Characterization of BoLA class II DQA and DQB by PCR-RFLP, cloning, and sequencing reveals sequence diversity in crossbred cattle

The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, revealing seven (HaeIII-A-G) and three (XbaI A...

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Bibliographic Details
Published in:Animal biotechnology 2023-11, Vol.34 (4), p.955-965
Main Authors: Parasar, Parveen, Bhushan, Bharat, Panigrahi, Manjit, Kumar, Harshit, Kaisa, Kaiho, Dutt, Triveni
Format: Article
Language:English
Subjects:
Alleles
Amino Acid Sequence
Amino acids
Animals
Cattle
Cattle - genetics
Cloning
Cloning, Molecular
diversity
DQB gene
Enzymes
Gene polymorphism
Genes
Genotypes
Nucleotides
PCR-RFLP
Phylogeny
Polymerase chain reaction
Polymerase Chain Reaction - veterinary
Polymorphism
Polymorphism, Restriction Fragment Length
restriction enzymes
Restriction fragment length polymorphism
sequence
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Summary:The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, revealing seven (HaeIII-A-G) and three (XbaI A-C) motifs, respectively. The BoLA-DQB gene was analyzed using PCR-RFLP with PstI and TaqI restriction enzymes, yielding five restriction motifs for each restriction enzyme (PstI-A-E and TaqI-A-E). In crossbred cattle, addition, deletion, and substitutions were observed in distinct sequences, resulting in variations in overall gene length. Changes in nucleotides at positions 64-80, 110-200, and 207-264 were largely responsible for polymorphism in DQA exon 2. The phylogenetic analysis predicted a high degree of nucleotide and amino acid changes in DQA exon 2-3 and DQB exon 2. DQA genes had a nucleotide dissimilarity of 0.3-25.4 percent, while DQB genes had a nucleotide dissimilarity of 1.5-14.3 percent. We cloned and sequenced 20 genotypes based on PCR-RFLP of the DQA and DQB genes. The current study observed variation in the DQA and DQB genes and will serve as a foundation for future research on the BoLA DQA and DQB genes.
ISSN:1049-5398
1532-2378
DOI:10.1080/10495398.2021.2006205