Factor analysis of evaluated and linearly scored traits in Swedish Warmblood horses.

Assessment protocols to describe the various aspects of conformation, gait and jumping traits on a linear scale were introduced at young horse tests for Swedish Warmblood horses in 2013. The traits scored on a linear scale are assumed to be less subjective and more easily compared across populations than the traditional evaluated traits that are scored relative to the breeding goal. However, the resulting number of traits is considerable, and several of the traits are correlated. The aim of this study was to investigate the interrelationship between the different evaluated and linearly scored traits in Swedish Warmbloods using factor analysis. In total, 20,935 horses born 1996-2017 had information on evaluated traits, and 5450 of these also had linearly scored trait records assessed since 2014 when the protocol was updated. A factor analysis with varimax rotation was performed separately for evaluated and linearly scored traits using the Psych package in R. Height at withers was included in both analyses. A total of four factors for evaluated traits and 14 factors for linearly scored traits were kept for further analysis. Missing values for individual traits in horses with linearly scored trait records were imputed based on correlated traits before factor scores were calculated using factor loadings. Genetic parameters for, and correlations between, the resulting underlying factors were estimated using multiple-trait animal models in the BLUPF90 package. Heritability estimates were on a similar level as for the traits currently used in the genetic evaluation, ranging from 0.05 for the factor for linearly scored traits named L.behaviour (dominated by traits related to behaviour) to 0.59 for the factor for evaluated traits named E.size (dominated by height at withers and conformation). For both types of traits, separate factors were formed for jumping and gait traits, as well as for body size. High genetic correlations were estimated between such corresponding factors for evaluated traits and factors for linearly scored traits. In conclusion, factor analysis could be used to reduce the number of traits to be included in multiple-trait genetic evaluation or in genomic analysis for warmblood horses. It can also contribute to a better understanding of the interrelationships among the assessed traits and be useful to decide on subgroups of traits to be used in several multiple-trait evaluations on groups of original traits.

Consequences of specialized breeding in the Swedish Warmblood horse population.

In many European warmblood studbooks, clear specialization toward either jumping or dressage horses is evident. The Swedish Warmblood (SWB) is also undergoing such specialization, creating a possible need for separate breeding programs and a discipline-specific Young Horse Test (YHT). This study investigated how far specialization of the SWB breed has proceeded and the potential consequences. Individuals in a population of 122,054 SWB horses born between 1980 and 2020 were categorized according to pedigree as jumping (J), dressage (D), allround (AR), or thoroughbred (Th). Data on 8,713 J horses and 6,477 D horses assessed for eight traits in YHT 1999-2020 were used to estimate genetic parameters within and between J and D horses and between different periods. Future scenarios in which young horses are assessed for either jumping or dressage traits at YHT were also analyzed. More than 80% of horses born in 1980-1985 were found to be AR horses, while 92% of horses born in 2016-2020 belonged to a specialized category. The average relationship within J or D category was found to increase during the past decade, whereas the relationship between these categories decreased. Heritability estimates for gait traits were 0.42-0.56 for D horses and 0.25-0.38 for J horses. For jumping traits, heritability estimates were 0.17-0.26 for J horses and 0.10-0.18 for D horses. Genetic correlations between corresponding traits assessed in J and D horses were within the range 0.48-0.81, with a tendency to be lower in the late study period. In the future scenarios, heritability and genetic variance both decreased for traits that were not assessed in all horses, indicating that estimation of breeding value and genetic progress for these traits could be affected by a specialized YHT. However, ranking of sires based on estimated breeding values (EBVs) and accuracy of EBVs was only slightly altered for discipline-specific traits. With continued specialization in SWB, specialization of the YHT should thus be considered.

Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects.

