Banner
Current IssueEditorial BoardOnline First ArticlesArchive
Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 52 issue 12 (december 2018) : 1684-1687,   Doi: 10.18805/ijar.B-902

Detection of Polymorphisms in the exon 2 region of the DRB3 gene in Naqu yaks

L
Luo-Bu Danjiu
T
Tian-Wu An
W
Wang-Dui Basang
Y
Yan-Bin Zhu
S
Shi-Cheng He
X
Xiao-Lin Luo
1Naqu Grassland Station, Naqu,852000, China.
Cite article:- Danjiu Luo-Bu, An Tian-Wu, Basang Wang-Dui, Zhu Yan-Bin, He Shi-Cheng, Luo Xiao-Lin (2018). Detection of Polymorphisms in the exon 2 region of the DRB3 gene in Naqu yaks. Indian Journal of Animal Research. 52(12): 1684-1687. doi: 10.18805/ijar.B-902.

ABSTRACT

In the present study, the second exon of the DRB3 gene of the major histocompatibility complex (MHC) from 94 Naqu yaks was amplified and sequenced, and its variation and phylogeny of nucleotides and haplotypes were analyzed. The results showed that 71 single-nucleotide polymorphism (SNPs) were identified, and 147 haplotypes were reconstructed. The average number of nucleotide differences was 16.80965, the nucleotide diversity was 0.05982, and the haplotype diversity was 0.9964. In addition, fewer haplotypes of exon 2 of DRB3 were shared among different ecotype strains, and a large number of privatized haplotypes (93.2%) were observed. Based on the results of the present study, the high genetic diversity of Naqu yaks could reflect their epidemic history and geographical distribution. In addition, the abundant diversity in the MHC region was estimated not only to enhance the current understanding of the status of genetic diversity for the conservation of Naqu yaks but also to improve the relative environmental suitability and disease-resistant breeding of these animals. 

