Common variants in the CPT1A gene are associated with cataracts in Northern breeds of domestic dog

Abstract

Primary hereditary cataract affects many purebred domestic dog breeds and is a major cause of visual impairment in dogs. Cataracts are common in Northern breeds such as the Siberian Husky, Alaskan Malamute and Samoyed, but their aetiology is currently unknown. Only two genetic loci are known to be causally related to primary hereditary cataracts in the dog. To search for genetic loci associated with cataracts in Northern breeds, we used a genome-wide association study approach in three breeds-Siberian Husky, Alaskan Malamute and Samoyed. Cases were defined as dogs with bilateral posterior polar subcapsular cataracts and controls were at least four years of age with no evidence of cataracts or other ocular abnormality. We found a genome-wide statistical association for cataracts in the Siberian Husky on canine chromosome 18 (P-value: 1.1 x 10 - 7), which was independently replicated in a second larger case-control set (P-value 9.8 x 10 - 29). The Samoyed breed also showed evidence for association in the same genomic region (P-value: 2.4 x 10 - 5). We subsequently used targeted resequencing of the associated region (6.5 Mb) in ten Siberian Huskies and whole genome sequencing of a Husky, Malamute, Samoyed and Norwegian Buhund case to conduct fine-mapping and screen for candidate causal variants. These analyses identified a region of linkage disequilibrium in the four breeds containing common variants in the carnitine palmitoyltransferase 1A (CPT1A) gene that are strongly associated with bilateral posterior polar subcapsular cataracts in the Siberian Husky, Samoyed, Icelandic Sheepdog and Norwegian Buhund and we demonstrate that CPT1A is expressed in the dog lens and retina through RNAseq. Our findings represent a novel locus for cataracts in dogs. However, further work is needed to elucidate the pathophysiology underlying the association between CPT1A and cataracts in Northern breeds.

Fig 1. Example of cataracts in the Siberian Husky.

(A) A three-year-old Husky with a typical PPSC showing a dense triangular polar opacity but also with radiating extensions of opacity along the posterior lens fibres; (B) A Husky first diagnosed with HC/PPSC at age 15 months. This image was obtained at age 9 years. Whilst the dog has nuclear sclerosis (a normal ageing change seen in dogs over 8 years of age), the cataract has also extended around the aged nucleus and cortical vacuoles are present.

Fig 2. Manhattan plots depicting the results of GWAS analyses.

(A) Siberian Husky (33 cases and 61 controls, 107,878 SNPs); (B) Siberian Husky replication set (152 cases and 149 controls, 81,230 SNPs); (C) Samoyed (23 cases and 25 controls, 103,719 SNPs); and (D) Alaskan Malamute (25 cases and 40 controls, 104,618 SNPs). Analyses for (A), (C) and (D) were conducted using a mixed model to adjust for overall population structure and relatedness within samples (see Materials and methods). For (B) analyses were conducted using GEMMA [10] to control for population substructure (see Materials and methods). The horizontal red dotted line denotes genome-wide statistical association using Bonferroni correction (P <  4.6 x 10^− 7 for (A), (C) and (D); and <  6.2 x 10^− 7 for (B)). Plots (A), (C) and (D) show BROADD2 data (Illumina canineHD). Plot (B) shows array data mapped to the CanFam 3.1 genome assembly. See S1 Table for LiftOver to other assemblies.

Fig 3. Partial CFA18 regional association plot of the genomic region surrounding the HC signal in the Siberian Husky (blue diamonds) and Samoyed (grey diamonds).

The horizontal red dotted line denotes genome-wide statistical association (P <  4.6 x 10^− 7), and the green line represents the empirical statistical threshold used to delineate the critical region in the Siberian Husky (P-value < 0.01). The vertical black dashed lines denote the start and end points of this critical region at chr18:51773736 bp and 58230092 bp (BROADD2 genome build; see S1 Table for LiftOver to other canine assemblies). The full CFA18 regional association plot is given in S5 Fig.