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Updated: Dec 13, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Diversity analysis at MHC class II DQA locus in buffalo (Bubalus bubalis) indicates extensive duplication and
Shailendra Kumar Mishra1, Saket Kumar Niranjan2, Ravinder Singh2
1ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India; School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201310, India.
Abstract:
Variation at MHC Class II-DQA locus in riverine and swamp buffaloes (Bubu) has been explored in this study. Through sequencing of buffalo DQA, 48 nucleotide variants identified from 17 individuals, reporting 42 novel alleles, including one pseudogene. Individual animal displayed two to seven variants, suggesting the presence of more than two Bubu-DQA loci, as an evidence of extensive duplication. dN values were found to be higher than dS values at peptide binding sites, separately for riverine and swamp buffaloes, indicating locus being under positive selection. Evolutionary analysis revealed numerous trans-species polymorphism with alleles from water buffalo assigned to at least three different loci (Bubu-DQA1, DQA2, DQA3). Alleles of both the sub-species intermixed within the cluster, showing convergent evolution of MHC alleles in bovines. The results thus suggest that both riverine and swamp buffaloes share con-current arrangement of DQA region, comparable to cattle in terms of copy number and population polymorphism.
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