Genome-Wide Association Study of Insect Bite Hypersensitivity in Swedish-Born Icelandic Horses

Equine allergic skin diseases: Clinical consensus guidelines of the World Association for Veterinary Dermatology

BACKGROUND

Allergic skin diseases are common in horses worldwide. The most common causes are insect bites and environmental allergens.

OBJECTIVES

To review the current literature and provide consensus on pathogenesis, diagnosis, treatment and prevention.

MATERIALS AND METHODS

The authors reviewed the literature up to November 2022. Results were presented at North America Veterinary Dermatology Forum (2021) and European Veterinary Dermatology Congress (2021). The report was available to member organisations of the World Association for Veterinary Dermatology for feedback.

CONCLUSIONS AND CLINICAL RELEVANCE

Insect bite hypersensitivity (IBH) is the best characterised allergic skin disease. An immunoglobulin (Ig)E response against Culicoides salivary antigens is widely documented. Genetics and environmental factors play important roles. Tests with high sensitivity and specificity are lacking, and diagnosis of IBH is based on clinical signs, seasonality and response to insect control. Eosinophils, interleukin (IL)-5 and IL-31 are explored as therapeutic targets. Presently, the most effective treatment is insect avoidance. Existing evidence does not support allergen-specific immunotherapy (ASIT) using commercially available extracts of Culicoides. Hypersensitivity to environmental allergens (atopic dermatitis) is the next most common allergy. A role for IgE is supported by serological investigation, skin test studies and positive response to ASIT. Prospective, controlled, randomised studies are limited, and treatment relies largely on glucocorticoids, antihistamines and ASIT based on retrospective studies. Foods are known triggers for urticaria, yet their role in pruritic dermatitis is unknown. Recurrent urticaria is common in horses, yet our understanding is limited and focussed on IgE and T-helper 2 cell response. Prospective, controlled studies on treatments for urticaria are lacking. Glucocorticoids and antihistamines are primary reported treatments.

Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse

Inbreeding depression is the reduction of performance caused by mating of close relatives. In livestock populations, inbreeding depression has been traditionally estimated by regression of phenotypes on pedigree inbreeding coefficients. This estimation can be improved by utilising genomic inbreeding coefficients. Here we estimate inbreeding depression for insect bite hypersensitivity (IBH) prevalence, the most common allergic horse disease worldwide, in Old Kladruber horse. In a deep pedigree with 3214 horses (187 genotyped), we used a generalised linear mixed model with IBH phenotype from 558 horses examined between 1996 and 2009 (1368 records). In addition to the classical pedigree information, we used the single-step approach that enabled joint use of pedigree and genomic information to estimate inbreeding depression overall genome and equine leucocyte antigen (ELA) class II region. Significant inbreeding depression was observed in all models fitting overall inbreeding coefficients (odds ratio between 1.018 and 1.074, P < 0.05) with the exception of Kalinowski's new inbreeding (P = 0.0516). The increase of ELA class II inbreeding was significantly associated with increased prevalence of IBH (odds ratio 1.018; P = 0.027). However, when fitted jointly with the overall inbreeding coefficient, the effect of ELA class II inbreeding was not significant (odds ratio 1.016; P = 0.062). Overall, the higher ELA class II and/or overall inbreeding (pedigree or genomic) was associated with increased prevalence of IBH in Old Kladruber horses. The single-step approach provides an efficient use of all the available pedigree, genomic, and phenotype information for estimation of overall and regional inbreeding effects.

Selection in the Finnhorse, a native all-around horse breed

Selection by breeders modifies the morphology, behaviour and performance of domesticated species. Here, we examined signs of selection in Finnhorse, the only native horse breed in Finland. We first searched divergent genomic regions between Finnhorses and other breeds, as well as between different breeding sections of the Finnhorse with data from Illumina Equine SNP70 BeadChip, and then studied several of the detected regions in more detail. We found altogether 35 common outlier SNPs between Finnhorses and other breeds using two different selection tests. Many of the SNPs were located close to genes affecting coat colour, performance, size, sugar metabolism, immune response and olfaction. We selected genes affecting coat colour (KIT, MITF, PMEL), performance (MSTN) and locomotion (DMRT3) for a more detailed examination. In addition, we looked for, and found, associations with height at withers and SNPs located close to gene LCORL. Among the four breeding sections of Finnhorses (harness trotters, riding horses, draught horses and pony‐sized horses), a single SNP located close to the DMRT3 gene was significantly differentiated and only between harness trotters and pony‐sized horses.

