Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: arjmand.farnaz@ut.ac.ir, y.devisty@ut.ac.ir

2 Corresponding Author, Department of Animal Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: hmoradis@ut.ac.ir

3 Department of Animal Science, Faculty of Agriculture,, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: moradim@ut.ac.ir

4 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran. E-mail: h-mohammadi64@araku.ac.ir

5 Aras International Campus, University of Tehran, Jolfa, Iran. E-mail: javannikkhah@yahoo.com

6 Department of Animal Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran. E-mail: y.devisty@ut.ac.ir

Abstract

Introduction: Bovine Leukemia Virus (BLV) infection is more common in dairy cattle herds. The main cause of leukosis is the disease that leads to the creation of cancerous lymphocytes in different organisms of the body and affects different species, including cattle. This disease reduces milk production and causes reproductive diseases, and finally the removal of infected animals. Due to trade restrictions and deaths caused by lymphosarcoma, it causes direct economic losses, which is also related to the decrease in milk production and the increase in the elimination rate. No treatment or vaccine is known for this disease so far. Therfore, studying the genomic regions related to susceptibility to BLV infection can be effective in controlling and treating this disease and genetic improvement of animals. This research aimed to perform a whole genom-wide association study (GWAS) study of cattle to identify genomic regions and candidate genes associated with BLV infection.
Material and Methods This study was conducted using Holstein cows that were naturally infected with BLV. For this purpose, blood samples of 150 Holstein cows in an industrial dairy cattle farm in Isfahan were collected, and DNA and serum of them were extracted. The prepared DNA samples were genotyped using k30 microarrays (SNPchip30k) (by Illumina). Quality control of sequences for rare allele frequency components (PMAF < 0.05), missing genotype (PMIND > 0.05), genotyping rate (PGENO > 0.05), and Hardy-Weinberg equilibrium (PH-W < 1×10-6) and significance test was performed by PLINK software. Analysis of the ontology of genes was done by the online database https://www.Uniprot.org and finally, the ontology diagram of genes was drawn and analyzed by the online database PANTHER.
Results and Discussion: After control analyzing, 145 cows (77 cases and 68 controls) and 22868 markers were left for further analysis, finally 8 markers higher than the significant threshold were identified, and most significant markers were located on chromosomes 17 and 21. Using ensemble sites and genecards, genes associated with significant selected markers were identified. The most important of them were GRK4, TP53BP1, SCAPER, GLRB, PDGFC, TNIP2, PSTPIP1, CEP350, MR1, TOM1L2, SREBF1, COPS and TNFRS13B. Gene Ontology (GO) analysis showed that these genes are more involved in protein-coding and play a role in regulating enzyme activities, intercellular exchanges, DNA stability, calcium activity, nervous system, and lipid activity. Also, according to other research, these genes played a role in cases such as infectious poison lesions, subclinical ketosis disease, BCS of cattle, fatty acid metabolism and fat deposition, various infections such as mastitis, and in meat traits and muscle stiffness in beef cattle. It should be noted that some of these genes were related to the pathways of innate immunity, humoral immunity, and cancer tumors.
Conclusion: Therefore, it can be concluded that whole genome wide association study analysis as well as gene ontology analysis to identify genomic regions related to viral infections such as leukemia can be effective in designing treatment methods and prevention methods and in choosing Genomics and breeding programs in Iranian dairy cows.

