Yermilov AA, Bakoev FS, Chesnokov DV, Belyakov VK, Kostyunina OV.

Animal Husbandry and Fodder Production. 2026. Vol. 109. No. 1. Р. 43-54.

doi: 10.33284/2658-3135-109-1-43

 

Original article

Genome-wide association study of semen quality in Holstein Bulls

 

Anton A Yermilov1, Faridun S Bakoev2, Dmitriy V Chesnokov3, Vladimir K Belyakov4,

Olga V Kostyunina5

1,2,3,4,5 LLC «WESTTRADE LTD», Moscow, Russia

1de_lamak@mail.ru

2bakoevfaridun@yandex.ru, https://orcid.org/0009-0001-6312-8947

3chesnokovdmitrii@yandex.ru, https://orcid.org/0009-0007-1061-5702

4bel.vk@yandex.ru, https://orcid.org/0000-0001-9487-1250

5kostolan@yandex.ru, https://orcid.org/0000-0001-8206-3221

            Abstract. Under intensive dairy farming conditions, the efficiency of artificial insemination directly depends on the reproductive potential of bull sires, which is assessed based on semen quality. Traditional phenotypic methods for evaluating ejaculates do not always provide a reliable prediction of fertility, necessitating the search for genetic predictors of reproductive traits. The aim of this study was to identify genomic regions and genes associated with sperm concentration and the proportion of rejected (unsuitable) ejaculates in Holstein bulls using a genome-wide association study (GWAS) approach. The analysis was performed using data from 104 Holstein bull sires, for which phenotypic values of the studied traits were calculated based on 3,928 semen samples collected between 2023 and 2024. Genotyping was carried out using the Illumina BovineSNP50v3 BeadChip, and after quality control, 38015 SNPs were retained for analysis. Heritability estimates, obtained via restricted maximum likelihood (REML) implemented in the GCTA software, revealed a moderately high genetic contribution: h² = 0.637 for sperm concentration and h² = 0.516 for the proportion of rejected ejaculates. GWAS, conducted using a mixed linear model association (MLMA) approach that accounted for the genomic relationship matrix (GRM), identified 360 significant SNPs associated with sperm concentration and 368 SNPs associated with ejaculate quality. The most significant associations were found in the genes MUC16, VWA3B, RECQL5, TMEM104, and RREB1, as well as in an intergenic region on chromosome 10 (rs109387674), previously linked to fertility and reproductive quantitative trait loci (QTL) in cattle. Functional annotation suggests that these genes are involved in key biological processes, including genomic stability maintenance, hormonal regulation, epithelial protection, and spermatogenesis. These findings enhance our understanding of the genetic architecture underlying reproductive traits in bulls and provide a foundation for developing genomic selection tools aimed at improving sire fertility, reducing economic losses due to ejaculate rejection, and strengthening the genetic self-sufficiency of domestic dairy cattle breeding.

Keywords: bull, ejaculate, sperm cell, sperm concentration, ejaculate rejection, GWAS

Acknowledgments:  the   work   was  supported  by  the  Russian  Science  Foundation,  Project  No. 24-16-00198.

            For citation: Yermilov AA, Bakoev FS, Chesnokov DV, Belyakov VK, Kostyunina OV. Genome-wide association study of semen quality in Holstein bulls. Animal Husbandry and Fodder Production. 2026;109(1):43-54. (In Russ.). https://doi.org/10.33284/2658-3135-109-1-43

References

 

