Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size.

Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long-term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome-wide ROH coverage (SROH ) within the range of 237.4-284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (SROH from 176.4-180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.

Novel insights into Sabino1 and splashed white coat color patterns in horses.

Within the framework of genome-wide analyses using the novel Axiom® genotyping array, we investigated the distribution of two previously described coat color patterns, namely sabino1 (SBI), associated with the KIT gene (KI16+1037A), and splashed white, associated with the PAX3 gene (ECA6:g.11429753C>T; PAX3C70Y ), including a total of 899 horses originating from eight different breeds (Achal Theke, Purebred Arabian, Partbred Arabian, Anglo-Arabian, Shagya Arabian, Haflinger, Lipizzan and Noriker). Based on the data we collected we were able to demonstrate that, besides Quarter horses, the PAX3C70Y allele is also present in Noriker (seven out of 189) and Lipizzan (three out of 329) horses. The SB1 allele was present in three breeds (Haflinger, 14 out of 98; Noriker, four out of 189; Lipizzan one out of 329). Furthermore, we examined the phenotypes of SB1- and PAX3C70Y -carrier horses for their characteristic white spotting patterns. None of the SB1/sb1-carrier horses met the criteria defining the Sabino1 pattern according to current applied protocols. From 10 heterozygous PAX3C70Y -carrier horses, two had nearly a splashed white phenotype. The results of this large-scale experiment on the genetic association of white spotting patterns in horses underline the influence of gene interactions and population differences on complex traits such as Sabino1 and splashed white.

Association between population structure and allele frequencies of the glycogen synthase 1 mutation in the Austrian Noriker draft horse.

The aim of this study was to determine the allele frequency of the glycogen synthase 1 (GYS1) mutation associated with polysaccharide storage myopathy type 1 in the Austrian Noriker horse. Furthermore, we examined the influence of population substructures on the allele distribution. The study was based upon a comprehensive population sample (208 breeding stallions and 309 mares) and a complete cohort of unselected offspring from the year 2014 (1553 foals). The mean proportion of GYS1 carrier animals in the foal cohort was 33%, ranging from 15% to 50% according to population substructures based on coat colours. In 517 mature breeding horses the mutation carrier frequency reached 34%, ranging on a wider scale from 4% to 62% within genetic substructures. We could show that the occurrence of the mutated GYS1 allele is influenced by coat colour; genetic bottlenecks; and assortative, rotating and random mating strategies. Highest GYS1 carrier frequencies were observed in the chestnut sample comprising 50% in foals, 54% in mares and 62% in breeding stallions. The mean inbreeding of homozygous carrier animals reached 4.10%, whereas non-carrier horses were characterized by an inbreeding coefficient of 3.48%. Lowest GYS1 carrier frequencies were observed in the leopard spotted Noriker subpopulation. Here the mean carrier frequency reached 15% in foals, 17% in mares and 4% in stallions and inbreeding decreased from 3.28% in homozygous non-carrier horses to 2.70% in heterozygous horses and 0.94% in homozygous carriers. This study illustrates that lineage breeding and specified mating strategies result in genetic substructures, which affect the frequencies of the GYS1 gene mutation.

The use of novel phenotyping methods for validation of equine conformation scoring results.

In this experiment, which is based on a cohort of 44 Lipizzan mares from the Austrian state stud farm of Piber, we present new statistical techniques for the analysis of shape and equine conformation using image data. In addition, we examined which strategies and procedures of image processing techniques led to a successful interpretation of the traits implemented in horse breeding programs. A total of 246 two-dimensional anatomical and somatometric landmarks were digitized from standardized photographs, and the variation of shape has been analyzed by the use of generalized orthogonal least-squares Procrustes (generalized Procrustes analysis (GPA)) procedures. The resulting shape variables have been regressed on the results from linear type trait classifications. In addition, the rating scores of six conformation classifiers were tested for agreement, yielding an inter-rater correlation (inter-class correlation) ranging from 0.41 to 0.68, respectively, a κ coefficient ranging from 0.16 to 0.53. From the 12 linear type traits assessed on a valuating scale, only the type-related traits (type, breed-type and harmony) revealed significant (P<0.05) results in the regression analysis of shape variables on linear type traits. The other nine traits were characterized by a lower agreement between classifiers and did not result in a significant 'shape regression'. Finally, the 'horse shape space' defined by shape variables resulting from GPA procedures offered the possibility to assist in trait definition and in the evaluation of ratings, and it is an adequate biological and objective scale to human perception of conformation, which is expressed in numerical data only.

Fragility non-hip fracture patients are at risk.

