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

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...

Full description

Saved in:
Bibliographic Details
Published in:Immunogenetics (New York) 2016-07, Vol.68 (6-7), p.439-447
Main Authors: Mishra, S. K., Niranjan, S. K., Banerjee, B., Dubey, P. K., Gonge, D. S., Mishra, B. P., Kataria, R. S.
Format: Article
Language:English
Subjects:
Alleles
Allergology
Amino Acid Sequence
Animals
Biological Evolution
Biomedical and Life Sciences
Biomedicine
Bubalus bubalis
Buffaloes - genetics
Cattle
Cell Biology
Chromosomes
Gene Function
Genes
Genetic diversity
Genetic Variation - genetics
Haplotypes
Haplotypes - genetics
Histocompatibility Antigens Class II - genetics
Human Genetics
Immunology
Original Article
Peptides
Phylogeny
Polymerase Chain Reaction
Polymorphism
Polymorphism, Restriction Fragment Length
Sequence Analysis, DNA - methods
Sequence Homology, Amino Acid
Species Specificity
Thermal cycling
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0093-7711
1432-1211
DOI:10.1007/s00251-016-0915-0