Polymorphism at the ovine major histocompatibility complex class II loci

A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak

Yak is an important livestock animal for the people indigenous to the harsh, oxygen‐limited Qinghai‐Tibetan Plateau and Hindu Kush ranges of the Himalayas. The yak genome was sequenced in 2012, but its assembly was fragmented because of the inherent limitations of the Illumina sequencing technology used to analyse it. An accurate and complete reference genome is essential for the study of genetic variations in this species. Long‐read sequences are more complete than their short‐read counterparts and have been successfully applied towards high‐quality genome assembly for various species. In this study, we present a high‐quality chromosome‐scale yak genome assembly (BosGru_PB_v1.0) constructed with long‐read sequencing and chromatin interaction technologies. Compared to an existing yak genome assembly (BosGru_v2.0), BosGru_PB_v1.0 shows substantially improved chromosome sequence continuity, reduced repetitive structure ambiguity, and gene model completeness. To characterize genetic variation in yak, we generated de novo genome assemblies based on Illumina short reads for seven recognized domestic yak breeds in Tibet and Sichuan and one wild yak from Hoh Xil. We compared these eight assemblies to the BosGru_PB_v1.0 genome, obtained a comprehensive map of yak genetic diversity at the whole‐genome level, and identified several protein‐coding genes absent from the BosGru_PB_v1.0 assembly. Despite the genetic bottleneck experienced by wild yak, their diversity was nonetheless higher than that of domestic yak. Here, we identified breed‐specific sequences and genes by whole‐genome alignment, which may facilitate yak breed identification.

A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb

Background

The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of ovine chromosome 20. The evolutionary consequence of such an inversion and an insertion (inversion/insertion) in relation to MHC function remains unknown. We previously constructed a BAC clone physical map for the ovine MHC exclusive of the insertion region. Here we report the construction of a high-density physical map covering the autosome insertion in order to address the question of what the inversion/insertion had to do with ruminants during the MHC evolution.

Results

A total of 119 pairs of comparative bovine oligo primers were utilized to screen an ovine BAC library for positive clones and the orders and overlapping relationships of the identified clones were determined by DNA fingerprinting, BAC-end sequencing, and sequence-specific PCR. A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb. Therefore, a continuous physical map covering the entire ovine autosome inversion/insertion region was successfully constructed. The map confirmed the bovine sequence assembly for the same homologous region. The DNA sequences of 185 BAC-ends have been deposited into NCBI database with the access numbers HR309252 through HR309068, corresponding to dbGSS ID 30164010 through 30163826.

Conclusions

We have constructed a high-density BAC clone physical map for the ovine autosome inversion/insertion between the MHC class IIa and IIb. The entire ovine MHC region is now fully covered by a continuous BAC clone contig. The physical map we generated will facilitate MHC functional studies in the ovine, as well as the comparative MHC evolution in ruminants.

A complete DNA sequence map of the ovine major histocompatibility complex

Background

The ovine Major Histocompatibility Complex (MHC) harbors clusters of genes involved in overall resistance/susceptibility of an animal to infectious pathogens. However, only a limited number of ovine MHC genes have been identified and no adequate sequence information is available, as compared to those of swine and bovine. We previously constructed a BAC clone-based physical map that covers entire class I, class II and class III region of ovine MHC. Here we describe the assembling of a complete DNA sequence map for the ovine MHC by shotgun sequencing of 26 overlapping BAC clones.

Results

DNA shotgun sequencing generated approximately 8-fold genome equivalent data that were successfully assembled into a finished sequence map of the ovine MHC. The sequence map spans approximately 2,434,000 nucleotides in length, covering almost all of the MHC loci currently known in the sheep and cattle. Gene annotation resulted in the identification of 177 protein-coding genes/ORFs, among which 145 were not previously reported in the sheep, and 10 were ovine species specific, absent in cattle or other mammals. A comparative sequence analyses among human, sheep and cattle revealed a high conservation in the MHC structure and loci order except for the class II, which were divided into IIa and IIb subregions in the sheep and cattle, separated by a large piece of non-MHC autosome of approximately 18.5 Mb. In addition, a total of 18 non-protein-coding microRNAs were predicted in the ovine MHC region for the first time.

