Horse Breeding goes Genomic

The overall breeding goal for Warmblood horses is high-level sport performance in show jumping and/or dressage, that originally developed from equestrian disciplines in the cavalry. Traditionally, breeding has in much relied on visual inspection by judges at young horse tests, and the breeder’s own selection of breeding stock. Estimated Breeding Values (EBVs) were introduced as a statistical tool to classify, and improve quantitative traits such as conformation, gaits, and show jumping. The emergence of molecular genetic knowledge made it possible to track down causative mutations associated with simple mendelian inherited disorders and traits, and to set up genetic tests for such mutations. Today, large-scale genomic techniques facilitate the possibility to find genetic associations also to multigenic, and multifactorial traits like sport performance. This means that selection should in theory aim at the whole genome, but such “genomic selection” is not yet at place in the horse breeding industry.

Genetic variation will be lower in chromosomal regions with higher selection pressure, and may comprise genes associated with the traits selected for. Such putative signatures of selection for sport performance were found in the genome of Swedish Warmblood horses (SWB) genotyped for 670,000 markers, when compared to the genome of Exmoor ponies. By calculating breed divergence as “Fixation index” (F_ST), “Runs of Homozygosity” (ROH), and “Cross-population Extended Haplotype Homozygosity” (XP-EHH), we revealed long homozygous regions in equine chromosomes, comprising genes possibly important for performance in sport horses. The detected genes are primarily involved in function of the nervous system, as well as muscle contraction and development, but further studies are needed to confirm functionality in the horse.

These days, breeding of Warmblood sport horses is more specialized on one or the other of the equestrian disciplines; dressage, and show jumping. Estimated breeding values (EBVs) for show jumping, already reveal two main SWB subpopulations, which we could confirm by calculating genetic differentiation, although there is still an overlap with a smaller population of non-specialized horses. Calculation of F_ST, revealed significantly divergent selection pressure on chromosome regions comprising genes controlling cell signaling in the central nervous system in dressage, compared to show jumping horses. The XP-EHH analysis uncovered positive selection on chromosome regions with genes involved in mobility, relaxed locomotion and sensitivity in dressage horses. In show jumping horses, positive selection, to a larger extent involve regions with genes associated with mentality, postsynaptic signaling, reward system, neuromuscular control of coordination, muscle growth and -function. Also, in this case, further studies are needed to confirm the functional role of these genes in Warmblood sport horses.

When applying strong selection, the lower genetic variation in some chromosome regions, could be considered as “regional inbreeding”, and increase the risk of accumulating mutations with negative effect on equine health and welfare. In my on-going project we use Whole Genome Trio Sequencing to unravel mutations causing microphthalmia or anophthalmia where one or both eyes are underdeveloped or missing. The prevalence is unknown, and the disorder may be underdiagnosed. It may be multigenic, why we use a combination of short- and long read sequencing, together with analysis of DNA modifications to detect both single mutations, structural variation, and epigenetic factors. When the inheritance of a disorder is verified, there is an enormous need for information, and dialogue with breeders and breed organizations, on how to tackle the new genetic information. Common questions are how to use heterozygous carriers in the breeding schemes, what is the risk of having an affected foal, etc. To be prepared for this, I use the autosomal recessive lethal mutation in the gene PLOD1, associated withthe Warmblood Fragile Foal Syndrome (WFFS), as an example to simulate how the allele frequencies change depending on strength of the selection pressure.

There are several challenges when implementing genetic and genomic knowledge in breeding of sport horses. Selection is not likely to act on one single, but rather on several, or even thousands of genes involved in complex biological networks. The breeder also has to consider if extreme selection could be linked to a higher incidence of injuries or inherited disorders. It is very difficult to determine if a deleterious mutation is “hitch-hiking” on an advantageous haplotype under selection, or if there is pleiotrophy acting. Genomic selection is routinely used in breeding of production animals, and horse breeders are aware of the method, but so far, the population structure, and the lack of suitable reference populations, has hindered the implementation in horse breeding. The results from my studies of equine genetics and genomics could be an important input in the future implementation of genomics in horse breeding.