MYu. Conservation of the Pridonskaya Down goat breed. Collected Scientific Papers of the Stavropol Research Institute of Animal Husbandry and Fodder 2007;1(1-1):121-123.
  6. Nogayev AA, Serekpayev NA. Goat breeding – the state and prospects of development in the Republic of Kazakhstan and the Akmola region. Herald of Science of S. Seifullin Kazakh Agrotechnical University. 2022;2-2(113):22-35. doi: 10.51452/kazatu.2022.2(113).1066
  7. Petrov SN, Deniskova TE, Dotsev AV. The use of STR markers for the genetic assessment of representatives of the genus Capra. Achievements of Science and Technology in Agro-Industrial Complex. 2023;37(9):74-79. doi: 10.53859/02352451_2023_37_9_74
  8. Deniskova TE, Dotsev AV, Selionova MI, Aibazov A-MM, Zinovieva NA. Search for signatures of selection in the genomes of domestic goats (Capra hircus L.) raised in Russia using detection of ROH    Sel'skokhozyaistvennaya  Biologiya  [Agricultural  Biology].   2024;59(4):620-632. doi: 10.15389/agrobiology.2024.4.620rus  doi: 10.15389/agrobiology.2024.4.620eng
  9. Petrov SN, Deniskova TE, Bakoev NF, Koshkina OA. Polymorphisms in the prion protein gene (PRNP) in some goat populations of Russia. Achievements of Science and Technology in Agro-Industrial Complex. 2025;39(3):61-66. doi: 10.53859/02352451_2025_39_3_61
  10. Goncharenko GM, Kargachakova TB, Grishina NB, Khoroshilova TS, Khalina OL. Down productivity and genotypic characteristics of BLG gene polymorphism and blood groups of goats in Gorny Altai. Vestnik University of Biotechnology. 2020;3:94- doi: 10.31677/2072-6724-2020-56-3-94-101
  11. Shaikenova KH, Assanbayev TSh, Sadenova MK, Ibrayev DK, Nazarova LM, Aisar ME. Results of the study of growth and development of Mountain Altai downy breed goats bred in the north-east of Kazakhstan. Herald of science of S.Seifullin Kazakh agrotechnical university: Multidisciplinary. 2025;(2):75-83. doi: 10.51452/kazatu.2025.2(125).1884
  12. Sambu-Hoo ChS, Makarova EYu. Tuvinian population soviet woolly breed goats' woolly productivity increase. Bulletin of KSAU. 2021;7(172):108-113. doi: 10.36718/1819-4036-2021-7-108-113
  13. Sandak-Huurak OO, Sat ChM. Wool productivity of crossbred Soviet Mohair breed of goats with coarse and semi-coarse wool in the Republic of Tuva. Sheep, Goats, Wool Business. 2020;1:27-28.
  14. An HJ, Cho SH, Ryu CS, Ko EJ, Park HW, Kim YR, et al. Genetic associations of miRNA variants (miR-10a, miR-30c, miR-181a, miR-499b) with primary ovarian insufficiency in Korean women. Maturitas. 2025;191:108153. doi: 10.1016/j.maturitas.2024.108153
  15. Boon H, Sjögren RJO, Massart J, Egan B, Kostovski E, Iversen PO, et al. MicroRNA-208b progressively declines after spinal cord injury in humans and is inversely related to myostatin expression. Physiol Rep. 2015;3(11):e12622. doi:10.14814/phy2.12622
  16. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi: 10.1093/gigascience/giab008
  17. Dang D, Zhang L, Gao L, Peng L, Chen J, Yang L. Analysis of genomic copy number variations through whole-genome scan in Yunling cattle. Front Vet Sci. 2024;11:1413504. doi: 3389/fvets.2024.1413504
  18. Deniskova TE, Dotsev AV., Selionova MI, Reyer H, Sölkner J, Fornara MS, et al. SNP-based genotyping provides insight into the West Asian origin of Russian local goats. Frontiers in Genetics. 2021;12:708740. doi: 10.3389/fgene.2021.708740
  19. DiTommaso T, Jones LK, Cottle DL, WTSI Mouse Genetics Program, Gerdin AK, Vancollie VE, Watt FM, et al. Identification of  genes important for cutaneous function revealed by  a  large  scale  reverse  genetic  screen  in  the    PLoS Genet. 2014;10(10):e1004705. doi: 10.1371/journal.pgen.1004705
  20. Fang L, Cai W, Liu S, Canela-Xandri O, Gao Y, Jiang J, et al. Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle. Genome Res. 2020;30(5):790-801. doi: 10.1101/gr.250704.119
  21. Freebern E, Santos DJA, Fang L, Jiang J, Parker Gaddis KL, Liu GE, et al. GWAS and fine-mapping of  livability  and  six  disease  traits  in  Holstein  BMC Genomics. 2020;21(1):41. doi: 10.1186/s12864-020-6461-z
  22. Gao J, Sun L, Liao R, Lyu Y, Zhang S, Xu J, et al. Genomic dissection of Chinese Yangtze River  Delta  white  goat  based  on  whole  genome sequencing. Animals (Basel). 2025;15(7):979. doi: 10.3390/ani15070979
  23. Girirajan S, Hauck PM, Williams S, Vlangos CN, Szomju BB, Solaymani-Kohal S, et al. Tom1l2 hypomorphic mice exhibit increased incidence of infections and tumors and abnormal immunologic response. Mamm Genome. 2008;19(4):246-262. doi: 10.1007/s00335-008-9100-6
  24. Gulen B, Blevins A, Kinch LN, Servage KA, Stewart NM, Gray HF, et al. FicD sensitizes cellular response to glucose fluctuations in mouse embryonic fibroblasts. Proc Natl Acad Sci USA. 2024;121(38):e2400781121. doi: 10.1073/pnas.2400781121
  25. Gwilliam K, Sperber M, Perry K, Rose KP, Ginsberg L, Paladugu N, et al. A cell type-specific approach to elucidate the role of miR-96 in inner ear hair cells. Front Audiol Otol. 2024;2:1400576. doi: 10.3389/fauot.2024.1400576
  26. Hu Y, Han Z, Guo H, Zhang N, Shen N, Jiang Y, et al. Identification of a novel germline PPP4R3A missense mutation Asp409Asn on familial non-medullary thyroid carcinoma. Biomedicines. 2024;12(1):244. doi: 10.3390/biomedicines12010244
  27. Jaton C, Schenkel FS, Sargolzaei M, Cánova A, Malchiodi F, Price CA, et al. Genome-wide association study and in silico functional analysis of the number of embryos produced by Holstein donors. J Dairy Sci. 2018;101(8):7248-7257. doi: 10.3168/jds.2017-13848