BACKGROUND: Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas. In spite of its harmful effect, a relatively high frequency of WFFS carriers has been found in Warmblood horses, suggesting a heterozygote advantage. Thus, in this study our aims were to: (1) estimate the frequency of WFFS carriers in the Swedish Warmblood breed (SWB), (2) estimate the effect of WFFS carrier genotype on performance traits in two SWB subpopulations bred for different disciplines, and (3) simulate the potential effects of balancing selection and different selection strategies on the frequency of carriers. METHODS: In total, 2288 SWB sport horses born between 1971 and 2020 were tested for the WFFS mutation and had estimated breeding values (EBV) for ten traditional evaluating and 50 linear descriptive traits. RESULTS: The frequency of WFFS carriers calculated from a pool of 511 randomly selected SWB horses born in 2017 was equal to 7.4% and ranged from 0.0 to 12.0% among the whole set of tested SWB horses, starting from 1971 till 2020. The effect of the WFFS carrier genotype was significant for several EBV mainly related to movements and dressage traits and especially for horses not bred for the show jumping discipline. Using simulation, we showed that balancing selection can maintain a recessive lethal allele in populations such as the SWB breed over generations and that the frequency is expected to slowly decrease in absence of balancing selection. Finally, we showed that selection against carrier sires can result in a more rapid decrease of the frequency of the mutant allele over time. CONCLUSION: Further research is needed to confirm the apparent association between equine performance and the WFFS carrier genotype. Identification of such associations or new causative mutations for horse performance traits can serve as new tools in horse breeding to select for healthy, sustainable, and better performing horses.

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.

BACKGROUND: The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests. RESULTS: A suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 × 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits tölt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans. CONCLUSIONS: Our results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.

Creating a communication space in the healthcare context: Children's perspective of using the eHealth service, Sisom.

According to the United Nation's Convention of the Rights of the Child, children have the right to participate in their own healthcare and make their opinions heard. The aim of this study was thus to explore the impact of using an eHealth service, Sisom, to gain the children's perspectives during their healthcare appointments. Data were gathered through individual interviews with a purposeful sample of 16 children, aged 6-13 years old, treated for different diseases and using the eHealth service, Sisom, during their healthcare appointments. The interviews were analysed using a constructivist grounded theory. The results showed that using Sisom made children's voice heard by creating a communication space in the healthcare setting. This meant that the children got involved in the communication, were acknowledged as an important person who could give the answers to questions and were given time. Implementing the use of Sisom is a way to make children's needs and preferences explicitly visible for decision-making in practice and thereby supporting the further development of child-centred care in practice.

A genome-wide scan for candidate lethal variants in Thoroughbred horses.

Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Variant analysis of whole-genome sequence data identified two SNPs in the 3'UTR of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations.

Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines.

The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010-2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.

Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds.

BACKGROUND: Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. RESULTS: We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. CONCLUSIONS: This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.

Signatures of selection in the genome of Swedish warmblood horses selected for sport performance.

BACKGROUND: A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. RESULTS: The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (FST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses. CONCLUSIONS: Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.

Car crash fatalities associated with fire in Sweden.

OBJECTIVE: To study the epidemiology and causes of death in fatal car crashes on Swedish roads in which the victim's vehicle caught fire. METHODS: The data set is from the Swedish Transport Administrations in-depth studies of fatal crashes 1998-2008. Autopsies from all cases provided data on injuries, toxicological analyses, and cause of death. RESULTS: In total, 181 people died in 133 burning cars, accounting for 5 percent of all deaths in passenger cars, sport utility vehicles, vans, and minibuses during 1998 to 2008. The cause of death for a third of the victims was fire related, as burns and/or smoke inhalation injuries, with no fatal trauma injuries. Twenty-five of these 55 deaths were persons 19 years or younger and included 15 of 18 rear seat deaths. Over half of the 181 deaths were in vehicles that had collided with another vehicle and, of these cases, half were killed in collisions with heavy vehicles. The percentage of drivers with illegal blood alcohol concentrations (27%) and suicides (5.5%) were not higher than in other fatal crashes on Swedish roads. The ignition point of the fire was indicated in only half of the cases and, of those, half started in the engine compartment and one fourth started around the fuel tank or lines. CONCLUSIONS: Car fires are a deadly postcrash problem. Reducing this risk would be primarily a responsibility for the automotive industry. A multifactor approach could be considered as follows: risk-reducing design, insulation, reduced flammability in motor compartment fluids and plastics, and automatic fire extinguishing equipment. Inspiration could be found in how, for example, the auto racing and aviation industries handle this problem.