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Research Article

volume 53 issue 12 (december 2019) : 1572-1576,   Doi: 10.18805/ijar.B-3768

Detection of polymorphism in the promoter region of TNF-alpha gene of water buffalo (Bubalus bubalis) and its association with disease resistance

A
Anurag Kumar
S
S.K. Mishra
S
S. Lavakumar
K
Karan Veer Singh
N
Namita Kumari
M
Monika Sodhi
M
M. Mukesh
S
S.K. Niranjan
A
Avnish Kumar
R
R.S. Kataria
1Indian Council of Agricultural Research, National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, India.
Cite article:- Kumar Anurag, Mishra S.K., Lavakumar S., Singh Veer Karan, Kumari Namita, Sodhi Monika, Mukesh M., Niranjan S.K., Kumar Avnish, Kataria R.S. (2019). Detection of polymorphism in the promoter region of TNF-alpha gene of water buffalo (Bubalus bubalis) and its association with disease resistance. Indian Journal of Animal Research. 53(12): 1572-1576. doi: 10.18805/ijar.B-3768.

ABSTRACT

Tumour necrosis factor (TNF), a proinflammatory cytokine, plays an important role in the regulation of cell differentiation, proliferation and death, as well as in innate and adaptive immune response. In this study we have sequence characterized upstream regulatory region of TNF-á gene of buffalo. Ten single polymorphic nucleotides (SNPs) -541A/T, -553A/G, -563,C/G, -619A/G, -659A/G, -706C/G, -730G/T, -794A/G, -898G/T, -981A/G) along with one indel at position -783 were identified. Further when analysed, among riverine and swamp types, 16 and 17 transcription factor–binding sites (TFBS) respectively were observed. Riverine and swamp buffaloes differed by PAX-2 transcription factor binding site at position -541 present in riverine and absent in swamp, important in the proliferation of multiple cell lines and development of organs. Comparative analysis of TNF-á upstream region revealed presence of additional NF-k binding site in buffalo and v-Myb binding site in cattle only. Genotyping of SNP -794A/G by tetra-ARMS PCR revealed variable allele frequencies among riverine and swamp buffaloes, however in clinical mastitis affected and non-affected Murrah buffaloes this SNP didn’t show any significant association with mastitis resistance. Overall study reveals the sequence variation in TNF-á promoter, possibly leading to modification of transcriptional regulation in swamp and riverine buffalo.