  28. Jiang J, Cole JB, Freebern E, Da Y, VanRaden PM, Ma L. Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls. Commun Biol. 2019;2(1):212. doi: 1038/s42003-019-0454-y
  29. Ke J, Chen C, Fei J, Luo K, Cheng Y, Yu H, et al. Genome-wide analysis of genetic loci and candidate genes related to teat number traits in Dongliao black pigs. Front Genet. 2025;16:1593395. doi: 10.3389/fgene.2025.1593395
  30. Kennedy JM, Fodil N, Torre S, Bongfen SE, Olivier J-F, Leung V, et al. CCDC88B is a novel regulator of maturation and effector functions of T cells during pathological inflammation. J Exp Med. 2014;211(13):2519-2535. doi: 10.1084/jem.20140455
  31. Li S, Ni H, Wang Y, Wu X, Bi J, Ou H, et al. Gain of bipolar disorder-related lncRNA AP1AR-DT in mice induces depressive and anxiety-like behaviors by reducing Negr1-mediated excitatory synaptic transmission. BMC Med. 2024;22(1):543. doi: 10.1186/s12916-024-03725-0
  32. Liu CL, Mou HL, Na RS, Wang X, Hu PF, Ceccobelli S, et al. Multiomic meta-analysis suggests a correlation between steroid hormone-related genes and litter size in goats. Anim Genet. 2024;55(5):779-787. doi: 10.1111/age.13464
  33. Liu Z, Cai Y, Deng M, Li D, Leng Q, Shi L, et al. Expression pattern of alkB homolog 5 in goat  testis  and  its  role  in  spermatogonial  stem    Cell  Tissue  Res.   2022;387(1):131-142. doi: 10.1007/s00441-021-03550-4
  34. Ma X, Zhang Q, La Y, Fu D, Jiang H, Bao P, et al. Differential abundance of brain mitochondrial proteins in yak and cattle: a proteomics-based study. Front Vet Sci. 2021;8:663031. doi: 10.3389/fvets.2021.663031
  35. Matsumura T, Semba K, Azuma S, Ikawa S, Gohda J, Akiyama T, Inoue J. TIFAB inhibits TIFA, TRAF-interacting protein with a forkhead-associated domain. Biochem Biophys Res Commun. 2004;317(1):230-23 doi: 10.1016/j.bbrc.2004.03.030
  36. Mu T, Hu H, Ma Y, Feng X, Zhang J, Gu Y. Regulation of key genes for milk fat synthesis in ruminants. Front Nutr. 2021;8:765147. doi: 3389/fnut.2021.765147
  37. Muroya S, Otomaru K, Oshima K, Oshima I, Ojima K, Gotoh T. DNA methylation of genes participating in hepatic metabolisms and function in fetal calf liver is altered by maternal undernutrition during gestation. Int J Mol Sci. 2023;24(13):10682. doi: 10.3390/ijms241310682
  38. Park BS, Im HL, Yoon NA, Tu TH, Park JW, Kim JG, et al. Developmentally regulated GTP-binding protein-2 regulates adipocyte differentiation. Biochem Biophys Res Commun. 2021;578:1-6. doi: 10.1016/j.bbrc.2021.08.081
  39. Qin J, Wang J, Chen J, Xu J, Liu S, Deng D, Li F. Homozygous variant in DRC3 (LRRC48) gene  causes  asthenozoospermia  and  male  J Hum Genet. 2024;69(8):401-409. doi: 10.1038/s10038-024-01253-6
  40. Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics. 2023;24(1):573. doi: 1186/s12864-023-09679-6
  41. Shinde H, McLeod KR, Lehmkuhler JW. Identification of metabolic pathways and hub genes associated with ultrasound subcutaneous fat and muscle depth of the longissimus muscle in cull beef cows using gene co-expression analysis. Animals (Basel). 2025;15(17):2636. doi: 3390/ani15172636
  42. Suchocki T, Czech B, Dunislawska A, Slawinska A, Derebecka N, Wesoly J, et al. SNP prioritization in targeted sequencing data associated with humoral immune responses in chicken. Poult Sci. 2021;100(11):101433. doi: 10.1016/j.psj.2021.101433
  43. Sun L, Yuan C, Guo T, Bai Y, Lu Z, Liu J. The accumulation of harmful genes within the ROH hotspot regions of the Tibetan sheep genome does not lead to genetic load. BMC Genomics. 2025;26(1):60. doi: 1186/s12864-025-11207-7
  44. Vasimuddin M, Misra S, Li H, Aluru S. Efficient architectureaware acceleration of BWA-MEM for multicore systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rio de Janeiro, Brazil, 20-24 May 2019 . IEEE;2019:314- doi: 10.1109/IPDPS.2019.00041
  45. Wei J, Lian H, Guo W, Chen YD, Zhang XN, Zang R, et al. SNX8 modulates innate immune response to DNA virus by mediating trafficking and activation of MITA. PLoS Pathog. 2018;14(10):e1007336. doi: 10.1371/journal.ppat.1007336
  46. Xiong J, Bao J, Hu W, Shang M, Zhang L. Whole-genome resequencing reveals genetic diversity  and  selection  characteristics of dairy goat. Front Genet. 2023;13:1044017. doi: 10.3389/fgene.2022.1044017
  47. Yang P, Shang M, Bao J, Liu T, Xiong J, Huang J, et al. Whole-genome resequencing revealed selective signatures for growth traits in Hu and Gangba sheep. Genes. 2024;15(5):551. doi: 10.3390/genes15050551
  48. Zhang F, Luo J, Shi C, Zhu L, He Q, Tian H, et al. Genome-wide analysis of the acyl-coenzyme A synthetase family and their association with the formation of goat milk flavour. Front Genet. 2022;13:980463. doi: 10.3389/fgene.2022.980463
  49. Zhao Y, Zhang X, Li F, Tian H, Zhang D, Li X, et al. The changes in genetic parameters and genomic selection of lambing rate in Hu sheep following marker-assisted selection. J Anim Breed Genet. 2026;143(3):465-478. doi: 1111/jbg.70036
  50. Zhou Z, Zhang K, Liu Z, Gao X, Huang K, Chen C, et al. ATPAF1 deficiency impairs ATP synthase assembly and mitochondrial respiration. Mitochondrion. 2021;60:129-141. doi: 10.1016/j.mito.2021.08.005
  51. Zimmermann S, Pfannkuch L, Al-Zeer MA, Bartfeld S, Koch M, Liu J, et al. ALPK1- and TIFA-dependent innate immune response triggered by the Helicobacter pylori type IV secretion system. Cell Rep. 2017;20(10):2384-2395. doi: 10.1016/j.celrep.2017.08.039

