The genetic architecture of the MHC class II region in British Texel sheep

Ali, Alsagher O.; Stear, Abigail; Fairlie‐Clarke, Karen; Brujeni, Gholamreza Nikbakht; Isa, Nur Mahiza Md; Salisi, Mohd Shahrom; Donskow‐Łysoniewska, Katarzyna; Groth, D. M.; Buitkamp, Johannes; Stear, M. J.

doi:10.1007/s00251-016-0962-6

Cited by 11 publications

(6 citation statements)

References 23 publications

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“…This study focuses on the DRB1, DQA1, DQB1, DQA2, DQB2, DQA3 and DQB3 loci in the class IIa region. A detailed description of the methods used to define class II genetic variants has been provided . In brief, genomic DNA was amplified by PCR with a variety of primers and sequenced by Sanger sequencing on an ABI 3130.…”

Section: Methodsmentioning

confidence: 99%

“…Haplotypes were determined from the known pedigrees. A comprehensive description of the alleles present in each haplotype has been published previously …”

Section: Methodsmentioning

confidence: 99%

“…A detailed description of the methods used to define class II genetic variants has been provided. 23 In brief, genomic DNA was amplified by PCR with a variety of primers and sequenced by Sanger sequencing on an ABI 3130. The absence of a detectable product was defined as a null allele.…”

Section: Detection Of Mhc Variationmentioning

confidence: 99%

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Association of MHC class II haplotypes with reduced faecal nematode egg count and IgA activity in British Texel sheep

Ali

Murphy

Stear

et al. 2019

Parasite Immunology

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Summary Nematode infection is one of the principal diseases suffered by sheep and the class II region of the MHC has been repeatedly associated with differences in susceptibility and resistance to infection. The aim of this study was to examine the association of MHC class II haplotypes in a flock of Texel sheep with faecal egg counts and antibody responsiveness. Two haplotypes carried the DRB1*11:01 allele which has previously been associated with reduced egg counts in Scottish Blackface and Suffolk sheep. One of the two haplotypes was associated with reduced egg counts in the Texel breed, and both haplotypes were associated with reduced IgA activity against an extract from fourth‐stage larvae. The reduced IgA activity is probably a consequence of reduced numbers of fourth‐stage larvae in sheep carrying the resistance allele. The association of specific MHC alleles with reduced egg counts, reduced worm numbers and decreased IgA activity provides a mechanism for the density‐dependent regulation of parasite growth and fecundity.

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Section: Methodsmentioning

confidence: 99%

“…Haplotypes were determined from the known pedigrees. A comprehensive description of the alleles present in each haplotype has been published previously …”

Section: Methodsmentioning

confidence: 99%

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Association of MHC class II haplotypes with reduced faecal nematode egg count and IgA activity in British Texel sheep

Ali

Murphy

Stear

et al. 2019

Parasite Immunology

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“…No single locus captures all MHC class IIa variation in the Soay sheep population. In addition, sequence-based genotyping of the DQ loci, especially the DQB loci, was complicated by cross-amplification amongst loci and variation in locus configuration (Ballingall et al 2015, 2018; Ali et al 2016; Dicks et al 2019). Sanger sequencing of multiple loci in large numbers of individuals would be costly and slow, yet such haplotypic data is necessary to carry out analyses of the evolutionary processes underlying the high variability in this region.…”

Section: Introductionmentioning

confidence: 99%

MHC class IIa haplotypes derived by high throughput SNP screening in an isolated sheep population

Dicks

Pemberton

Ballingall

et al. 2020

Preprint

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Investigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant SNP haplotype. The panel of 13 SNPs was genotyped in 5951 sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of a recombinant SNP haplotype.

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“…A number of additional gene duplications within the ovine DQ region have been recently been reported (Ali et al 2017, Ballingall et al 2018b. It is not yet clear if these represent functional duplications or gene fragments that co-amplify with the primers used.…”

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confidence: 99%

Allelic nomenclature for the duplicated MHC class II DQ genes in sheep

et al. 2018

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The principal MHC class II molecules involved in the presentation of peptides to the antigen specific receptors on CD4 + T cells genes in sheep are derived from DR and DQ genes. Allelic nomenclature systems for the DRB1 and its partner DRA loci are available for Ovid's; however, no official nomenclature is available for the DQ genes which creates ambiguity within the research community. Ovine MHC haplotypes include at least two pairs of DQA and DQB genes, termed DQA1, DQB1 and DQA2, DQB2 and both sets are polymorphic and both seem to be functional. In a number of haplotypes, the DQA1 locus appears to be absent (DQA1-null) and is replaced by a second locus termed DQA2-like. Here, we identify families of alleles based on sequence similarity and phylogenetic clustering which correspond to each of the DQA and DQB genes identified in previous genomic and transcript analyses of homozygous animals. Using such criteria to cluster sequences, we have named 82 full-length and partial cDNA transcripts derived from domestic sheep (Ovis aries) which correspond to alleles at the Ovar-DQA1, DQA2, DQA2-like, DQB1, DQB2 and DQB2-like genes and provide associated sequence resources available to the research community through the IPD-MHC Database. This sets the basis for naming and annotation of DQ genes within the ovine MHC and may be used as a template for DQ genes in other ruminant species which will ultimately support research in livestock infectious disease.

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The genetic architecture of the MHC class II region in British Texel sheep

Cited by 11 publications

References 23 publications

Association of MHC class II haplotypes with reduced faecal nematode egg count and IgA activity in British Texel sheep

Association of MHC class II haplotypes with reduced faecal nematode egg count and IgA activity in British Texel sheep

MHC class IIa haplotypes derived by high throughput SNP screening in an isolated sheep population

Allelic nomenclature for the duplicated MHC class II DQ genes in sheep

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