REFERENCES

  1. Acevedo-Whitehouse K, Gulland FMD, Bowen L (2018). MHC class II DRB diversity predicts antigen recognition and is associated with disease severity in California sea lions naturally infected with Leptospira interrogans. Infect Genet Evol. 57:158-165. 
  2. Acevedo-Whitehouse K, Gulland FMD, Bowen L.MHC class II DRB diversity predicts antigen recognition and is associated with disease severity in California sea lions naturally infected with Leptospira interrogans. Infect Genet Evol. 2018, 57:158-165.
  3. Birnbaum ME, Mendoza JL, Sethi DK, Dong S, Glanville J, Dobbins J, Ozkan E, Davis MM, Wucherpfennig KW, Garcia KC (2014). Deconstructing the peptide-MHC specificity of T cell recognition.Cell. 157(5):1073-87.
  4. China National Commission of Animal Genetic Resources (2011). Animal genetic resources in China: Sheep and goats. Beijing: Chinese Agricultural Press,
  5. Cornwall DH, Kubinak JL, Zachary E, Stark DL, Seipel D, Potts WK (2017). Experimental manipulation of population-level MHC diversity controls pathogen virulence evolution in Mus musculus. J Evol Biol. doi: 10.1111/jeb.13225
  6. E GX, Huang YF, Zhao YJ, Ma YH, Na RS, Zhang JH, Gao HJ, Wu X. (2015). Genetic variability of ten Chinese indigenous goats using MHC-linked microsatellite markers.Vet Immunol Immunopathol. 167(3-4):196-9. 
  7. E GX, Huang YF, Zhao YJ, Na RS (2015). Variability with altitude of major histocompatibility complex-related microsatellite loci in goats from Southwest China. Genet Mol Res., 14(4):14629-36.
  8. Excoffier, L., and H.E.L. Lischer (2010). Arlequin 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10: 564–567.
  9. Gabriel SS, Bon N, Chen J, Wekerle T, Bushell A, Fehr T, Cippà PE (2016).Distinctive Expression of Bcl-2 factors in regulatory T Cells determines a pharmacological target to induce immunological tolerance. Front Immunol. 7: 73. doi: 10.3389/    fimmu.2016.00073. eCollection 2016.
  10. Kang XZ, Erdemtu, Jiang JQ, Chen ZM, Liu TY, Yitegeltu, Sharhu, Tu Y (2014). Research progress on major histocompatibility complex (MHC) gene. China Animal Husbandry & Veterinary Medicine, 41(5): 28-33.
  11. Kumar S, Stecher G, Tamura K. MEGA7 (2016) Molecular Evolutionary genetics analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016, 33(7):1870-4.
  12. Lai SJ, Wang L, Liu YP, Li XW (2005). Study on Mitochondrial DNA genetic polymorphism of some yak breeds in china. Acta Genetica Sinica. 32(5): 463-470.
  13. Lewin HA, Russell GC, Glass EJ (1999). Comparative organization and function of the major histocompatibility complex of domesticated cattle. Immunol Rev. 167:145-58.
  14. Miretti MM, Ferro JA, Lara MA, Contel EP (2001). Restriction fragment length polymorphism (RFLP) in exon 2 of the BoLA-DRB3 gene in South American cattle. Biochem Genet. 39(9-10):311-24.
  15. Nei M. and Kumar S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, New York.
  16. Osborne AJ, Pearson J, Negro SS, Chilvers BL, Kennedy MA, Gemmell NJ (2015). Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics. Mol Ecol. 24(7):1419-32. doi: 10.1111/mec.13128.
  17. Posada D j(2008). ModelTest: Phylogenetic model averaging. Mole Biol Evol. 25: 1253-1256
  18. Rojana-udomsart A, Mitrpant C, James I, Witt C, Needham M, Day T, Kiers L, Corbett A, Martinez P, Wilton SD, Mastaglia FL (2013). Analysis of HLA-DRB3 alleles and supertypical genotypes in the MHC Class II region in sporadic inclusion body myositis. J Neuroimmunol. 254(1-2):174-7. doi: 10.1016/j.jneuroim.2012.09.003
  19. Rozas, J. and Rozas, R. DnaSP, (1995). DNA sequence polymorphism: an interactive program for estimating Population Genetics parameters from DNA sequence data. Comput. Applic. Biosci. 11: 621-625.
  20. Sambrook J, and Russell D (2001). Molecular Cloning: A Laboratory Manual (M), 3rd ed. Clod Spring Harbor Laboratory Press. New York:
  21. Sha RN, An TW, E GX, Han JL (2016). Polymorphism study on DRB3 Gene Exon 2 in Tianzhu White yak and Gannan Yak Arlud. China Animal Husbandry & Veterinary Medicine. 43(3): 746-753
  22. Slatkin, M (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics. 139: 457-462.
  23. Song QQ, Zhong JC, Zhang CF, Xin JW, Ji QM, Chai ZX (2014). Analysis on genetic diversity and phyletic evolution of mitochondrial DNA from Tibetan yaks. Acta Theriologica Sinica. 34(4): 356-365.
  24. Tajima, F (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123 (3): 585–95.
  25. Takahata N, Nei M (1990). Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics. 124(4):967-78.
  26. Tian ZL (2016). Polymorphism and Sequence Characteristics in BoL A-DRB1 and DRB2 Genes in Yak (M). Lanzhou: Gansu Agricultural University.
  27. Zhang Y, Huang B (2017). The Development and Diversity of ILCs, NK Cells and Their Relevance in Health and Diseases. Adv Exp Med Biol. 1024: 225-244. 
  28. Jukes T.H. and Cantor C.R (1969). Evolution of protein molecules. In Munro HN, editor, Mammalian Protein Metabolism, pp. 21-132, Academic Press, New York.
  29. Felsenstein J (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39: 783-791. 
Published In
Indian Journal of Animal Research
Article Metrics
Metrics Icon
0
Views
0
Citations
Reviewed By
Share Article
Download Article
In this Article
    Contact us
    Follow us