Conclusion

An ovine MHC DNA sequence map was successfully assembled by shotgun sequencing of 26 overlapping BAC clone. This makes the sheep the second ruminant species for which the complete MHC sequence information is available for evolution and functional studies, following that of the bovine. The results of the comparative analysis support a hypothesis that an inversion of the ancestral chromosome containing the MHC has shaped the MHC structures of ruminants, as we currently observed in the sheep and cattle. Identification of relative large numbers of microRNAs in the ovine MHC region helps to provide evidence that microRNAs are actively involved in the regulation of MHC gene expression and function.

Polymorphism of the DQA2 gene in goats

Variation in the caprine DQA2 gene was investigated using PCR-single-strand conformational polymorphism (SSCP) and DNA sequencing. Eleven DQA2 alleles were defined by SSCP patterns from 23 goats. All the caprine alleles shared high sequence homology to ovine DQA2 sequences, and exhibited a pattern of polymorphism similar to DQA2 alleles from sheep and cattle but different from caprine DQA1 sequences. Thirty-eight AA positions in the alpha1 domain of caprine DQA2 molecules were polymorphic, and a high degree of polymorphism was observed in the putative antigen-binding region, with 74% of the positions being polymorphic. Phylogenetic analysis of caprine, ovine, and bovine DQA sequences revealed that the caprine DQA2 sequences identified here grouped with ovine DQA2, bovine DQA2, DQA3, and DQA4 sequences but are separate from the group of caprine DQA1 alleles. Nine of the caprine DQA2 sequences were more similar to ovine DQA2 alleles, whereas the remaining two were more closely related to ovine DQA2-like and bovine DQA3 alleles. This finding suggests that the caprine DQA2 sequences may represent two loci, which probably arose by either gene duplication or gene conversion events. Allelic lineages were evident for both DQA2 and DQA2-like loci, supporting the trans-species mode of evolution of major histocompatibilitly complex genes. The high level of polymorphism and similarity between caprine and ovine DQA2 alleles suggests that the DQA2 gene may play an important role in immune responses to shared pathogens.

Transcriptional profiling of Ovis aries identifies Ovar-DQA1 allele frequency differences between nematode-resistant and susceptible selection lines

Gastrointestinal nematodes are a major cause of disease in grazing livestock; however, individual animals differ in their response to infection. To identify genes whose expression correlates with resistance status, transcriptional profiling of resistant and susceptible sheep was undertaken. Transcription profiles were taken at three time points during the growth of lambs. The number of genes differentially expressed increased as animals were exposed to longer nematode challenge. Almost 300 genes, with a variety of functions, were differentially expressed overall, although genes more highly expressed in resistant animals typically had major histocompatibility complex (MHC) II, free radical scavenging or smooth muscle-specific functions. The Ovar-DQA1 gene was 8.4-fold more highly expressed in resistant animals. This was due in part to a higher frequency of DQA1 null alleles in susceptible animals. The null allele of DQA1 was also associated with susceptibility in a separate selection flock, presenting the hypothesis that failure to present parasite antigens to immune cells led to nematode susceptibility. To test this hypothesis, commercial rams from three breeds were genotyped for the null allele of DQA1. The homozygous null allele was associated with susceptibility in only one of the three breeds tested indicating that the null allele does not cause susceptibility to intestinal parasites per se but is probably in linkage disequilibrium with additional polymorphisms in the MHC region. A combination of these polymorphisms may contribute to susceptibility in some populations. The extent of linkage disequilibrium between polymorphisms may vary from breed to breed or population to population.

