Sequence diversity of major histo-compatibility complex class II DQA1 in Indian Tharparkar cattle: novel alleles and in-silico analysis.

Autor: Sahoo NR; Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India., Kumar P; Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India., Khan MF; Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India., Mourya R; Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India., Ravikumar GVPPS; Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.; National Institute of Animal Biotechnology, Hyderabad, Telangana, India., Tiwari AK; Central Instrumentation Facility, Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
Jazyk: angličtina
Zdroj: HLA [HLA] 2019 Jun; Vol. 93 (6), pp. 451-461. Date of Electronic Publication: 2019 Apr 04.
DOI: 10.1111/tan.13521
Abstrakt: Exon 2 of MHC class II gene codes for the first domain of the molecule that forms the peptide-binding groove and its polymorphism partly explains functional MHC diversity. A 850 bp DQA1 gene fragment spanning from intron I to exon III was typed by sequencing of 40 Tharparkar cattle of various agro-climatic zones of northern India along with 10 Tharparkar crossbreds. On analysis of nucleotide sequences, a total of 30 polymorphic sites (1 insertion and 29 SNPs) were identified in 14 MHC alleles leading to amino acid changes in 5 places in 249 bp (exon 2). Five new BoLa DQA1 alleles were identified and reported. The within group mean distance was highest in Tharparkar herd of Bikaner (0.045) and lowest (0.020) in that of Surathgarh (breeding tract) whereas, between groups mean distance was highest in Bikaner Tharparkar-Suratgarh Tharparkar pair. There was excess of nonsynonymous over synonymous nucleotide substitutions in the present study. The effects of these substitutions were predicted using I-Mutant and Panther online resources. The mean ratio of dN/dS was found to be >1.0 at 12 codons with two mutation hotspots at 13th codon (P = 0.002) and 64th codon (P = 0.01). The phylo-geographic analysis revealed that alleles 5, 7 and 13 formed a different cluster with alleles 7 and 13 grouped by the most frequent allele (BoLa-DQA*1401).
(© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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