title: High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes.
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.
authors.affiliation: National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
authors.forename: S K
authors.initials: SK
authors.lastname: Mishra
authors.affiliation: National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India. saketniranjan@gmail.com.
authors.forename: S K
authors.initials: SK
authors.lastname: Niranjan
authors.affiliation: School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India.
authors.forename: B
authors.initials: B
authors.lastname: Banerjee
authors.affiliation: Immune Regulation, World Premier International Research Center, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka Prefecture, 5650871, Japan.
authors.forename: P K
authors.initials: PK
authors.lastname: Dubey
authors.affiliation: National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
authors.forename: D S
authors.initials: DS
authors.lastname: Gonge
authors.affiliation: Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
authors.forename: B P
authors.initials: BP
authors.lastname: Mishra
authors.affiliation: National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India. katariaranji@yahoo.co.in.
authors.forename: R S
authors.initials: RS
authors.lastname: Kataria
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D002020:Buffaloes / Q000235:genetics*; D002417:Cattle; D014644:Genetic Variation / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D000949:Histocompatibility Antigens Class II / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA / Q000379:methods; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
chemical_list: D000949:Histocompatibility Antigens Class II
keywords: Allelic diversity; Bubalus bubalis; Duplicated haplotype; MHC-DQA; Peptide-binding site; Phylogeny