Haplotype analysis of the DQA genes in sheep: Evidence supporting recombination between the loci1

The ovine class II major histocompatibility complex mediates specific immune responses to exogenous antigens in sheep. A number of ovine class II loci have been identified, and most of them appear to be polymorphic. In this study we investigated the DQA1 locus of 520 sheep and the DQA2 locus of over 40,000 sheep, finding 12 sequences and 22 sequences, respectively, using DQA1- and DQA2-specific PCR primers. Among the DQA2 sequences, 2 groups of sequences can be found: those that share homology with the DQA2 sequences from closely related species and those that cluster with bovine DQA3 and DQA4 sequences and have been called DQA2-like in sheep. The occurrence of these DQA2-like sequences was once again confirmed to correspond with the absence of detectable DQA1 sequences, suggesting that they are found at the same location as DQA1. Within the sheep studied, 37 haplotypes could be detected, 23 being haplotypes of DQA1 and DQA2 sequences and with frequencies ranging from 0.38 to 9.27%, and 14 being haplotypes of DQA2 and DQA2-like sequences and with frequencies ranging from 0.03 to 14.53%. We discovered 12 DQA1-DQA2 combinations that were derived from 5 DQA1 alleles and 4 DQA2 alleles, and 8 DQA2-DQA2-like combinations from 5 DQA2 alleles and 2 DQA2-like sequences. The frequency of occurrence of recombined DQA1-DQA2 sequences and recombined DQA2-DQA2-like sequences is similar, once again suggesting the DQA2-like sequences are found at the DQA1 locus.

Allelic variation of the ovine Toll-like receptor 4 gene

The family of Toll-like receptors (TLRs) is responsible for recognition of pathogen-associated molecular patterns (PAMPs), and Toll-like receptor 4 (TLR4) recognizes not only exogenous ligands such as the lipopolysaccharide (LPS) of Gram-negative bacteria, but also a number of endogenous ligands. Variation in the nucleotide sequence of the ovine TLR4 gene was investigated by amplification of a fragment containing a putative ligand-binding region using polymerase chain reaction (PCR), followed by single-strand conformational polymorphism (PCR-SSCP) analysis and DNA sequencing. Four novel SSCP patterns, representing four different sequences, were identified. Either one or two different sequences were detected in individual sheep and all the sequences identified shared high homology to the TLR4 sequences from a variety of species, suggesting that these sequences represent allelic variants of the ovine TLR4 gene. Fourteen single nucleotide polymorphisms (SNPs) were detected, and 79% (11 of 14) of SNPs were non-synonymous substitutions that would result in amino acid changes. Variation detected here might have an impact on pattern recognition and hence affect the immune response to pathogens.

A BAC clone-based physical map of ovine major histocompatibility complex

An ovine bacterial artificial chromosome (BAC) library containing 190,000 BAC clones was constructed and subsequently screened to construct a BAC-based physical map for the ovine major histocompatibility complex (MHC). Two hundred thirty-three BAC clones were selected by 84 overgo probes designed on human, mouse, and swine MHC sequence homologies. Ninety-four clones were ordered by DNA fingerprinting to form contigs I, II, and III that correspond to ovine MHC class I-class III, class IIa, and class IIb. The minimum tiling paths of contigs I, II, and III are 15, 4, and 4 BAC clones, spanning approximately 1900, 400, and 300 kb, respectively. The order and orientation of most BAC clones in each contig were confirmed by BAC-end sequencing. An open gap exists between class IIa and class III. This work helps to provide a foundation for detailed study of ovine MHC genes and of evolution of MHCs in mammals.

