Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.

Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and affected foals are usually killed. In order to identify the causal mutation we subjected six confirmed Swedish cases and a DNA pool consisting of 21 control individuals to whole genome resequencing. We screened for polymorphisms where the cases and the control pool were fixed for opposite alleles and observed this signature for only 25 SNPs, most of which were scattered on genome assembly unassigned scaffolds. Read depth analysis at these loci revealed homozygosity or compound heterozygosity for two partially overlapping large deletions in the pseudoautosomal region (PAR) of chromosome X/Y in cases but not in the control pool. One of these deletions removes the entire coding region of the SHOX gene and both deletions remove parts of the CRLF2 gene located downstream of SHOX. The horse reference assembly of the PAR is highly fragmented, and in order to characterize this region we sequenced bacterial artificial chromosome (BAC) clones by single-molecule real-time (SMRT) sequencing technology. This considerably improved the assembly and enabled size estimations of the two deletions to 160-180 kb and 60-80 kb, respectively. Complete association between the presence of these deletions and disease status was verified in eight other affected horses. The result of the present study is consistent with previous studies in humans showing crucial importance of SHOX for normal skeletal development.

Associations of health status and conformation with longevity and lifetime competition performance in young Swedish Warmblood riding horses: 8,238 cases (1983-2005).

OBJECTIVE: To determine associations of health status and conformation with competition longevity and lifetime performance in young Swedish Warmblood riding horses. DESIGN: Cohort study and genetic analysis. ANIMALS: 8,238 horses. PROCEDURES: Horses were examined for health, conformation, and performance from 1983 to 2005, when they were 4 to 5 years old, and competition results from 1983 to 2012 were evaluated. Associations between conformation, health, and talent scores of young horses and longevity (years in competition) and lifetime performance were analyzed. Odds ratios of competing later in life among horses with joint flexion test reactions were determined. Genetic correlations between young horse health, conformation, and talent scores and longevity and lifetime performance were determined. RESULTS: Good overall 4- to 5-year-old health, conformation, and talent scores for performance were phenotypically and genetically associated with greater longevity and lifetime performance. Good health was genetically correlated (rg = 0.3) to longevity and lifetime performance. Among conformation traits, body type and movements in the trot were most strongly associated with future longevity; these were genetically correlated (rg = 0.2 to 0.3) to longevity and lifetime performance. Intermediate-sized horses were associated with highest longevity and lifetime performance. Positive flexion test results were associated with lower ORs (OR, 0.59 for moderate to severe and 0.76 for minor reactions) of competing later in life, compared with no reaction, and were associated with lower longevity (0.4 years). CONCLUSIONS AND CLINICAL RELEVANCE: Horses with good health and conformation at a young age had better longevity in competitions than the mean. Positive correlations suggested that improvement of health and conformation of young horses will enhance their future athletic talent and performance.

Prevalence of clinical findings at examinations of young Swedish warmblood riding horses.

BACKGROUND: Soundness of an individual horse is important for animal welfare and owner economy. However, knowledge of health status in normal horse populations is limited due to lack of systematic health recordings. The aim of the investigation was to study the prevalence of veterinary clinical findings in 4-5-year-old Swedish warmblood riding horses, and their influence on overall health scores, where associations to future longevity has been indicated. RESULTS: The prevalence of clinical findings in 8,281 horses examined during 1983-2005 was studied according to a standardised protocol and related to overall health scores in linear statistical models. Effects of sex, age, examination event and changes over time were included. In total, 49% of the horses had clinical findings of medical health (MED), 42% in hooves (HOOF) and 74% of palpatory orthopaedic health (PALP). However, only 6%, 3% and 24% had moderate or severe findings, of MED, HOOF and PALP, respectively. Flexion test reactions were reported in 21% of the horses (5% moderate/severe), heavily influencing the overall score (H2). One fifth of these horses also had findings of unprovoked lameness while 83% had PALP findings (44% with moderate/severe findings). Acute clinical signs, i.e. heat or soreness, had a large influence on the H2 score but were rare, whereas more common clinical findings had smaller effects on overall health. Large variations in recorded health results were observed among events. A decrease in findings has occurred since 1983, in particular for PALP findings. CONCLUSIONS: Results of occurrence and relevance of evaluated clinical findings could be used for advice on preventive actions to keep horses sound, and possibly for benchmarking, and genetic evaluation of health traits. The distinct effect of event on recorded clinical findings emphasises that further harmonisation of veterinary examinations are desirable.

Genetic analysis of clinical findings at health examinations of young Swedish warmblood riding horses.

BACKGROUND: Soundness is important for welfare and utility of the riding horse. Musculoskeletal disorders are the most common causes of interruption in training and of culling. Despite great importance, heritability of a majority of health traits in horses has previously not been estimated. The objective was to perform genetic analyses of medical and orthopaedic health traits in young riding horses, including estimates of heritability and genetic correlations between health traits, and to reveal possibilities for genetic evaluation of stallions for progeny health. RESULTS: The heritability of health traits was estimated using records from 8,238 Swedish warmblood riding horses examined as 4-5 year olds at the Riding Horse Quality Test in 1983-2005. The analyses were performed using multi-trait linear mixed animal models. The heritabilities of palpatory orthopaedic health (PALP), including effusion, swelling, heat, soreness and stiffness/atrophy, and hoof examination results (HOOF), of hoof shape and hoof wall quality, were 0.12 and 0.10, respectively. The genetic variation in these traits resulted in distinct health differences between progeny groups of stallions. The highest heritability among clinical signs of PALP was found for synovial effusions at 0.14. For systemic locations, joint related findings had the highest heritability; 0.13. The heritabilities of medical health and locomotion examination results were low, 0.02 and 0.04, respectively. A genetic improvement of health status has occurred over time but accounts only partly for the decrease in clinical findings of health during the studied period. CONCLUSIONS: The genetic variation found in PALP and HOOF implies distinct differences between progeny groups. Thus, there are possibilities for improvement of these traits in the population through selection. The weak and non-significant correlation between PALP and HOOF suggests that both traits need to be selected for in practical breeding to improve both traits. Some genetic improvements over time have already been achieved, possibly due to regular stallion health inspections and an indirect selection for lifetime performance. For further improvements stallion breeding values for health may be introduced, based on RHQT examinations, complementary to present breeding values for performance.