Investigation of Computationally Predicted Structural Polymorphisms in Gaited Horses

Improved understanding of variation in genome structure is crucial to provide insight into genomic influence on phenotypic traits. In a previously conducted analysis, six re-sequenced horse genomes were inspected for single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). SVs, specifically inversions, are usually hard to detect but have been linked to major phenotypical variations in the horse. For example, the Tobiano white spotting pattern is caused by a paracentric inversion on the Equus caballus chromosome 3, likely disrupting a promoter region of the KIT gene. INDELs are the second most common form of genomic variation. An example of an INDEL is the deletion in MYO5A gene which causes Lavender Foal Syndrome.

Further analysis of the data provided by the previous study demonstrated that regions of the genome under selection in the three gaited horse breeds possessed unique genes ontology (GO) terms for biological processes in locomotion. Notably one of the hits - a computationally predicted insertion fragment - is similar between two of these horses, but is not present in the other four horses nor in Twilight, the horse reference genome.

With about 14,075 annotated SVs and an average of 357,000 homozygous alternative INDELs amongst the six re-sequenced horses, such diversity has the capacity to be a major source of phenotypic variation in the horse. Further investigations will assess gene-disrupting SVs and INDELs in the equine genome and its associations with phenotypic effects.