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High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes

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Abstract

In this study, genetic diversity analysis of MHC class II-DQA locus helped in identification of 25 new Bubu-DQA nucleotide sequences in swamp buffaloes (Bubalus bubalis carabanesis, Bubu). Phylogenetic analysis revealed the distribution of the buffalo DQA sequences in two major clusters of DQA1 and DQA2 genes, sharing common lineages with corresponding cattle alleles, possibly due to trans-species evolution. However, a highly divergent sequence, Bubu-DQA*2501, homologous to cattle (BoLA) DQA3 allele, was identified, indicating the existence of an additional locus; putative DQA3 in buffalo. PCR-RFLP analysis revealed extensive duplication of DQA locus in swamp buffaloes, sharing DQA1, DQA2, and DQA3 alleles in different combinations in duplicated haplotypes. Higher dN than dS values and Wu–Kabat variability at peptide-binding regions in Bubu-DQA indicated high polymorphism with balancing selection. Levels of genetic diversity within DQA sequences and duplication in a small population of swamp buffalo indicate the genetic richness of the species, important for fitness.

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Acknowledgments

The authors wish to acknowledge the support received from Director of NBAGR and NDRI, Karnal, for use of facilities. Technical assistance provided by Mr. Naresh Kumar Yadav is also duly acknowledged.

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Authors and Affiliations

  1. National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India

    S. K. Mishra, S. K. Niranjan, D. S. Gonge & R. S. Kataria

  2. School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India

    B. Banerjee

  3. Immune Regulation, World Premier International Research Center, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka Prefecture, 5650871, Japan

    P. K. Dubey

  4. Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India

    B. P. Mishra

Authors
  1. S. K. Mishra
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  2. S. K. Niranjan
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  3. B. Banerjee
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  4. P. K. Dubey
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  5. D. S. Gonge
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  6. B. P. Mishra
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  7. R. S. Kataria
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Corresponding authors

Correspondence to S. K. Niranjan or R. S. Kataria.

Electronic supplementary materials

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ESM 1

Supplementary Figure 1: Mismatch distribution for Bubu-DQA and BoLA-DQA. Vertical axis, showing frequencies and horizontal axis showing mean number of pairwise differences. (DOCX 36 kb)

ESM 2

Supplementary Table 1: Bubu-DQA alleles, their types, size and variation. Supplementary Table 2: Distribution of different DQA alleles in animals having selected haplotype (DOCX 25 kb)

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Mishra, S.K., Niranjan, S.K., Banerjee, B. et al. High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes. Immunogenetics 68, 439–447 (2016). https://doi.org/10.1007/s00251-016-0915-0

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  • DOI: https://doi.org/10.1007/s00251-016-0915-0

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