The diversity of bovine MHC class II DRB3 and DQA1 alleles in different herds of Japanese Black and Holstein cattle in Japan

Miyasaka, T.; Takeshima, Shin‐nosuke; Matsumoto, Yuki; Kobayashi, Naohiko; Matsuhashi, Tomohiro; Miyazaki, Yasuo; Tanabe, Yasutaka; Ishibashi, Ko; Sentsui, Hiroshi; Aida, Yoko

doi:10.1016/j.gene.2010.10.007

Cited by 54 publications

(69 citation statements)

References 37 publications

(54 reference statements)

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“…We have identified highly antigenic CD4 + T-cell epitopes on T4SS proteins VirB9-1, VirB9-2, and VirB10 presented by BoLA class II DR and DQ molecules that are encoded by alleles prevalent among Holstein cattle worldwide. Similar frequencies of the MHC class II alleles studied here were found for Holstein cattle in Japan, where the combined frequencies were 81.2%, 86.9%, 90.3%, and 95.2% in four populations studied (Miyasaka et al, 2011; Takeshima et al, 2003), in Ontario, Canada, where the combined frequency was 89.5% (Sharif et al, 1998), in Iran, where the combined frequencies were 73.2%, 75.5%, 78.1%, and 80.2% in several studies (Nassiry et al, 2008; Pashimi et al, 2009), and in Europe, where the combined frequency was 89.5% (Nassiry et al, 2008). Inclusion of VirB9-1, VirB9-2, and VirB10 peptides linked together in a multiple-antigen and peptide-based vaccine will not only provide more than one immunogenic peptide, but will offer the opportunity for increased T-cell dependent IgG responses upon infection if B cell epitopes are also included (Morse et al, 2012).…”

Section: Discussionsupporting

confidence: 83%

Breadth of the CD4+ T cell response to Anaplasma marginale VirB9-1, VirB9-2 and VirB10 and MHC class II DR and DQ restriction elements

et al. 2012

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MHC class II molecules influence antigen-specific CD4+ T-lymphocyte responses primed by immunization and infection. CD4+ T-cell responses are important for controlling infection by many bacterial pathogens including Anaplasma marginale, and are observed in cattle immunized with the protective A. marginale outer membrane (OM) vaccine. Immunogenic proteins that comprise the protective OM vaccine include type IV secretion system (T4SS) proteins VirB9-1, VirB9-2, and VirB10, candidates for inclusion in a multi-epitope vaccine. Our goal was to determine the breadth of the VirB9-1, VirB9-2, and VirB10 T-cell response and MHC class II restriction elements in six cattle with different MHC class II haplotypes, defined by DRB3, DQA, and DQB allele combinations for each animal. Overlapping peptides spanning each T4SS protein were tested in T-cell proliferation assays with autologous antigen presenting cells (APC) and artificial APC expressing combinations of bovine DR and DQ molecules. Twenty immunostimulatory peptides were identified; three representing two or more epitopes in VirB9-1, ten representing eight or more epitopes in VirB9-2, and seven representing seven or more epitopes in VirB10. Of eight DRA/DRB3 molecules, four presented 15 peptides, which was biased as DRA/DRB3*1201 presented ten and DRA/DRB3*1101 presented four peptides. Four DQA/DQB molecules composed of two intrahaplotype and two interhaplotype pairs presented seven peptides, of which five were uniquely presented by DQ molecules. In addition,three functional mixed isotype (DQA/DRB3) restriction elements were identified. The immunogenicity and broad MHC class II presentation of multiple VirB9-1, VirB9-2, and VirB10 peptide epitopes justify their testing as a multi-epitope vaccine against A. marginale.

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Section: Discussionsupporting

confidence: 83%

Breadth of the CD4+ T cell response to Anaplasma marginale VirB9-1, VirB9-2 and VirB10 and MHC class II DR and DQ restriction elements

et al. 2012

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“…The use of polymorphisms within genes is fast gaining attention as a complement to the current methods of selection because of their association with traits of interest in animals, especially those that affect livestock diseases (Miyasaka et al, 2011;Yakubu, 2015). However, the effects of nsSNPs in the DQA1 gene in goats have not been predicted to date in silico.…”

Section: Discussionmentioning

confidence: 99%

Modelling functional and structural impact of non-synonymous single nucleotide polymorphisms of the DQA1 gene of three Nigerian goat breeds

Yakubu¹,

Donato²,

Imumorin³

2017

SA J. An. Sci.

