Polymorphism of the MHC-DQA2 gene in the Chios dairy sheep population and its association with footrot

Genome-wide association with footrot in hair and wool sheep

Ovine footrot is an infectious disease with important contributions from Dichelobacter nodosus and Fusobacterium necrophorum. Footrot is characterized by separation of the hoof from underlying tissue, and this causes severe lameness that negatively impacts animal wellbeing, growth, and profitability. Large economic losses result from lost production as well as treatment costs, and improved genetic tools to address footrot are a valuable long-term goal. Prior genetic studies had examined European wool sheep, but hair sheep breeds such as Katahdin and Blackbelly have been reported to have increased resistance to footrot, as well as to intestinal parasites. Thus, footrot condition scores were collected from 251 U.S. sheep including Katahdin, Blackbelly, and European-influenced crossbred sheep with direct and imputed genotypes at OvineHD array (>500,000 single nucleotide polymorphism) density. Genome-wide association was performed with a mixed model accounting for farm and principal components derived from animal genotypes, as well as a random term for the genomic relationship matrix. We identified three genome-wide significant associations, including SNPs in or near GBP6 and TCHH. We also identified 33 additional associated SNPs with genome-wide suggestive evidence, including a cluster of 6 SNPs in a peak near the genome-wide significance threshold located near the glutamine transporter gene SLC38A1. These findings suggest genetic susceptibility to footrot may be influenced by genes involved in divergent biological processes such as immune responses, nutrient availability, and hoof growth and integrity. This is the first genome-wide study to investigate susceptibility to footrot by including hair sheep and also the first study of any kind to identify multiple genome-wide significant associations with ovine footrot. These results provide a foundation for developing genetic tests for marker-assisted selection to improve resistance to ovine footrot once additional steps like fine mapping and validation are complete.

Allele/haplotype variation in the MHC-DQA2 gene in Spanish sheep and its association with footrot susceptibility

Footrot is a contagious disease that affects the hoof of sheep and other ungulates. The severity of the disease varies from a slight limp to the death of the individual due to injuries that prevent them from feeding. Variants of the Major Histocompatibility Complex (MHC)-DQA2 gene (MHC-DQA2) have been associated with a greater or lesser susceptibility to footrot in Greek, New Zealand and German sheep. In this study, variation in ovine MHC-DQA2, the absence or presence of footrot and the severity of infection was analysed in 117 Spanish Merino, Black Merino and Churra Lebrijana sheep. A total of 21 alleles/haplotypes and 65 genotypes were found with different frequencies in these breeds. As found in other studies, the MHC-DQA2 allele *1101 appeared to be associated with increased susceptibility to footrot, while allele *1201 appeared to be associated with decreased susceptibility. Overall this would suggest the ovine MHC plays a role in controlling susceptibility to footrot infection and that there are breed differences in susceptibility. Sheep might therefore be able to be selected by their MHC-DQA2 alleles/haplotypes to reduce the incidence of the disease in flocks.

A Cross-Sectional Epizootiological Study and Risk Assessment of Foot-Related Lesions and Lameness in Intensive Dairy Sheep Farms

Simple Summary

Foot-related lameness is one of the most significant welfare issues in farm animals. Contrary to dairy cows and meat sheep breeds, epizootiological data on foot-lesions and associated lameness in dairy sheep are scarce. In this study, data were collected from 30 representative intensive dairy sheep farms. Multivariate statistical analysis was used to produce a typology of intensive farming systems which resulted in the assignment of farms in two distinct clusters. Six hundred adult ewes were randomly selected from six flocks (three flocks per cluster) and a cross-sectional study was implemented to investigate the epizootiology and potential risk factors of foot-related lameness, foot-lesions and diseases. Ovine interdigital dermatitis and infectious footrot were the most common infectious foot diseases, while white line disease and hoof wall cracks were the most prevalent non-infectious lesions. Infectious footrot was the main cause of lameness and increased with age, whereas body condition score was associated with increased prevalence of ovine interdigital dermatitis. Comparisons between the clusters regarding foot-related lameness, foot-diseases and lesions at the animal, the limb, and the hoof level are presented, and relevant literature, mechanisms, hypotheses, and challenges of the field are discussed.