REFERENCES

  1. Aboelenin, M.M., Mahrous, K.F., Rashed, M.A. and Sallam, M.A. (2017). Molecular characterization of tumor necrosis factor- A (TNFA) gene in Egyptian river buffaloes.  Arab Univ. J. Agric. Sci.. 25(2): 367-375. 
  2. Asghar, T., Yoshida, S., Kennedy S., Negoro, K., Zhuo, W., Hamana, S., et al. (2004).The tumor necrosis factor-á promoter-1031C polymorphism is associated with decreased risk of endometriosis in a Japanese population. Hum. Reprod. 19(11): 2509-2514.
  3. Benedict, C.A., Banks, T.A., Ware, C.F. (2003) Death and survival: viral regulation of TNF signaling pathways. (2003). Curr. Opin. Immunol. 15(1): 59-65.
  4. Bojarojæ-Nosowicz, B., Kaczmarczyk, E., Stachura, A., Kotkiewicz, M. (2011). Polymorphism in the promoter region of the tumor necrosis factor-alpha gene in cattle herds naturally infected and uninfected with the Bovine Leukemia Virus. Pol. J. Vet. Sci. 14(4): 671-673.
  5. Chekmenev, D.S., Haid, C., Kel, A.E. (2005). P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res. 33(suppl_2): 432-7.
  6. Cheng, Y., Huang, C., Tsai, H. (2016). Relationship of bovine TNF-á gene polymorphisms with the risk of bovine tuberculosis in Holstein cattle. J. Vet. Med. Sci. 78(5): 727-732.
  7. Deshpande, A., Nolan, J.P., White, P.S., Valdez, Y.E., Hunt, W.C., Peyton, C.L., et al. (2005) TNF-á promoter polymorphisms and susceptibility to human papillomavirus 16–associated cervical cancer. J. Infect. Dis. 191(6): 969-976.
  8. Eccles, M.R., He, S., Legge, M., Kumar, R., Fox, J., Zhou, C., et al. (2004). PAX genes in development and disease: the role of PAX2 in urogenital tract development. Int. J. Dev. Biol. 46(4): 535-544.
  9. Knight, J.C., Udalova, I., Hill, A.V., Greenwood, B.M., Peshu, N., Marsh, K., et al. (1999). A polymorphism that affects OCT-1 binding to the TNF-á promoter region is associated with severe malaria. Nat. Genet. 22(2): 145.
  10. Konnai, S., Usui, T., Ikeda, M., Kohara, J., Hirata, T.I., Okada, K., et al. (2006). Tumor necrosis factor-alpha genetic polymorphism may contribute to progression of bovine leukemia virus-infection. Microbes Infect. 8(8): 2163-2171.
  11. Manly, B.F. (1986). Randomization and regression methods for testing for associations with geographical, environmental and biological distances between populations. Res. Popul. Ecol. 28(2): 201-18.
  12. Mingala, C.N., Konnai, S., Cruz, L.C., Onuma, M., Ohashi, K. (2009). Comparative moleculo-immunological analysis of swamp-and riverine-type water buffaloes responses. Cytokine, 46(2): 273-282.
  13. Peakall, R.O. and, Smouse, P.E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Resour. 6(1): 288-95.
  14. Ranjan, S., Bhushan, B., Panigrahi, M., Kumar, A., Deb, R., Kumar, P., et al. (2015). Association and expression analysis of single nucleotide polymorphisms of partial tumor necrosis factor alpha gene with mastitis in crossbred cattle. Anim. Biotechnol. 26(2): 98-104.
  15. Sambrook, J.R and Russell, D.W. (2001). Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor Press, Cold Spring Harbor.
  16. Singh, D., Kumar, S., Singh, B., Bardhan, D. (2014). Economic losses due to important diseases of bovines in central India. Vet. World, 7(8).
  17. Thakur, S., Singh, M., Aseri, G.K., Verma, A., Vineeth, M.R., Rayees, M., Arya, A. (2017). Identification of point mutation in TLR2 gene and its association with mastitis in water buffalo. Indian J. Anim. Res. 52(9).
  18. Van Heel, D.A., Udalova, I.A., De Silva, A.P., McGovern, D.P., Kinouchi, Y., Hull, J., et al. (2002). Inflammatory bowel disease is associated with a TNF-á polymorphism that affects an interaction between the OCT1 and NF-êB transcription factors. Hum Mol. Genet. 11(11): 1281-1289.
  19. Wen, Y., Cheng, X., Zhao, S. (2018). Nucleotide variants of the NRAMP1 gene in pigs and their effects on disease resistance. Indian J. Anim. Res. 52 (4): 490-496.
  20. Werth, V.P., Zhang, W., Dortzbach, K., Sullivan, K. (2000). Association of a Promoter Polymorphism of Tumor Necrosis Factor-á with Subacute Cutaneous Lupus Erythematosus and Distinct Photoregulation of Transcription1. J. Invest. Dermatol. 115(4): 726-730.
  21. Wojdak-Maksymiec K., Szyda, J., Strabel, T. (2013). Parity-dependent association between TNF-á and LTF gene polymorphisms and clinical mastitis in dairy cattle. BMC Vet Res. 9(1): 114.
  22. Yea, S.S., Yang, Y.I., Jang, W.H., Lee, Y.J., Bae, H.S., Paik, K.H. (2001). Association between TNF-á promoter polymorphism and Helicobacter pylori cagA subtype infection. J. Clin. Pathol. 54(9): 703-706. 
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Indian Journal of Animal Research
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    Research Article

    volume 53 issue 12 (december 2019) : 1572-1576,   Doi: 10.18805/ijar.B-3768

    Detection of polymorphism in the promoter region of TNF-alpha gene of water buffalo (Bubalus bubalis) and its association with disease resistance

