Genomic analyses in Cavalier King Charles spaniels identify loci associated with clinical signs of Chiari-like malformation and Syringomyelia

Background: Chiari-like malformations (CM) and syringomyelia (SM) are common in Cavalier King Charles spaniels (CKCS) leading to variable manifestations of pain and scratch. Inheritance studies suggest a polygenic mode of inheritance and association studies have identified loci associated with the presence of SM on MRI. Given the poor correlation of clinical signs of CMSM with MRI findings, we hypothesized that an association study with clinical signs as the phenotype could reveal new loci of interest. The objectives of this study were to perform genome-wide association studies on CKCS using SM and clinical sign phenotypes of pain and scratch and to use whole genome sequencing (WGS) to identify variants in regions of interest. We collected DNA on 174 CKCS. Owners completed questionnaires to establish the clinical pain and scratch phenotype and magnetic resonance imaging (MRI) was used to identify CM and SM (linear T2 hyperintensity greater than 2 mm in height) in all dogs. Dogs were genotyped using the Axiom K9 HD (710,000 snps) array. GWAS analyses were performed using GEMMA and categorical and quantitative approaches were used to define clinical phenotypes. Whole genome sequencing (WGS) was performed on an Illumina HiSeq 4000 high-throughput sequencing system. Results: There were no regions associated with SM presence. The presence of signs of pain and scratch was associated with a region on Canis familiaris autosome (CFA) 26 downstream of ZWINT, previously associated with skull changes in CKCS with SM, although genome-wide significance was not reached. Loci were also associated with quantitative pain and scratch scores on CFA 13, 2 and 38. There were 66 variants that segregated with phenotype including 2 missense variants that were predicted to have moderate effects on ZWINT function. Conclusions: The identification of a locus on CFA26 using the clinical phenotype of pain and scratch that coincided with a locus identified in a morphological study provides strong support for this as a region of interest.