Allelic diversity at MHC class II DQ loci in buffalo (Bubalus bubalis): Evidence for duplication

Niranjan, S. K.; Deb, S. M.; Kumar, Subodh; Mitra, Abhijit; Sharma, Alisha; Sakaram, D.; Naskar, S.; Sharma, Deepak; Sharma, Sita R.

doi:10.1016/j.vetimm.2010.07.014

Cited by 13 publications

(9 citation statements)

References 28 publications

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“…The d N and d S are estimated by the modified Nei-Gojobori method. a : present study; b : Chen et al [34]; c : Goda et al [36]; d : Marsden et al [91]; e : Castro-Prieto et al [92]; f : Becker et al [93]; g : Niranjan et al [94]; h : Sena et al [95]; i : Diaz et al [96]; j : Meyer-Lucht and Sommer [97]; k : An individual that has the putative pseudogene, Urth-DQB*3201 , is excluded. * : The number of MHC variants may be derived from multiple loci.…”

Section: Resultsmentioning

confidence: 99%

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

et al. 2012

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BackgroundThe major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations.ResultsAmong 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected.ConclusionsThe low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that the Japanese black bears may also retain more potential resistance against pathogens than other endangered mammalian species. To prevent further decline of potential resistance against pathogens, a conservation policy for the Japanese black bear should be designed to maintain MHC rare variants in each local population.

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Section: Resultsmentioning

confidence: 99%

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

et al. 2012

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“…MHC genes, encoding the MHC molecules are prime candidates for the investigation of genetic variation in the host resistance to infection. These genes have attracted much attention in farm animals due to the need of improved methods of disease control through the design of novel vaccines and selection of disease resistant animals (NIRANJAN et al, 2010). In vertebrates, the MHC is vital for foreign antigen recognition and the immune response to infections.…”

Section: Introductionmentioning

confidence: 99%

“…The MHC class II genes encode polymorphic cell-surface glycoproteins comprising non-covalently linked α and β subunits. DQ genes of MHC class II region encode for α (DQA) and β (DQB) chains of the molecule (NIRANJAN et al, 2010). The second exon has been shown to be highly polymorphic and under positive selection, and the class II DQA gene has recently attracted more attention (AMILLS et al, 2008;JUNYING et al, 2008;MIYASAKA et al, 2011;HOU et al, 2011;DENG et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Nucleotide sequence variability analysis of Major Histocompatibility Complex Class II DQA1 gene in Nigerian goats

et al. 2017

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Wheto and I. G. Imumorin (2017): Nucleotide sequence variability analysis of major histocompatibility complex class II DQA1 gene in Nigerian goats. Vol 49, No.3,[865][866][867][868][869][870][871][872][873][874] Major Histocompatibility Complex (MHC) molecules loaded with peptides derived from invading pathogens are recognised by the immune system to produce a highly effective and specific response against foreign pathogens. A 310-bp fragment of exon 2 of the MHC Class II DQA1 gene was amplified in 27 animals made up of three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SH)]. Twenty amino acid polymorphic sites were found in Nigerian goats. Comparison of predicted amino acid residues of DQA1 exon 2 alleles of Nigerian goats with similar alleles from other caprine species revealed considerable congruence in amino acid 866 GENETIKA, Vol. 49, No3, 865-874, 2017 substitution pattern. A significant positive selection signature was detected at the DQA1 locus of Nigerian goats in that non-synonymous substitutions occurred at a faster rate compared to synonymous substitutions (dN:dS ratio = 1.28 ; Z-Statistics= 1.634; P<0.05). The evolutionary tree constructed using UPGMA, revealed that the southern WAD goat appeared to be more related to the northern RS than SH goat at the DQA1 locus. It will be interesting therefore, for future studies to investigate the association of the genetic variants in DQA1 gene of Nigerian goats with resistance/susceptiblity to diseases in order to conserve these precious animal genetic resources.

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“…Maximum (27) amino acid differences between two were observed in the b1 domain. Other authors also found higher substitutions in b1 domain of DQB sequences within and between the species (Traul et al 2005;Niranjan et al 2010). Within the b1 domain, nine out of 23 peptide binding sites (PBS) were substituted in Bubu-DQB compared to BoLA-DQB*0101 sequence.…”

Section: Resultsmentioning

confidence: 88%

Genetic characterisation of buffalo MHC (Bubu)-DQB cDNA molecule

Niranjan

Deb

Kumar

et al. 2011

Journal of Applied Animal Research

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A 771 nucleotide long cDNA molecule corresponding to major histocompatibility complex (MHC)-DQB gene was amplified, cloned and sequenced from water buffalo (Bubalus bubalis). Open reading frame of the Bubu-DQB sequence was short by three nucleotides from the DQB genes of the other ruminants. Nucleotide similarity of Bubu-DQB was highest with cattle DQB alleles (84Á97%), followed by goat (88.8%) and sheep (87.5%). The sequence comparison revealed that the DQB gene was highly variable in buffalo particularly, in exon 2 (b1 domain). A total of 45 amino acid substitutions were identified in Bubu-DQB compared to cattle DQB*0101 sequence, with a maximum (27) in b1 domain. The residues involved in antigen binding and heterodimer formation were found to be different in buffalo DQB sequence compared to other species. Phylogenetic study showed that the Bubu-DQB has evolved prior to the diversification of common DQB alleles in ruminants. Our study revealed the high genetic variation in the DQB gene in buffalo, which might have generated to recognise species specific antigens.

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Allelic diversity at MHC class II DQ loci in buffalo (Bubalus bubalis): Evidence for duplication

Cited by 13 publications

References 28 publications

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

Nucleotide sequence variability analysis of Major Histocompatibility Complex Class II DQA1 gene in Nigerian goats

Genetic characterisation of buffalo MHC (Bubu)-DQB cDNA molecule

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