Keywords

Reference
Abdalla, E. A., Peñagaricano, F., Byrem, T. M., Weigel, K. A., & Rosa, G. J. M. (2016). Genome‐wide association mapping and pathway analysis of leukosis incidence in a US Holstein cattle population. Animal genetics, 47(4), 395-407.‏
Abdullahi Arpanahi, R., Pakdel, A., & Zandi Bagche Mariam, M. B. (2013). From the infinitesimal inheritance model with partial effects (modelInfinitesimal) to genomic selection. New genetics, 7(29-2). (in Perian).
Badour, K., Zhang, J., Shi, F., McGavin, M. K., Rampersad, V., Hardy, L. A., Field, D., & Siminovitch, K. A. (2003). The Wiskott-Aldrich syndrome protein acts downstream of CD2 and the CD2AP and PSTPIP1 adaptors to promote formation of the immunological synapse. Immunity, 18(1), 141-154.‏
Blasiak, J., Szczepańska, J., Sobczuk, A., Fila, M., & Pawlowska, E. (2021). RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair. International Journal of Molecular Sciences, 22(21), 11440.‏
Brym, P., Bojarojć-Nosowicz, B., Oleński, K., Hering, D. M., Ruść, A., Kaczmarczyk, E., & Kamiński, S. (2016). Genome-wide association study for host response to bovine leukemia virus in Holstein cows. Veterinary Immunology and Immunopathology, 175, 24-35.‏
Carignano, H. A., Roldan, D. L., Beribe, M. J., Raschia, M. A., Amadio, A., Nani, J. P., & Miretti, M. M. (2018). Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle. BMC genomics, 19(1), 1-15.‏
Carlson, G. (2002). Diseases of the hematopoietic and hemolymphatic systems. Large Animal Internal Medicine, ed, 3, 1042-1043.
Chen, Q. Z., Yang, M. Y., Liu, X. Q., Zhang, J. N., Mi, S. Y., Wang, Y. J., & Yu, Y. (2022). Blood transcriptome analysis and identification of genes associated with supernumerary teats in Chinese Holstein cows. Journal of Dairy Science, 105(12), 9837-9852.‏
Falini, B., Martino, G., & Lazzi, S. (2022). A comparison of the International Consensus and 5th World Health Organization classifications of mature B-cell lymphomas. Leukemia, 1-17.‏
Gao, Y., Jiang, J., Yang, S., Cao, J., Han, B., Wang, Y., & Sun, D. (2018). Genome-wide association study of Mycobacterium avium subspecies paratuberculosis infection in Chinese Holstein. BMC genomics, 19(1), 1-10.
Girirajan, S., Hauck, P. M., Williams, S., Vlangos, C. N., Szomju, B. B., Solaymani-Kohal, S., & Elsea, S. H. (2008). Tom1l2 hypomorphic mice exhibit increased incidence of infections and tumors and abnormal immunologic response. Mammalian Genome, 19(4), 246-262.‏
Goddard, M. E., & Hayes, B. J. (2009). Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics, 10(6), 381-391.
Goldfinch, N. G. (2010). Characterisation of mucosal associated invariant T-cells and MR1 in ruminants.‏
González-Rodríguez, A., Munilla, S., Mouresan, E. F., Cañas-Álvarez, J. J., Díaz, C., Piedrafita, J., & Varona, L. (2016). On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations. Genetics Selection Evolution, 48(1), 1-12.‏
Hemmatzadeh, F., & Momtaz, H. (2007). Detection of bovine Leukemia virus antigens expressed in lymph node tumors that induce humoral immunity in cow. Journal of Veterinary Research, 62(3), 281-284.
Kim, E. S., Sonstegard, T. S., & Rothschild, M. F. (2015). Recent artificial selection in US Jersey cattle impacts autozygosity levels of specific genomic regions. BMC genomics, 16(1), 1-10.‏
Kościuczuk, E. M., Lisowski, P., Jarczak, J., Krzyżewski, J., Zwierzchowski, L., & Bagnicka, E. (2014). Expression patterns of β-defensin and cathelicidin genes in parenchyma of bovine mammary gland infected with coagulase-positive or coagulase-negative Staphylococci. BMC Veterinary Research, 10(1), 1-14.‏
Liu, D., Chen, Z., Zhao, W., Guo, L., Sun, H., Zhu, K., & Pan, Y. (2021). Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits. BMC genomics, 22(1), 1-19.‏
Lou, Y., & Huang, Z. (2020). microRNA‑15a‑5p participates in sepsis by regulating the inflammatory response of macrophages and targeting TNIP2. Experimental and therapeutic medicine, 19(4), 3060-3068.‏
Malchiodi, F., Brito, L. F., Schenkel, F. S., Christen, A. M., Kelton, D. F., & Miglior, F. (2018). Genome-wide association study and functional analysis of infectious and horn type hoof lesions in Canadian Holstein cattle. In Proceedings of the World Congress on Genetics Applied to Livestock Production.‏