    Research Article

    volume 52 issue 12 (december 2018) : 1684-1687,   Doi: 10.18805/ijar.B-902

    Detection of Polymorphisms in the exon 2 region of the DRB3 gene in Naqu yaks

    L
    Luo-Bu Danjiu
    T
    Tian-Wu An
    W
    Wang-Dui Basang
    Y
    Yan-Bin Zhu
    S
    Shi-Cheng He
    X
    Xiao-Lin Luo
    1Naqu Grassland Station, Naqu,852000, China.
    Cite article:- Danjiu Luo-Bu, An Tian-Wu, Basang Wang-Dui, Zhu Yan-Bin, He Shi-Cheng, Luo Xiao-Lin (2018). Detection of Polymorphisms in the exon 2 region of the DRB3 gene in Naqu yaks. Indian Journal of Animal Research. 52(12): 1684-1687. doi: 10.18805/ijar.B-902.

    ABSTRACT

    In the present study, the second exon of the DRB3 gene of the major histocompatibility complex (MHC) from 94 Naqu yaks was amplified and sequenced, and its variation and phylogeny of nucleotides and haplotypes were analyzed. The results showed that 71 single-nucleotide polymorphism (SNPs) were identified, and 147 haplotypes were reconstructed. The average number of nucleotide differences was 16.80965, the nucleotide diversity was 0.05982, and the haplotype diversity was 0.9964. In addition, fewer haplotypes of exon 2 of DRB3 were shared among different ecotype strains, and a large number of privatized haplotypes (93.2%) were observed. Based on the results of the present study, the high genetic diversity of Naqu yaks could reflect their epidemic history and geographical distribution. In addition, the abundant diversity in the MHC region was estimated not only to enhance the current understanding of the status of genetic diversity for the conservation of Naqu yaks but also to improve the relative environmental suitability and disease-resistant breeding of these animals. 