Genetics of Immune Disease in the Horse

Host defenses against infection by viruses, bacteria, fungi, and parasites are critical to survival. It has been estimated that upwards of 7% of the coding genes of mammals function in immunity and inflammation. This high level of genomic investment in defense has resulted in an immune system characterized by extraordinary complexity and many levels of redundancy. Because so many genes are involved with immunity, there are many opportunities for mutations to arise that have negative effects. However, redundancy in the mammalian defense system and the adaptive nature of key immune mechanisms buffer the untoward outcomes of many such deleterious mutations.

Genetics of Skin Disease in Horses

Equine skin diseases are common, causing increased costs and reduced welfare of affected horses.Genetic testing, if available, can complement early detection, disease diagnosis, and clinical treatment and offers horse breeders the possibility to rule out carrier status. The mechanisms of complex disease can be investigated by using the latest state-of-the-art genomic technologies. Genome-based strategies may also serve as an efficient and cost-effective strategy for the management of the disease severity levels, with particular interest in complex traits such as insect bite hypersensitivity, chronic progressive lymphedema, and melanoma.

How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species

Background

PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and pet species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown.

Results

We introduce the genome coverage parameter to appropriately estimate F_ROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK’s minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings.

Conclusions

In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis’ validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

Genome-wide association study for insect bite hypersensitivity susceptibility in horses revealed novel associated loci on chromosome 1

Equine insect bite hypersensitivity (IBH) is a pruritic skin allergy caused primarily by biting midges, Culicoides spp. IBH susceptibility has polygenic inheritance and occurs at high frequencies in several horse breeds worldwide, causing increased costs and reduced welfare of affected horses. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) associated with equine IBH susceptibility. After quality control, 33,523 SNPs were included in a Bayesian genome-wide association study on 177 affected and 178 unaffected Icelandic horses. We report associated regions in E. caballus (ECA) 1, 3, 15 and 18, overlapping with known IBH QTLs in horses, and novel regions containing several genes, together explaining 11.46% of the total genetic variance. For validation, three SNPs on ECA 1 and ECA X (explaining the largest percentage of genetic variance) within 1-mb genomic windows for IBH were genotyped in an independent population of 280 Exmoor ponies. The associated genomic region (152-153 mb) on ECA 1 was confirmed in Exmoor ponies and contains the AQR gene involved in splicing processes and a long non-coding RNA. This study confirms the polygenic nature of IBH susceptibility and suggests a role of transcriptional regulatory mechanisms (e.g., alternative splicing) for IBH predisposition in these horse breeds.

Genomic Regions Associated with IgE Levels against Culicoides spp. Antigens in Three Horse Breeds

Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective, independent, and quantitative phenotype to improve the power to detect genetic variants that underlie IBH. Genotypes of 200 Shetland ponies, 127 Icelandic horses, and 223 Belgian Warmblood horses were analyzed while using a mixed model approach. No single-nucleotide polymorphism (SNP) passed the Bonferroni corrected significance threshold, but several regions were identified within and across breeds, which confirmed previously identified regions of interest and, in addition, identifying new regions of interest. Allergen-specific IgE levels are a continuous and objective phenotype that allow for more powerful analyses when compared to a case-control set-up, as more significant associations were obtained. However, the use of a higher density array seems necessary to fully employ the use of IgE levels as a phenotype. While these results still require validation in a large independent dataset, the use of allergen-specific IgE levels showed value as an objective and continuous phenotype that can deepen our understanding of the biology underlying IBH.

MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites

The Icelandic horse has been maintained as a closed population in its eponymous homeland for many generations, with no recorded introductions of new horses of any breed since the year 1000 CE. Here we determined the diversity of major histocompatibility complex (MHC) haplotypes in 156 Icelandic horses from two groups, based on a panel of 12 polymorphic intra-MHC microsatellites tested in families of various composition. We identified a total of 79 MHC haplotypes in these two groups, including one documented intra-MHC recombination event from a total of 147 observed meioses. None of these MHC haplotypes have been previously described in any other horse breed. Only one MHC homozygote was found in the entire population studied. These results indicate a very high level of MHC heterozygosity and haplotype diversity in the Icelandic horse. The environment in Iceland is remarkable for its lack of common agents of equine infectious disease, including equine herpesvirus type 1, influenza virus, and streptococcus equi. The driving forces for maintenance of MHC heterozygosity in Icelandic horses must thus be sought outside of these major horse pathogens. Based on our results, we propose that intra-MHC recombination may play a major role in the generation of novel haplotypes.

A prospective study on insect bite hypersensitivity in horses exported from Iceland into Switzerland

BACKGROUND

Insect bite hypersensitivity (IBH) is an IgE-mediated dermatitis caused by bites of Culicoides spp., which occurs frequently in horses imported from Iceland to continental Europe. IBH does not occur in Iceland because Culicoides species that bite horses are not present. However, Simulium vittatum (S. vittatum) are found in Iceland. In Europe, blood basophils from IBH-affected horses release significantly more sulfidoleukotrienes (sLT) than those from healthy controls after in vitro stimulation with Culicoides nubeculosus (C. nubeculosus) and S. vittatum. Aims of the study were: (I) using the sLT release assay, to test if horses living in Iceland were sensitized to S. vittatum and (II) to determine in a longitudinal study in horses imported from Iceland to Switzerland whether the sLT release assay would allow to predict which horses would develop IBH.