Abstract

Foot-related lameness, foot-diseases and lesions are emerging issues in dairy sheep; however, relevant epizootiological studies are scarce, and risk factors have not been elucidated. The objectives of this cross-sectional study were (i) to address this dearth of knowledge by investigating the epizootiology of lameness-related foot-lesions and diseases, and (ii) to assess the impact of potential risk factors on foot health, in intensive dairy sheep farms. Thirty farms were assigned in two representative clusters using a multivariate statistical analysis. Three farms per cluster and 100 multiparous milking ewes per farm (total n = 600) were selected and enrolled in the study. Foot-related lameness, ovine interdigital dermatitis (OID), infectious footrot (IFR), white line disease, hoof wall cracks, as well as health and welfare traits were recorded. Overall prevalence of foot-related lameness was 9.0% and was primarily associated with IFR; however, additional infectious and non-infectious foot diseases and lesions also contributed. Among infectious foot diseases, OID was the most prevalent (21.3%) followed by IFR (8.0%); WLD and hoof wall cracks were the most prevalent non-infectious foot-lesions (37.7% and 15.3%, respectively). IFR and OID prevalence increased with age (p < 0.05) and BCS (p < 0.01), respectively, suggesting that host-related factors and husbandry practices are important determinants of its occurrence.

Ovine footrot: A review of current knowledge

Footrot is a contagious foot disease mainly affecting sheep. It is caused by the Gram-negative anaerobic bacterium Dichelobacter nodosus. Warm, wet environmental conditions favour development of footrot, and under perfect conditions, it takes just 2-3 weeks from infection to manifestation of clinical signs. Affected sheep show lameness of various degrees and often graze while resting on their carpi. Local clinical signs vary in severity and extent from interdigital inflammation (benign footrot) to underrunning of the complete horn shoe in advanced stages of virulent footrot. Laboratory diagnosis ideally involves collection of four-foot interdigital swab samples followed by competitive real time PCR, allowing for detection of the presence of D. nodosus and differentiation between benign and virulent strains. Laboratory-based diagnostics at the flock level based on risk-based sampling and pooling of interdigital swab samples are recommended. The list of treatment options of individual sheep includes careful removal of the loose undermined horn, local or systemic administration of antimicrobials, systemic administration of non-steroidal anti-inflammatories (NSAIDs) and disinfectant footbathing. Strategies for control at the flock level are manifold and depend on the environmental conditions and the procedures traditionally implemented by the respective country. Generally, measures consist of treatment/culling of infected sheep, vaccination and prevention of reinfection of disease-free flocks. Gaining deeper insight into the beneficial effects of NSAIDs, screening for eco-friendly footbath solutions, developing better vaccines, including the development of a robust, reproducible infection model and elucidation of protective immune responses, as well as the elaboration of effective awareness training programs for sheep farmers, are relevant research gaps.

Aetiology, Risk Factors, Diagnosis and Control of Foot-Related Lameness in Dairy Sheep

During the last twenty years, considerable research efforts have recognized the consequences of foot-related lameness primarily in cattle, and meat and wool sheep. Despite the lack of extensive epidemiological studies, field observations and isolated research reports in dairy sheep have suggested that the problem might be more severe in semi-intensive and intensive farming systems. Footrot, contagious ovine digital dermatitis, ovine interdigital dermatitis, white line disease, and pedal joint abscess are the most common causes of foot-related lameness. Dichelobacter nodosus, Fusobacterium necrophorum, Treponema spp., and Actinomyces pyogenes are the most significant foot-related lameness-associated pathogens. Despite a documented hereditary predisposition, environmental factors are the most important in determining the occurrence of foot-related lameness. Moist and warm environment, increased parity and milk yield, inappropriate housing conditions and infrastructures, inadequate hygiene status, imbalanced nutrition, and insufficient foot care are the most critical risk factors. Furthermore, a foot-lameness control plan should include targeted implementation of claw trimming and footbathing, evidence-based planning of hygiene measures in preventive veterinary practices (i.e., antibiotic administration, vaccinations against footrot), selective breeding to footrot resistance, and, most importantly, the continuous training of farming personnel. Controlling foot-lameness in dairy sheep is critical in determining the well-being of animals, and strongly affects the farm's profitability and sustainability.

