Progressive retinal atrophy (PRA), caused by aberrant functioning of rod/cone photoreceptors leads to blindness. Different types of photoreceptor abnormalities with different ages of onset and progression have been reported in dogs, even in the same breed, and new ones are constantly discovered in Labrador retriever. We collected samples from 3 affected dogs and 3 unaffected siblings, along with the unaffected parents of the same litter. Homozygosity mapping detected six candidate regions >1Mb. Whole-genome sequencing detected an homozygous 3-bp deletion in the coding region of GTPBP2, CFA12 - a GTP-binding protein (CFA12:12,246,348) c.1606_1608del, p.Ala536del).       
            The variant was absent from the online EVA database, the Dog Biomedical Variants Database, and the Dog10k variants database. Testing 75 healthy dogs from the same kennel detected wild type and carrier individuals. More than 600 Labradors from the general population (USA) were genotyped wild type for the variant. The variant was absent from the online EVA database, the Dog Biomedical Variants Database, and the Dog10k variants database. GTPBP2 is associated with Jaberi-Elahi syndrome in Homo sapiens, and splice variants in Mus musculus are associated with neurodegeneration; in both cases photoreceptor degeneration may be included in its manifestation.         
            Heterologous cellular systems were transfected with cDNA encoding WT or A536del mutant GTPBP2 protein and immunoblot analysis of total cell lysate with antibodies to GTPBP2 showed that the expression level of the GTPBP2 mutant protein A536del is slightly but not significantly reduced, compared to the WT form. Instead, the cellular distribution of GTPBP2 protein was investigated by using immunofluorescent methods and confocal analysis of cells transfected with WT or A536del GTPBP2 protein revealed that the WT form is diffuse throughout the cytoplasm of cells, while the mutant form resulted in the formation of cytosolic aggregates in almost 70-80% of cells. We therefore show a non-syndromic, retinal-specific phenotype occurring in a large animal model, associated with a deletion in a conserved Alanine, in a conserved interval outside the GTP domain of GTPBP2, suggesting a potentially novel role of the sequence on cellular localization of the protein.

Blood samples were gathered and DNA extracted as for standard protocol (BACC2 kit)

SNPdata:  genotype data Type from 220k CanineHD array (Illumina). 

Libraries of 300 bp insert size were prepared and illumina HiSeq2500 paired-end reads (2x100 bp) were collected (one lane per sample). Fastq files were generated using Casava 1.8. A total of 561.77 millions reads (100 bp paired-end reads) for the four libraries were collected for the sequenced dogs from a shotgun fragment library (corresponding to an average coverage of the genome of 28.2x and 27.6x for the cases, and 26.7x and 28.4x for the parents).