Allelic diversity and locus duplication at the MHC Class II DQ sub‐region in the Indian yak population

Abstract

In bovines, MHC-DQ loci are highly polymorphic and duplicated, which broadens the immunological repertoire. 1-3 Here, we report on the diversity at the DQ subregion in the yak (Bos grunniens, Bogr).Thirty-seven yaks were sampled in Arunachal Pradesh (India). After amplification of exon 2 from the DQA and DQB genes, 30 samples yielded readable nucleotide sequences covering both genes (Table S1). Twelve DQA and DQB PCR products with heterogeneous sequences were cloned, and six random positive clones were sequenced for each sample. Sequences of PCR products from homozygous samples and cloned sequences were submitted to NCBI (accession nos. KP999914-43, KP233802).We identified 13 DQA alleles in 13 animals and 18 DQB alleles in 22 animals. Nucleotide diversity at exon 2 was higher in DQA (0.130) than in DQB (0.074) alleles. Ten peptide binding sites 4 in DQB and three in DQA had a Wu-Kabat variability index of greater than 4, suggesting a major role of the DQB locus in adaptive selection (Fig. 1). The dN/dS values for DQA (0.63) and DQB (4.08) indicated that only DQB is under positive selection.Three yaks were found to be homozygous, and 10 were heterozygous and/or duplicated at both DQA and DQB (Table S1). The other 17 yaks were heterozygous or duplicated at either DQA or DQB. More than two alleles for both DQA and DQB in three yaks indicated duplication of both loci, which for DQA has also been observed in water buffalo. 5 For DQB, locus duplication could be confirmed in at least four yaks by the presence of more than two alleles. Phylogenetic analysis revealed different major clusters and an intermingling of DQA and DQB alleles respectively from yak and other bovines (Fig. S1). The yak DQA alleles belong to the DQA1 (alleles 3, 5 to 10, 12 and 13) or DQA2 (alleles 1, 2, 4 and 11) haplogroups. DQB allele 8 has a separate position, and other yak DQB alleles again are grouped into two major clusters. Both phylograms demonstrate that the DQ alleles are shared by bovine species and often evolved by duplication.Acknowledgements: The authors acknowledge the funding support received from the ICAR-NBAGR director under institute project No. 7.56.