Diversity of the ovine DQA2 gene1

Variation in the ovine DQA2 gene was investigated in approximately 2,000 sheep from six breeds. Fragments of DNA containing the ovine DQA2 exon 2 were amplified using PCR. Single-strand conformational polymorphism analysis and DNA sequence analysis were employed to detect genetic variation. Twenty-three nucleic acid sequences, encoding 22 DQA2 amino acid sequences, were identified. This increases the number of alleles identified from 10 to 23. In some cases, three or four unique sequences were isolated from individual sheep, suggesting that these DQA2 sequences may represent two loci. Phylogenetic tree analysis revealed that 5 of these 23 sequences were more closely related to cattle DQA3 or DQA4 sequences than to other sheep DQA2 sequences. These sequences clustered together and were called DQA2-like to differentiate them from other DQA2 sequences. There was no evidence of DQA5-like sequences in sheep. Information theory-based analysis indicated that some of the DQA2-like sequences had low information content at splice sites, suggesting that these alleles may have low functional activity. Allelic lineages were observed not only at the DQA2 locus, but also at the DQA2-like locus, supporting the trans-species mode of evolution of MHC genes. Comparison of the allelic sequences suggests that polymorphism seems to have arisen largely by point mutation and gene conversion, and a recent gene conversion event seems to have occurred between the DQA2 and DQA2-like loci. The high level of sequence polymorphism detected and varied number of loci demonstrate the extensive diversity of the ovine DQA2 gene.

Allelic polymorphism in the ovine DQA1 gene1

Variation in the ovine DQA1 gene was investigated by amplification of exon 2 using PCR, followed by single-strand conformational polymorphism (SSCP) analysis, cloning, and DNA sequencing. Fourteen novel SSCP patterns, representing 14 different sequences, were identified. Eight of these 14 sequences were identical to published DQA1 sequences from sheep, whereas the remaining six were novel but similar to the published DQA1 sequences from sheep and cattle. These six new sequences exhibited conserved region and variable region patterns similar to the published sheep DQA1 sequences, but were different than the published DQA2 sequences from sheep. All of these 14 putative sheep DQA1 sequences fulfilled the criteria used by the established bovine leukocyte antigens major histocompatibility complex nomenclature committee for assignment as new alleles. Comparison of the available DQA1 sequences from sheep and cattle revealed several clusters of ovine DQA1 sequences, and some sheep alleles were more similar to cattle alleles than other sheep alleles. The occurrence of trans-species polymorphism suggests the action of balancing selection at the DQA1 locus. Twenty-four percent of the nucleotide positions showed variation within exon 2, and this variation seems to have arisen largely by point mutation and gene conversion. The nonsynonymous and synonymous substitution rates were similar in both the putative antigen-binding site codons and the putative nonantigen-binding site codons. The extensive polymorphism reported in this article is consistent with polymorphism reported at the bovine DQA1 locus.

Evolution of the ovine MHC DQA region

Southern hybridisation was used to define an apparent gene duplication event at the ovine DQA2 locus. Approximately 500 sheep from five different breeds were genotyped at their DQA1 and DQA2 loci. A subset of these were selected for further characterisation. Southern hybridisation of TaqI digested DNA revealed no DQA1 region in some sheep. It was also noted in these DQA1 null animals the DQA2 specific probe hybridised to two bands. An EcoRV-RFLP designed to distinguish copy number confirmed this duplication of the DQA2 region. The results showed that the duplication was exclusively associated with the DQA1 null haplotype and occurred only in alleles DQA2-F, -G, -I and -J. Comparison with bovine MHC genes revealed that they also contained a DQA1 null haplotype and that this haplotype was associated with a putative DQA3 gene. The potential for an ovine DQA3 locus is discussed.

Association between alleles of the ovine major histocompatibility complex and resistance to footrot

Variation in natural resistance to footrot may be genetically derived, implying that genetic markers for resistance may exist and allow selection of superior animals. In this study association between variation within the ovine MHC class II region and resistance to footrot was investigated in two trials. Half-sib progeny were subjected to a field challenge with footrot and their condition subsequently recorded. The animals were then typed at their MHC class II loci to investigate associations between inherited paternal haplotype and footrot status. In the first trial an association between MHC haplotype and footrot status was observed across all animals (P = 0.005), when the self-curing and resistant animals were combined (P = 0.002) and when the self-curing animals were excluded from the analysis (P = 0.001). No association was observed in the second trial, a result attributed to the dry weather conditions which led to poor disease transmission and unreliable disease classification.