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There are two types of 1-day field tests available for young Swedish Warmblood sport horses; one test for 3-year olds and one more advanced test for 4-year olds. Conformation, gaits and jumping ability are evaluated at both tests. Studies on various genetic parameters were based on about 20 000 tested horses. The data for 4-year olds consisted of 30 years of testing. The aims of the study were to estimate genetic parameters for results from different time periods, and to estimate heritabilities for, and genetic correlations between, traits scored in the two tests. The judgement of traits was shown to have been changed during the 30 years of testing, resulting in changes in higher heritabilities in, and stronger genetic correlations between, later time periods. In the first time period, records showed higher residual and lower genetic variances than in the subsequent time periods. Genetic correlations between traits recorded in the first and last time period deviated considerably from unity. Further studies are needed to investigate how to treat data from the early period in genetic evaluations. Heritabilities were moderate to high for conformation traits (0.24 to 0.58) at both types of tests, except for correctness of legs (0.08). The heritabilities for gait traits were also moderate to high (0.37 to 0.53). For jumping traits, the heritabilities ranged between 0.17 and 0.33. The highly positive genetic correlations (0.82 to 0.99) between corresponding traits tested at the simpler test for 3-year olds and at the ridden test of 4-year olds implied that it would be desirable to include the test results of 3-year olds into the genetic evaluation as breeding values for Swedish Warmbloods for many years has only been based on results from 4-year olds.

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.

For many years, the breeding value estimation for Swedish riding horses has been based on results from Riding Horse Quality Tests (RHQTs) of 4-year-olds only. Traits tested are conformation, gaits and jumping ability. An integrated index including competition results is under development to both get as reliable proofs as possible and increases the credibility of the indexes among breeders, trainers and riders. The objectives of this study were to investigate the suitability of competition data for use in genetic evaluations of horses and to examine how well young horse performance agrees with performance later in life. Competition results in dressage and show jumping for almost 40 000 horses from the beginning of the 1960s until 2006 were available. For RHQT data of 14 000 horses judged between 1988 and 2007 were used. Genetic parameters were estimated for accumulated competition results defined for different age groups (4 to 6 years of age, 4 to 9 years of age and lifetime), and for different birth year groups. Genetic correlations were estimated between results at RHQT and competitions with a multi-trait animal model. Heritabilities were higher for show jumping than dressage and increased with increasing age of the horse and amount of information. For dressage, heritabilities increased from 0.11 for the youngest group to 0.16 for lifetime results. For show jumping corresponding values increased from 0.24 to 0.28. Genetic correlations between competition results for the different age groups were highly positive (0.84 to 1.00), as were those between jumping traits at RHQT and competition results in show jumping (0.87 to 0.89). For dressage-related traits as 4-year-old and dressage competition results the estimated genetic correlations were between 0.47 and 0.77. We suggest that lifetime results from competitions should be integrated into the genetic evaluation system. However, genetic parameters showed that traits had changed during the over 35-year period covered due to the development of the sport, which needs to be considered in future genetic evaluations.Keywords: riding horses, dressage, show jumping, performance test, genetic parameters ImplicationsTo estimate reliable breeding values of Swedish Warmblood horses and to reduce bias due to pre-selection of horses for competition, it is important to integrate all available information from both young horse tests and competitions. Lifetime competition results are recommended and high genetic correlations were estimated between results in competition and results from tests of 4-year-old. The equestrian sport has changed during the 20th century, and this study shows that competition results do not mean the same throughout the 35-year long period of recording. Future studies will investigate how to handle competition data from different time periods in genetic evaluations.

BackgroundCopy 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.ResultsWe 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.ConclusionsThis 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.