    A
    Anurag Kumar
    S
    S.K. Mishra
    S
    S. Lavakumar
    K
    Karan Veer Singh
    N
    Namita Kumari
    M
    Monika Sodhi
    M
    M. Mukesh
    S
    S.K. Niranjan
    A
    Avnish Kumar
    R
    R.S. Kataria
    1Indian Council of Agricultural Research, National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, India.
    Cite article:- Kumar Anurag, Mishra S.K., Lavakumar S., Singh Veer Karan, Kumari Namita, Sodhi Monika, Mukesh M., Niranjan S.K., Kumar Avnish, Kataria R.S. (2019). Detection of polymorphism in the promoter region of TNF-alpha gene of water buffalo (Bubalus bubalis) and its association with disease resistance. Indian Journal of Animal Research. 53(12): 1572-1576. doi: 10.18805/ijar.B-3768.

    ABSTRACT

    Tumour necrosis factor (TNF), a proinflammatory cytokine, plays an important role in the regulation of cell differentiation, proliferation and death, as well as in innate and adaptive immune response. In this study we have sequence characterized upstream regulatory region of TNF-á gene of buffalo. Ten single polymorphic nucleotides (SNPs) -541A/T, -553A/G, -563,C/G, -619A/G, -659A/G, -706C/G, -730G/T, -794A/G, -898G/T, -981A/G) along with one indel at position -783 were identified. Further when analysed, among riverine and swamp types, 16 and 17 transcription factor–binding sites (TFBS) respectively were observed. Riverine and swamp buffaloes differed by PAX-2 transcription factor binding site at position -541 present in riverine and absent in swamp, important in the proliferation of multiple cell lines and development of organs. Comparative analysis of TNF-á upstream region revealed presence of additional NF-k binding site in buffalo and v-Myb binding site in cattle only. Genotyping of SNP -794A/G by tetra-ARMS PCR revealed variable allele frequencies among riverine and swamp buffaloes, however in clinical mastitis affected and non-affected Murrah buffaloes this SNP didn’t show any significant association with mastitis resistance. Overall study reveals the sequence variation in TNF-á promoter, possibly leading to modification of transcriptional regulation in swamp and riverine buffalo.

