Allelic diversity at MHC class II DQ loci in buffalo (Bubalus bubalis): evidence for duplication.
The genetic diversity of MHC class II DQ genes was investigated in riverine buffalo (Bubalus bubalis) by PCR-RFLP and sequencing. Highly variable regions (exons 2-3) of DQ genes were amplified from 152 buffaloes and genotyped by PCR-RFLP. Alleles identified by differential restriction patterns were sequenced for the characterization. PCR-RFLP was a rapid method to discriminate between DQA1 and duplicated DQA2 genes in buffalo, however, the method appeared to be inadequate for determining the more complicated DQB genotypes. A total of 7 and 10 alleles were identified for DQA and DQB loci, respectively. Nucleotide as well as amino acid variations among DQ alleles particularly at peptide binding regions were high. Such variations were as expected higher in DQB than DQA alleles. The phylogenetic analysis for both genes revealed the grouping of alleles into two major sub-groups with higher genetic divergence. High divergence among DQ allelic families and the isolation of two diverse DQA and DQB sequences from individual samples indicated duplication of DQ loci was similar in buffalo to other ruminants.
Niranjan
Saket K
SK
Animal Genetics Division, Indian Veterinary Research Institute, Izatnagar, UP 243122, India. saketniranjan@gmail.com
Deb
Sitangsu M
SM
Kumar
Subodh
S
Mitra
Abhijit
A
Sharma
Arjava
A
Sakaram
Durgam
D
Naskar
Soumen
S
Sharma
Deepak
D
Sharma
Sita R
SR
D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002020:Buffaloes / Q000235:genetics* / Q000276:immunology*; D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D005802:Genes, MHC Class II; D014644:Genetic Variation; D000949:Histocompatibility Antigens Class II / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D017386:Sequence Homology, Amino Acid
D017931:DNA Primers; D000949:Histocompatibility Antigens Class II