Mekata, H., & Yamamoto, M. (2022). Single-Nucleotide Polymorphism on Spermatogenesis Associated 16 Gene-Coding Region Affecting Bovine Leukemia Virus Proviral Load. Veterinary Sciences, 9(6), 275.‏
Meuwissen, T. H., Hayes, B. J., & Goddard, M. (2001). Prediction of total genetic value using genome-wide dense marker maps. genetics, 157(4), 1819-1829.‏
Mohammadi, V., Atyabi, N., & Nikbakht, B. G. (2011). Seroprevalence of bovine leukemia virus in some dairy farms in Iran. Global Veterinaria, 7(3), 305-309.
Nafikov, R. A., Schoonmaker, J. P., Korn, K. T., Noack, K., Garrick, D. J., Koehler, K. J., & Beitz, D. C. (2013). Sterol regulatory element binding transcription factor 1 (SREBF1) polymorphism and milk fatty acid composition. Journal of dairy science, 96(4), 2605-2616.‏
Pierce, K. D., Handford, C. A., Morris, R., Vafa, B., Dennis, J. A., Healy, P. J., & Schofield, P. R. (2001). A nonsense mutation in the α1 subunit of the inhibitory glycine receptor associated with bovine myoclonus. Molecular and Cellular Neuroscience, 17(2), 354-363.‏
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.‏
Radostits, O. M., Gay, C. C., Blood, D. C., & Hinchcliff, K. W. (2000). Mastitis In: Veterinary Medicine, A Textbook of the Diseases of Cattle, Sheep, Pigs, Goats and Horses. Edn. 9th publ. Book power with Saunders, London, 611-613.‏
Radostits, O. M., Gay, C. C., Hinchcliff, K. W., & Constable, P. D. (2007). A textbook of the diseases of cattle, horses, sheep, pigs and goats. Veterinary medicine, 10, 2045-2050.
Reginald, J. (1999). Bovine Leukemia Virus. Current Veterinary therapy (Food Animal Practice). 4th ed. Sounders Company, pp: 296-299.
Reigstad, L. J., Varhaug, J. E., & Lillehaug, J. R. (2005). Structural and functional specificities of PDGF‐C and PDGF‐D, the novel members of the platelet‐derived growth factors family. The FEBS journal, 272(22), 5723-5741.‏
Sahana, G., Guldbrandtsen, B., Thomsen, B., Holm, L. E., Panitz, F., Brøndum, R. F., & Lund, M. S. (2014). Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle. Journal of dairy science, 97(11), 7258-7275.‏
Saifi Abad Shapouri, M. (2005). Viral diseases of cattle. Author: Robert Karz, first edition, Shahid Chamran University of Ahvaz Printing and Publishing Department, 157-171.(in Persian)
Salzer, U., Bacchelli, C., Buckridge, S., Pan-Hammarström, Q., Jennings, S., Lougaris, V., & Grimbacher, B. (2009). Relevance of biallelic versus monoallelic TNFRSF13B mutations in distinguishing disease-causing from risk-increasing TNFRSF13B variants in antibody deficiency syndromes. Blood, The Journal of the American Society of Hematology, 113(9), 1967-1976.‏
Sender, G., Korwin-Kossakowska, A., Pawlik, A., Hameed, K. G. A., & Oprzadek, J. (2013). Genetic Basis of Mastitis Resistance in Dairy Cattle-A Review/Podstawy Genetyczne Odpornosci Krow Mlecznych Na Zapalenie Wymienia-Artykul Przegladowy. Annals of Animal Science, 13(4), 663.‏
Soares, R. A. N., Vargas, G., Duffield, T., Schenkel, F., & Squires, E. J. (2021). Genome-wide association study and functional analyses for clinical and subclinical ketosis in Holstein cattle. Journal of Dairy Science, 104(9), 10076-10089.‏
Soupene, E., & Kuypers, F. A. (2019). ACBD6 protein controls acyl chain availability and specificity of the N-myristoylation modification of proteins [S]. Journal of lipid research, 60(3), 624-635.
Taghizadeh, S., Gholizadeh, M., Moradi, M. H., Costilla, R., Moore, S., & Di Gerlando, R. (2022). Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds. Scientific Reports, 12(1), 1-12.‏
Takeshima, S. N., Sasaki, S., Meripet, P., Sugimoto, Y., & Aida, Y. (2017). Single nucleotide polymorphisms in the bovine MHC region of Japanese Black cattle are associated with bovine leukemia virus proviral load. Retrovirology, 14(1), 1-7.‏
Taye, M., Kim, J., Yoon, S. H., Lee, W., Hanotte, O., Dessie, T., & Kim, H. (2017). Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef. BMC genetics, 18(1), 1-14.‏
Teo, Y. Y., Fry, A. E., Clark, T. G., Tai, E. S., & Seielstad, M. (2007). On the usage of HWE for identifying genotyping errors. Annals of Human genetics, 71(5), 701-703.‏
Zhao, J., Liu, Z., Liu, T., Nilsson, S., & Nistér, M. (2008). Identification and expression analysis of an N-terminally truncated isoform of human PDGF-C. Experimental cell research, 314(14), 2529-2543.