Information about the authors:

Tatyana E Deniskova, Cand. Sci. (Biology), Leading Researcher, Head of the Laboratory of Molecular Genetics of Farm Animals, Federal Research Center for Animal Husbandry named after Academy Member LK Ernst, 60 Dubrovitsy village, Podolsk City district, Moscow region, 142132, Russia.

Alexandra S Abdelmanova, Dr. Sci. (Biology), Senior Researcher, Laboratory of Genetic Monitoring of Livestock Resources, Federal Research Center for Animal Husbandry named after Academy Member LK Ernst, 60 Dubrovitsy village, Podolsk City district, Moscow region, 142132, Russia.

Olga A Koshkina, Cand. Sci. (Biology), Researcher, the Laboratory of Molecular Genetics of Farm Animals, Federal Research Center for Animal Husbandry named after Academy Member LK Ernst, 60 Dubrovitsy village, Podolsk City district, Moscow region, 142132, Russia.

Arsen V Dotsev, Cand. Sci. (Biology), Leading Researcher, Head of Laboratory of Functional and Evolutionary Animal Genomics, Federal Research Center for Animal Husbandry named after Academy Member LK Ernst, 60 Dubrovitsy village, Podolsk City district, Moscow region, 142132, Russia.

Natalia A Zinovieva, Dr Sci. (Biology), Professor, Academician of the Russian Academy of Sciences, Director, Federal Research Center for Animal Husbandry named after Academy Member LK Ernst, 60 Dubrovitsy village, Podolsk City district, Moscow region, 142132, Russia.

The article was submitted 03.05.2026; approved after reviewing 24.07.2026; accepted for publication 14.09.2026.

Download