  1. Naryshkina EN, Ignatieva LP, Zaripov OG, Levchenko MV, Sermyagin AA. Reproduction traits of Simmental cows obtained from sires of local and imported lines. Animal Husbandry and Fodder Production. 2025;108(1):50-59. doi: 10.33284/2658-3135-108-1-50
  2. Tulinova OV, Romanova EA. Impact of classifier qualification on the results of linear assessment of cattle. Animal Husbandry and Fodder Production. 2025;108(3):95-112. doi: 10.33284/2658-3135-108-3-95
  3. Abril-Parreño L, Carthy TR,  Keogh  K,  Štiavnická  M,  O’Meara  C, Lonergan P, Kenny DA, Fair S. Genome-wide association study reveals candidate markers related to field fertility and semen quality traits in Holstein-Friesian bulls. Animal. 2023;17(7):100841. doi: 10.1016/j.animal.2023.100841
  4. Buitenhuis B, Janss LLG, Poulsen NA, Larsen LB, Larsen MK, Sørensen P. Genome-wide association and biological pathway analysis for milk-fat composition in Danish Holstein and Danish Jersey cattle. BMC Genomics. 2014;15:1112. doi: 10.1186/1471-2164-15-1112
  5. Buitenhuis B, Poulsen NA, Gebreyesus G, Larsen LB. Estimation of genetic parameters and detection of chromosomal regions affecting the major milk proteins and their post translational modifications in Danish Holstein and Danish Jersey cattle. BMC Genet. 2016;17:114. doi: 1186/s12863-016-0421-2
  6. Cesarani A, Corte Pause F, Hidalgo J, Garcia A, Degano L, Vicario D, Macciotta NPP, Stradaioli G. Genetic background of semen parameters in Italian Simmental bulls. Ital J Anim Sci. 2023;22(1):76-83. doi: 10.1080/1828051X.2022.2160665
  7. Fortes MRS, Reverter A, Nagaraj SH, Zhang Y, Jonsson NN, Barris W, Lehnert SA, Boe-Hansen GB, Hawken RJ. A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle. J Anim Sci. 2011;89(6):1669-1683. doi: 10.2527/jas.2010-3681
  8. Gautason E, Þórarinsdóttir Þ, Sahana G. Haplotypes affecting stillbirth and fertility in Icelandic Dairy Cattle. J Appl Genetics. 2025;66:1053-1064. doi: 10.1007/s13353-025-00978-0
  9. Jung M, Rüdiger K, Schulze M. In vitro measures for assessing boar semen fertility. Reprod Domest Anim. 2015;50(S2):20- doi: 10.1111/rda.12533
  10. Khan MZ, Chen W, Naz S, Liu X, Liang H, Chen Y, Kou X, Liu Y, Ashraf I, Han Y, Peng Y, Wang C, Zahoor M. Determinant genetic markers of semen quality in livestock. Front Endocrinol (Lausanne). 2024;15:1456305. doi: 10.3389/fendo.2024.1456305
  11. Kunii H, Kubo T,  Asaoka N, Balboula AZ, Hamaguchi Y, Shimasaki T, Bai H, Kawahara M, Kobayashi H, Ogawa H, Takahashi M. Loop-mediated isothermal amplification (LAMP) and machine learning application for early pregnancy detection using bovine vaginal mucosal membrane. Biochem Biophys Res Commun. 2021;569:179-186. doi: 10.1016/j.bbrc.2021.07.015
  12. Li W, Mi S,  Zhang J,  Liu X, Chen S, Liu S, Feng X, Tang Y, Li Y, Liu L, Fang L, Zhang S, Yu Y. Integrating  sperm  cell  transcriptome and seminal plasma metabolome to analyze the molecular regulatory mechanism of sperm motility in Holstein stud bulls. J Anim Sci. 2023;101:skad214. doi: 10.1093/jas/skad214
  13. Marete A, Lund MS, Boichard D, Ramayo-Caldas Y. A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds. PLoS One. 2018;13(7):e0199931. doi: 10.1371/journal.pone.0199931
  14. Moore SG, Pryce JE, Hayes BJ, Chamberlain AJ, Kemper KE, Berry DP, McCabe M, Cormican P, Lonergan P, Fair T, Butler ST. Differentially expressed genes in endometrium and corpus luteum of Holstein cows selected for high and low fertility are enriched for sequence variants associated with fertility. Biol Reprod. 2016;94(1):19. doi: 10.1095/biolreprod.115.132951