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The DQA1 gene is a member of the highly polymorphic MHC class II locus that is responsible for the differences among individuals in immune response to infectious agents. In this study, the authors performed a comprehensive computational analysis of the functional and structural impact of non-synonymous or amino acid-changing single nucleotide polymorphisms (SNPs) (nsSNPs) that are deleterious to the DQA1 protein in Nigerian goats. A 310-bp fragment of exon 2 of the DQA1 gene was amplified and sequenced in 27 unrelated animals that are representative of three major Nigerian goat breeds (nine each of West African Dwarf, Red Sokoto, and Sahel of both sexes) using genomic DNA. Forty-two nsSNPs were identified from the alignment of the deduced amino acid sequences. Based on the PANTHER, PROVEAN and PolyPhen-2 algorithms, there was consensus in identifying the mutants I26D, E114V and V115F as being deleterious. Further, differences between the native and the mutant proteins in the subsequent molecular trajectory analysis (stabilizing and flexible residue composition, total grid energy, solvation energy, coulombic energy, solvent accessibility, and protein-protein interaction properties) revealed E114V and V115F to be highly deleterious. Combined mutational analysis comparing the amutant (I26D, E114V and V115F mutations collectively) with the native protein also showed changes that could affect protein function and structure. Further wet-lab confirmatory analysis in a pathological association study involving a larger population of goats is required at the DQA1 locus. This would lay a sound foundation for breeding disease-resistant individuals in the future. ______________________________________________________________________________________

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“…In this present study, the expression level of BOLA-DQA1 was higher in high milk yielders than in low milk yielders. Other research has reported that the BOLA-DQA1 gene was associated with resistance to mastitis progression [24]. …”

Section: Discussionmentioning

confidence: 99%

Whole blood transcriptional profiling comparison between different milk yield of Chinese Holstein cows using RNA-seq data

et al. 2016

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BackgroundThe objective of this research was to investigate the variation of gene expression in the blood transcriptome profile of Chinese Holstein cows associated to the milk yield traits.ResultsWe used RNA-seq to generate the bovine transcriptome from the blood of 23 lactating Chinese Holstein cows with extremely high and low milk yield. A total of 100 differentially expressed genes (DEGs) (p < 0.05, FDR < 0.05) were revealed between the high and low groups. Gene ontology (GO) analysis demonstrated that the 100 DEGs were enriched in specific biological processes with regard to defense response, immune response, inflammatory response, icosanoid metabolic process, and fatty acid metabolic process (p < 0.05). The KEGG pathway analysis with 100 DEGs revealed that the most statistically-significant metabolic pathway was related with Toll-like receptor signaling pathway (p < 0.05). The expression level of four selected DEGs was analyzed by qRT-PCR, and the results indicated that the expression patterns were consistent with the deep sequencing results by RNA-Seq. Furthermore, alternative splicing analysis of 100 DEGs demonstrated that there were different splicing pattern between high and low yielders. The alternative 3’ splicing site was the major splicing pattern detected in high yielders. However, in low yielders the major type was exon skipping.ConclusionThis study provides a non-invasive method to identify the DEGs in cattle blood using RNA-seq for milk yield. The revealed 100 DEGs between Holstein cows with extremely high and low milk yield, and immunological pathway are likely involved in milk yield trait. Finally, this study allowed us to explore associations between immune traits and production traits related to milk production.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2901-1) contains supplementary material, which is available to authorized users.

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The diversity of bovine MHC class II DRB3 and DQA1 alleles in different herds of Japanese Black and Holstein cattle in Japan

Cited by 54 publications

References 37 publications

Breadth of the CD4+ T cell response to Anaplasma marginale VirB9-1, VirB9-2 and VirB10 and MHC class II DR and DQ restriction elements

Breadth of the CD4+ T cell response to Anaplasma marginale VirB9-1, VirB9-2 and VirB10 and MHC class II DR and DQ restriction elements

Modelling functional and structural impact of non-synonymous single nucleotide polymorphisms of the DQA1 gene of three Nigerian goat breeds

Whole blood transcriptional profiling comparison between different milk yield of Chinese Holstein cows using RNA-seq data

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