Characterisation of major histocompatibility complex class IIa haplotypes in an island sheep population

The ovine MHC class IIa is known to consist of six to eight loci located in close proximity on chromosome 20, forming haplotypes that are typically inherited without recombination. Here, we characterise the class IIa haplotypes within the Soay sheep (Ovis aries) on St. Kilda to assess the diversity present within this unmanaged island population. We used a stepwise sequence-based genotyping strategy to identify alleles at seven polymorphic MHC class IIa loci in a sample of 118 Soay sheep from four cohorts spanning 15 years of the long-term study on St. Kilda. DRB1, the most polymorphic MHC class II locus, was characterised first in all 118 sheep and identified six alleles. Using DRB1 homozygous animals, the DQA (DQA1, DQA2 and DQA2-like) and DQB (DQB1, DQB2 and DQB2-like) loci were sequenced, revealing eight haplotypes. Both DQ1/DQ2 and DQ2/DQ2-like haplotype configurations were identified and a single haplotype carrying three DQB alleles. A test sample of 94 further individuals typed at the DRB1 and DQA loci found no exceptions to the eight identified haplotypes and a haplotype homozygosity of 21.3%. We found evidence of historic positive selection at DRB1, DQA and DQB. The limited variation at MHC class IIa loci in Soay sheep enabled haplotype characterisation but showed that no single locus could capture the full extent of the expressed variation in the region.

Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea

The swine leukocyte antigens (SLAs) are the multigene families related to immune responses. Little is known about the effect of the DRA gene on diarrheal disease. This study reported the genetic diversity of the DRA gene in exons 1, 3 and 4 in 290 Chinese Yantai black pigs. No variation was identified in exon 3. In exon 1, three genotypes and two alleles were identified, generated by two single nucleotide polymorphisms (SNPs). In exon 4, there were eight genotypes and five alleles containing seven SNPs were detected with four SNPs being novel SNPs. The low polymorphism found in swine DRA is consistent with the concept that the DRA gene is highly conserved among all mammalian species. Statistical analyses indicated that the genotypes of exon 1 were not significantly associated with piglet diarrhea (p > 0.05); however, genotypes C₄C₄ (1.80 ± 0.33) and A₄E₄ (1.66 ± 0.25) of exon 4 were significantly susceptible to diarrhea (p < 0.01). These indicate that the particular genotypes of the DRA gene are susceptible to diarrheal disease, which provides valuable information for disease-resistance breeding in swine.

Genome-wide association study of footrot in Texel sheep

Background

This is the first study based on a genome-wide association approach that investigates the links between ovine footrot scores and molecular polymorphisms in Texel sheep using the ovine 50 K SNP array (42 883 SNPs (single nucleotide polymorphisms) after quality control). Our aim was to identify molecular predictors of footrot resistance.

Methods

This study used data from animals selected from a footrot-phenotyped Texel sheep population of 2229 sheep with an average of 1.60 scoring records per animal. From these, a subset of 336 animals with extreme trait values for footrot was selected for genotyping based on their phenotypic records. De-regressed estimated breeding values (EBV) for footrot were used as pseudo-phenotypes in the genome-wide association analysis.

Results

Seven SNPs were significant on a chromosome-wise level but the association analysis did not reveal any genome-wise significant SNPs associated with footrot. Based on the current state of knowledge of the ovine genome, it is difficult to clearly link the function of the genes that contain these significant SNPs with a potential role in resistance/susceptibility to footrot. Linkage disequilibrium (LD) was analysed as one of the factors that influence the power of detecting QTL (quantitative trait loci). A mean LD of 0.20 (r² at a distance of 50 kb between two SNPs) in the population analysed was estimated. LD declined from 0.15 to 0.07 and to 0.04 at distances between two SNPs of 100, 1000 and 2000 kb, respectively.

Conclusions

Based on a relatively small number of genotyped animals, this study is a first step to search for genomic regions that are involved in resistance to footrot using the ovine 50 K SNP array. Seven SNPs were found to be significant on a chromosome-wise level. No major genome-wise significant QTL were identified.