RESULTS

Horses in Iceland, even when living in high S. vittatum areas, were usually not sensitized to S. vittatum or C. nubeculosus. Incidence of IBH in the 145 horses from the longitudinal study was 51% and mean time until IBH developed was 2.5 ± 1 year. Before import and after the first summer following import, there were no significant differences in sLT release between the endpoint healthy (H) and IBH groups. After the 2nd summer, when the number of clinically affected horses increased in the endpoint IBH group, a significantly higher sLT release after stimulation with C. nubeculosus but not with S. vittatum was observed. After the 3rd and 4th summer, the endpoint IBH group had a significantly higher sLT release with C. nubeculosus and S. vittatum than the endpoint H group. Some of the horses that remained healthy became transiently positive in the sLT release assay upon stimulation of their peripheral blood leucocytes with C. nubeculosus.

CONCLUSIONS

Horses in Iceland are not sensitized to S. vittatum. In horses that develop IBH, sensitization to S. vittatum is secondary to sensitization to C. nubeculosus and probably a result of an immunological cross-reactivity. A sLT release assay cannot be used to predict which horses will develop IBH. A transient positive reaction in the sLT release assay observed in horses that remained healthy suggests that immunoregulatory mechanisms may control an initial sensitization of the healthy horses.

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity

Background

Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide.

Results

Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH.

Conclusions

CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0657-0) contains supplementary material, which is available to authorized users.

Genetic parameters of insect bite hypersensitivity in the Old Grey Kladruber horse

The objective of this study was to assess the genetic parameters of insect bite hypersensitivity (IBH) in the Old Grey Kladruber horse, an original Czech warmblood horse breed. Insect bite hypersensitivity is a recurrent allergic skin disease affecting horses worldwide. Its etiology is multifactorial. The defect is genetically controlled, and the starting impulse is a bite by midges of the spp. and less frequently spp. Knowledge about the associated genes is limited. Horses were kept by the National Stud in Kladruby (1,146 measurements) and by 10 private breeders (63 measurements). The horses were visually scored by the same inspector over a period of 13 yr from 1996 to 2009. A linear logistic model with a binary variable was used for subsequent statistical analysis. The fixed effects of the farm, year of evaluation, age of evaluation, and sex were significant, and the nonsignificant effect was the intensity of greying. The animals from the National Stud were more strongly affected by IBH than animals from private studs. The National Stud is located near the Labe River, at an altitude of 206 m; there are bottomland pastures in the vicinity, blind river arms, and numerous pools and marshes, and the climate is mild. These conditions are convenient for horse keeping but also for the propagation of . The stallions were less affected than the mares. The occurrence in years of age was influenced by selection; scoring began in the first year of age, and when the young animal was repeatedly positive, it was eliminated from breeding. The estimated h differed significantly from 0, and the direct h were 0.626 in the animal model with a maternal effect, 0.359 in the animal model without a maternal effect, and 0.363 in the animal model without correlation between direct and maternal effect. The maternal h was 0.305. The estimated repeatabilities were 0.636 with a maternal effect, 0.615 without a maternal effect, and 0.623 without correlation. The h of IBH was found to be medium to high, so there is a possibility to reduce the prevalence of IBH by selection.

Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH)

While susceptibility to hypersensitive reactions is a common problem amongst humans and animals alike, the population structure of certain animal species and breeds provides a more advantageous route to better understanding the biology underpinning these conditions. The current study uses Exmoor ponies, a highly inbred breed of horse known to frequently suffer from insect bite hypersensitivity, to identify genomic regions associated with a type I and type IV hypersensitive reaction. A total of 110 cases and 170 controls were genotyped on the 670K Axiom Equine Genotyping Array. Quality control resulted in 452,457 SNPs and 268 individuals being tested for association. Genome-wide association analyses were performed using the GenABEL package in R and resulted in the identification of two regions of interest on Chromosome 8. The first region contained the most significant SNP identified, which was located in an intron of the DCC netrin 1 receptor gene. The second region identified contained multiple top SNPs and encompassed the PIGN, KIAA1468, TNFRSF11A, ZCCHC2, and PHLPP1 genes. Although additional studies will be needed to validate the importance of these regions in horses and the relevance of these regions in other species, the knowledge gained from the current study has the potential to be a step forward in unraveling the complex nature of hypersensitive reactions.