Leveraging Emerging Genomic Technologies For The Benefit Of The Domestic Horse

Abstract

The domestic horse has played an important role in human history and serves as a valuable model organism for genetic studies. Generations of selective breeding have created several key population and genomic advantages for study. The completion of the horse reference genome sequence in 2009 further strengthened the utility of the horse as a genetic model. However, in order to continue deriving the maximum benefit from research, it is vital to incorporate novel genomic technologies. We applied three such methodologies in the following projects. Chromosomal aberrations can lead to congenital abnormalities, embryonic loss, and infertility. Detection of small deviations - such as aneuploidy in the acrocentric chromosomes, mosaicisms, or partial chromosomal structural variation can be difficult with typical cytogenetics techniques. The Illumina Equine SNP50 BeadChip was utilized for molecular karyotyping, assessing copy number variation at fifty thousand loci simultaneously throughout the genome. This method successfully diagnosed aberrations in three cases where the traditional FISH was not possible. Laminitis is a devastating disease of the hoof that is the second leading cause of both lameness and euthanasia in the horse. The etiology is poorly understood, and published research has focused on a small number of known gene targets. Due to the poor quality of current equine gene annotation, RNA-seq of lamellar tissue was undertaken to provide a more robust set of targets. De novo transcriptome assembly generated a valuable gene annotation resource for the future study of laminitis. Leopard complex spotting is a unique collection of pigmentation patterns in which a single autosomal allele (LP) allows for the expression of other modifying loci. RNA-seq was used to supplement typical gene mapping approaches for characterizing PATN1, a major effect modifier of LP. A targeted set of variants was produced for finemapping a 16 Mbp region associated with the phenotype. These genotypes identified a SNP in the 3'UTR of RFWD3 that may be utilized by horse breeders for the identification of non-LP horses that carry PATN1. These three projects demonstrate the benefit of next-generation technologies. High-throughput methods facilitate rapid high-resolution evaluation of the entire genome, providing a comprehensive tool for future research.