INTRODUCTION: Fragility fractures are a growing worldwide health care problem. Hip fractures have been clearly associated with poor outcomes. Fragility fractures of other bones are common reasons for hospital admission and short-term disability, but specific long-term outcome studies of non-hip fragility fractures are rare. The aim of our trial was to evaluate the 1-year outcomes of non-hip fragility fracture patients. METHODS: This study is a retrospective cohort review of 307 consecutive older inpatient non-hip fracture patients. Patient data for analysis included fracture location, comorbidity prevalence, pre-fracture functional status, osteoporosis treatments and sociodemographic characteristics. The main outcomes evaluated were 1-year mortality and post-fracture functional status. RESULTS: As compared to the expected mortality, the observed 1-year mortality was increased in the study group (17.6 vs. 12.2 %, P = 0.005). After logistic regression, three variables remained as independent risk factors for 1-year mortality among non-hip fracture patients: malnutrition (OR 3.3, CI 1.5-7.1), Charlson comorbidity index (CCI) (OR 1.3, CI 1.1-1.5) and the Parker Mobility Score (PMS) (OR 0.85, CI 0.74-0.98). CCI and PMS were independent risk factors for a high grade of dependency after 1 year. Management of osteoporosis did not significantly improve after hospitalization due to a non-hip fragility fracture. CONCLUSION: The outcomes of older non-hip fracture patients are comparable to the poor outcomes of older hip fracture patients, and appear to be primarily related to comorbidities, pre-fracture function and nutritional status. The low rate of patients on osteoporosis medications likely reflects the insufficient recognition of the importance of osteoporosis assessment and treatment in non-hip fracture patients. Increased clinical and academic attention to non-hip fracture patients is needed.

Ophthalmological findings in a closed herd of Lipizzaners.

REASONS FOR PERFORMING THE STUDY: There are no studies on the ophthalmic health status in the Lipizzaner breed. OBJECTIVE: To perform an ophthalmological survey in a closed herd in 3 housing systems. MATERIALS: All horses at the Federal Stud Piber, Heldenberg and the Spanish Riding School Vienna were subjected to ophthalmological examination. Findings were documented and correlated with factors such as age, gender, location and housing situation. The interrelation of abnormalities of different regions was determined by calculating accuracy. Pedigree analysis of horses affected by cataract was performed. RESULTS: A total of 267 horses met the inclusion criteria of this study. Of these, 172 horses were stabled in Piber, 72 in Vienna and 23 in Heldenberg. Ophthalmological examination revealed 203 cases with ocular findings, predominantly involving the conjunctiva (44.6%), cornea (21.7%) and fundus (37.5%). In 24 (8.9%) horses a diagnosis of cataract was made. There was no interrelation between different eye diseases. Horses stabled at Piber were significantly more affected by conjunctival and fundic abnormalities. Fewer abnormalities were found in horses stabled in open boxes. Access to free stalls resulted in more cases of conjunctivitis. Pedigree analysis showed no evidence of inbreeding as a cause of cataract formation. CONCLUSION AND POTENTIAL RELEVANCE: Acquired corneal abnormalities were over-represented in this study. This survey may serve as a basis for further research on the pathogenesis of ophthalmic diseases in Lipizzaners.

Pedigree analysis in the Austrian Noriker draught horse: genetic diversity and the impact of breeding for coat colour on population structure.

The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average co-ancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.

Individual-based assessment of population structure and admixture in Austrian, Croatian and German draught horses.

All over Europe, the number of draught horses has decreased drastically during the last 50 years. As a prerequisite for efficient management decisions, we analysed the conservation status in Austrian (Noriker Carinthia - NC, Noriker Salzburg - NS), Croatian (Croatian Coldblood - C, Posavina horse - P) and German (Altmaerkisch Coldblood - A, Black Forest horse - BF, Mecklenburg Coldblood - M, Rhenish German Draught horse - R, Saxon Thuringa Coldblood - ST, Schleswig Draught horse - Sch, South German Coldblood - SG) draught horses (434) using multilocus genotypic information from 30 (effectively 27) microsatellite loci. Populations located in areas with less intensive agricultural production (C, NC, NS, P and SG) had greater diversity within the population and estimated effective population size than A, BF, Sch, M, R and ST populations. The PCA plots revealed that populations form five separate groups. The 'Noriker' group (NC, NS and SG) and the 'Rhenish' group (A, M, R and ST) were the most distinctive (pairwise F(ST) values ranged from 0.078 to 0.094). The 'Croatian' group (C and P) was in the centre, while the BF and Sch populations formed two out-groups. A posterior Bayesian analysis detected further differentiation, mainly caused by political and geographical factors. Thus, it was possible to separate the South German Coldblood from the Austrian Noriker population where no subpopulation structure was detected. The admixture analysis revealed imprecise classification between C and P populations. A small but notable separation of R from A, M and ST populations was detected, while Sch and BF populations remained as out-groups. The information obtained should aid in making efficient conservation decisions.