Whole Genome Sequencing of Two Unrelated Arabian Foals with Occipitoatlantoaxial Malformation

A group of rare developmental craniocervical junction abnormalities in horses are termed occipitoatlantoaxial malformations (OAAM). These vertebral deformities involve the occiput, first and second cervical vertebrae. Hoxd3-null mice display a similar phenotype as the familial OAAM-affected Arabian horses and recently, our laboratory identified an intergenic deletion in the HOXD region in an Arabian foal with OAAM. The aim of this study is to identify additional putative functional variants associated with OAAM in Arabian horses. Two Arabian colts (20-30 days of age) were identified with OAAM at necropsy. Tissue samples were collected and DNA isolated. Genomic libraries were prepared and sequenced on an Illumina HiSeq 2500, generating 125 bp PE reads at ~12x coverage. Sequence data was trimmed using Trimmomatic. Subsequently, remaining high-quality reads were mapped to the EquCab2.0 reference genome using the Burrows-Wheeler Aligner (BWA), sorted and indexed using SAMtools. Aligned reads were examined for any possible structural variants within the HOXD region as compared to seven unaffected Arabian horses using the Integrated Genomic Viewer (IGV). Additionally, variants (SNPs and insertions/deletions) were called genome-wide using the Genome Analysis Toolkit (GATK). Results suggest that genetic heterogeneity within the HOXD region may contribute to the OAAM phenotype in Arabian horses.