    REFERENCES

    1. Acevedo-Whitehouse K, Gulland FMD, Bowen L (2018). MHC class II DRB diversity predicts antigen recognition and is associated with disease severity in California sea lions naturally infected with Leptospira interrogans. Infect Genet Evol. 57:158-165. 
    2. Acevedo-Whitehouse K, Gulland FMD, Bowen L.MHC class II DRB diversity predicts antigen recognition and is associated with disease severity in California sea lions naturally infected with Leptospira interrogans. Infect Genet Evol. 2018, 57:158-165.
    3. Birnbaum ME, Mendoza JL, Sethi DK, Dong S, Glanville J, Dobbins J, Ozkan E, Davis MM, Wucherpfennig KW, Garcia KC (2014). Deconstructing the peptide-MHC specificity of T cell recognition.Cell. 157(5):1073-87.
    4. China National Commission of Animal Genetic Resources (2011). Animal genetic resources in China: Sheep and goats. Beijing: Chinese Agricultural Press,
    5. Cornwall DH, Kubinak JL, Zachary E, Stark DL, Seipel D, Potts WK (2017). Experimental manipulation of population-level MHC diversity controls pathogen virulence evolution in Mus musculus. J Evol Biol. doi: 10.1111/jeb.13225
    6. E GX, Huang YF, Zhao YJ, Ma YH, Na RS, Zhang JH, Gao HJ, Wu X. (2015). Genetic variability of ten Chinese indigenous goats using MHC-linked microsatellite markers.Vet Immunol Immunopathol. 167(3-4):196-9. 
    7. E GX, Huang YF, Zhao YJ, Na RS (2015). Variability with altitude of major histocompatibility complex-related microsatellite loci in goats from Southwest China. Genet Mol Res., 14(4):14629-36.
    8. Excoffier, L., and H.E.L. Lischer (2010). Arlequin 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10: 564–567.
    9. Gabriel SS, Bon N, Chen J, Wekerle T, Bushell A, Fehr T, Cippà PE (2016).Distinctive Expression of Bcl-2 factors in regulatory T Cells determines a pharmacological target to induce immunological tolerance. Front Immunol. 7: 73. doi: 10.3389/    fimmu.2016.00073. eCollection 2016.
    10. Kang XZ, Erdemtu, Jiang JQ, Chen ZM, Liu TY, Yitegeltu, Sharhu, Tu Y (2014). Research progress on major histocompatibility complex (MHC) gene. China Animal Husbandry & Veterinary Medicine, 41(5): 28-33.
    11. Kumar S, Stecher G, Tamura K. MEGA7 (2016) Molecular Evolutionary genetics analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016, 33(7):1870-4.
    12. Lai SJ, Wang L, Liu YP, Li XW (2005). Study on Mitochondrial DNA genetic polymorphism of some yak breeds in china. Acta Genetica Sinica. 32(5): 463-470.
    13. Lewin HA, Russell GC, Glass EJ (1999). Comparative organization and function of the major histocompatibility complex of domesticated cattle. Immunol Rev. 167:145-58.
    14. Miretti MM, Ferro JA, Lara MA, Contel EP (2001). Restriction fragment length polymorphism (RFLP) in exon 2 of the BoLA-DRB3 gene in South American cattle. Biochem Genet. 39(9-10):311-24.
    15. Nei M. and Kumar S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, New York.
    16. Osborne AJ, Pearson J, Negro SS, Chilvers BL, Kennedy MA, Gemmell NJ (2015). Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics. Mol Ecol. 24(7):1419-32. doi: 10.1111/mec.13128.
    17. Posada D j(2008). ModelTest: Phylogenetic model averaging. Mole Biol Evol. 25: 1253-1256
    18. Rojana-udomsart A, Mitrpant C, James I, Witt C, Needham M, Day T, Kiers L, Corbett A, Martinez P, Wilton SD, Mastaglia FL (2013). Analysis of HLA-DRB3 alleles and supertypical genotypes in the MHC Class II region in sporadic inclusion body myositis. J Neuroimmunol. 254(1-2):174-7. doi: 10.1016/j.jneuroim.2012.09.003
    19. Rozas, J. and Rozas, R. DnaSP, (1995). DNA sequence polymorphism: an interactive program for estimating Population Genetics parameters from DNA sequence data. Comput. Applic. Biosci. 11: 621-625.
    20. Sambrook J, and Russell D (2001). Molecular Cloning: A Laboratory Manual (M), 3rd ed. Clod Spring Harbor Laboratory Press. New York:
    21. Sha RN, An TW, E GX, Han JL (2016). Polymorphism study on DRB3 Gene Exon 2 in Tianzhu White yak and Gannan Yak Arlud. China Animal Husbandry & Veterinary Medicine. 43(3): 746-753
    22. Slatkin, M (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics. 139: 457-462.
    23. Song QQ, Zhong JC, Zhang CF, Xin JW, Ji QM, Chai ZX (2014). Analysis on genetic diversity and phyletic evolution of mitochondrial DNA from Tibetan yaks. Acta Theriologica Sinica. 34(4): 356-365.
    24. Tajima, F (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123 (3): 585–95.
    25. Takahata N, Nei M (1990). Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics. 124(4):967-78.
    26. Tian ZL (2016). Polymorphism and Sequence Characteristics in BoL A-DRB1 and DRB2 Genes in Yak (M). Lanzhou: Gansu Agricultural University.
    27. Zhang Y, Huang B (2017). The Development and Diversity of ILCs, NK Cells and Their Relevance in Health and Diseases. Adv Exp Med Biol. 1024: 225-244. 
    28. Jukes T.H. and Cantor C.R (1969). Evolution of protein molecules. In Munro HN, editor, Mammalian Protein Metabolism, pp. 21-132, Academic Press, New York.
    29. Felsenstein J (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 39: 783-791. 
    In this Article
      Contact us
      Follow us
      Published In
      Indian Journal of Animal Research

      Editorial Board

      View all (0)