  15. Reyer H, Abou-Soliman I, Schulze M, Henne H, Reinsch N, Schoen J, Wimmers, K. Genome-wide association analysis of semen characteristics in piétrain boars. Genes. 2024;15(3):382. doi: 10.3390/genes15030382
  16. Riley DG, Gill  CA,  Boldt  CR, Funkhouser RR, Herring AD, Riggs PK, Sawyer JE, Lunt DK, Sanders JO. Crossbred steer temperament as yearlings and whole genome association of steer temperament as yearlings and calf temperament post-weaning. J Anim Sci. 2016;94(4):1408-1414. doi: 10.2527/jas.2015-0041
  17. Robertson MJ, Chambers C, Spanner EA, de Graaf SP, Rickard JP. The assessment of sperm DNA integrity: implications for assisted reproductive technology fertility outcomes across livestock species. Biology. 2024;13(7):539. doi: 10.3390/biology13070539
  18. Selvaraju S, Parthipan S, Somashekar L, Binsila BK, Kolte AP, Arangasamy A, Ravindra JP, Krawetz SA. Current status of sperm functional genomics and its diagnostic potential of fertility in bovine (Bos taurus). Syst Biol Reprod Med. 2018;64(6):484- doi: 10.1080/19396368.2018.1444816
  19. Selvaraju S, Parthipan S, Somashekar L, Kolte AP, Krishnan Binsila B, Arangasamy A, Ravindra JP. Occurrence and functional significance of the transcriptome in bovine (Bos taurus) spermatozoa. Sci Rep. 2017;7:42392. doi: 10.1038/srep42392
  20. Somashekar L, Selvaraju S, Parthipan S, Patil SK, Binsila BK, Venkataswamy MM, Karthik Bhat S, Ravindra JP. Comparative sperm protein profiling in bulls differing in fertility and identification of phosphatidylethanolamine-binding protein 4, a potential fertility marker. Andrology. 2017;5(5):1032-1051. doi: 10.1111/andr.12404
  21. Wagener K, Pothmann H, Prunner I, Peter S, Erber R, Aurich C, Drillich M, Gabler C. Endometrial mRNA expression of selected pro-inflammatory factors and mucins in repeat breeder cows with and without subclinical endometritis. Theriogenology. 2017;90:237-244. doi: 10.1016/j.theriogenology.2016.12.013
  22. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: A tool for genome-wide complex trait analysis. Am J Hum Genet. 2011;88(1):76-82. doi: 10.1016/j.ajhg.2010.11.011
  23. Yang J, Zaitlen NA, Goddard ME, Visscher PM, Price AL. Advantages and pitfalls in the application of mixed-model association methods. Nat Genet. 2014;46(2):100-106. doi: 10.1038/ng.2876
  24. Yin H, Zhou C, Shi S, Fang L, Liu J, Sun D, Jiang L, Zhang S. Weighted Single-Step Genome-Wide Association Study of Semen Traits in Holstein Bulls of China. Front Genet. 2019;10:1053. doi: 10.3389/fgene.2019.01053

Information about the authors: 

Anton A Yermilov, Cand. Sci. (Biology), Senior Researcher, WESTTRADE LLC, Russia, Moscow, 1st Varshavsky proezd, 1A, building 9, 115201, tel.: +7 (916) 888-68-67.

Faridun S Bakoev, Bioinformatician, WESTTRADE LLC, Russia, Moscow, 1st Varshavsky proezd, 1A, building 9, 115201, tel.: +7 (961) 438-80-58.

Dmitriy V Chesnokov, Research Specialist, WESTTRADE LLC, Russia, Moscow, 1st Varshavsky proezd, 1A, building 9, 115201, tel.: +7 (903) 789-41-40.

Vladimir K Belyakov, Dr. Sci. (Medicine), General Director, WESTTRADE LLC, Russia, Moscow, 1st Varshavsky proezd, 1A, building 9, 115201, tel.: +7 (916) 737-66-77.

Olga V Kostyunina, Dr. Sci. (Biology), Chief Researcher, WESTTRADE LLC, Russia, Moscow, 1st Varshavsky proezd, 1A, building 9, 115201, tel.: +79037415635.

The article was submitted 28.10.2025; approved after reviewing 21.01.2026; accepted for publication 16.03.2026.

Download