    REFERENCES

    1. Aboelenin, M.M., Mahrous, K.F., Rashed, M.A. and Sallam, M.A. (2017). Molecular characterization of tumor necrosis factor- A (TNFA) gene in Egyptian river buffaloes.  Arab Univ. J. Agric. Sci.. 25(2): 367-375. 
    2. Asghar, T., Yoshida, S., Kennedy S., Negoro, K., Zhuo, W., Hamana, S., et al. (2004).The tumor necrosis factor-á promoter-1031C polymorphism is associated with decreased risk of endometriosis in a Japanese population. Hum. Reprod. 19(11): 2509-2514.
    3. Benedict, C.A., Banks, T.A., Ware, C.F. (2003) Death and survival: viral regulation of TNF signaling pathways. (2003). Curr. Opin. Immunol. 15(1): 59-65.
    4. Bojarojæ-Nosowicz, B., Kaczmarczyk, E., Stachura, A., Kotkiewicz, M. (2011). Polymorphism in the promoter region of the tumor necrosis factor-alpha gene in cattle herds naturally infected and uninfected with the Bovine Leukemia Virus. Pol. J. Vet. Sci. 14(4): 671-673.
    5. Chekmenev, D.S., Haid, C., Kel, A.E. (2005). P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res. 33(suppl_2): 432-7.
    6. Cheng, Y., Huang, C., Tsai, H. (2016). Relationship of bovine TNF-á gene polymorphisms with the risk of bovine tuberculosis in Holstein cattle. J. Vet. Med. Sci. 78(5): 727-732.
    7. Deshpande, A., Nolan, J.P., White, P.S., Valdez, Y.E., Hunt, W.C., Peyton, C.L., et al. (2005) TNF-á promoter polymorphisms and susceptibility to human papillomavirus 16–associated cervical cancer. J. Infect. Dis. 191(6): 969-976.
    8. Eccles, M.R., He, S., Legge, M., Kumar, R., Fox, J., Zhou, C., et al. (2004). PAX genes in development and disease: the role of PAX2 in urogenital tract development. Int. J. Dev. Biol. 46(4): 535-544.
    9. Knight, J.C., Udalova, I., Hill, A.V., Greenwood, B.M., Peshu, N., Marsh, K., et al. (1999). A polymorphism that affects OCT-1 binding to the TNF-á promoter region is associated with severe malaria. Nat. Genet. 22(2): 145.
    10. Konnai, S., Usui, T., Ikeda, M., Kohara, J., Hirata, T.I., Okada, K., et al. (2006). Tumor necrosis factor-alpha genetic polymorphism may contribute to progression of bovine leukemia virus-infection. Microbes Infect. 8(8): 2163-2171.
    11. Manly, B.F. (1986). Randomization and regression methods for testing for associations with geographical, environmental and biological distances between populations. Res. Popul. Ecol. 28(2): 201-18.
    12. Mingala, C.N., Konnai, S., Cruz, L.C., Onuma, M., Ohashi, K. (2009). Comparative moleculo-immunological analysis of swamp-and riverine-type water buffaloes responses. Cytokine, 46(2): 273-282.
    13. Peakall, R.O. and, Smouse, P.E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Resour. 6(1): 288-95.
    14. Ranjan, S., Bhushan, B., Panigrahi, M., Kumar, A., Deb, R., Kumar, P., et al. (2015). Association and expression analysis of single nucleotide polymorphisms of partial tumor necrosis factor alpha gene with mastitis in crossbred cattle. Anim. Biotechnol. 26(2): 98-104.
    15. Sambrook, J.R and Russell, D.W. (2001). Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor Press, Cold Spring Harbor.
    16. Singh, D., Kumar, S., Singh, B., Bardhan, D. (2014). Economic losses due to important diseases of bovines in central India. Vet. World, 7(8).
    17. Thakur, S., Singh, M., Aseri, G.K., Verma, A., Vineeth, M.R., Rayees, M., Arya, A. (2017). Identification of point mutation in TLR2 gene and its association with mastitis in water buffalo. Indian J. Anim. Res. 52(9).
    18. Van Heel, D.A., Udalova, I.A., De Silva, A.P., McGovern, D.P., Kinouchi, Y., Hull, J., et al. (2002). Inflammatory bowel disease is associated with a TNF-á polymorphism that affects an interaction between the OCT1 and NF-êB transcription factors. Hum Mol. Genet. 11(11): 1281-1289.
    19. Wen, Y., Cheng, X., Zhao, S. (2018). Nucleotide variants of the NRAMP1 gene in pigs and their effects on disease resistance. Indian J. Anim. Res. 52 (4): 490-496.
    20. Werth, V.P., Zhang, W., Dortzbach, K., Sullivan, K. (2000). Association of a Promoter Polymorphism of Tumor Necrosis Factor-á with Subacute Cutaneous Lupus Erythematosus and Distinct Photoregulation of Transcription1. J. Invest. Dermatol. 115(4): 726-730.
    21. Wojdak-Maksymiec K., Szyda, J., Strabel, T. (2013). Parity-dependent association between TNF-á and LTF gene polymorphisms and clinical mastitis in dairy cattle. BMC Vet Res. 9(1): 114.
    22. Yea, S.S., Yang, Y.I., Jang, W.H., Lee, Y.J., Bae, H.S., Paik, K.H. (2001). Association between TNF-á promoter polymorphism and Helicobacter pylori cagA subtype infection. J. Clin. Pathol. 54(9): 703-706. 
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