No abstract

The progressive retinal atrophy (PRA) is an inherited eye disease and characterized by progressive retinal degeneration which leads to impaired vision in dogs. Using targeted next generation sequencing of nine PRA cases and six controls, we have identified SNPs in PDC, PDE6A and PDE6B, which were not previously associated with PRA. The gene in which the highest mutations found was PDE6A (113 and 104 SNPs), followed by PDE6B, PDC and RHO in all dog breeds and Spitz-only respectively. Five SNPs identified in PDC gene of Spitz-only breed showed significant association with PRA. However, no pathogenetically relevant mutations were found in RHO gene for PRA. The SNP in PDE6B chr3: 91763017 (G/A) in Spitz-only breed, and PDE6A chr4: 5912574 (T/C) and PDC chr7: 19511750 (T/A) were associated with PRA in the breeds of dog studied. Our results show that PRA is genetically heterogeneous and is caused by multiple, distinct mutations.

Progressive retinal atrophy (PRA) is one of the major causes of retinal photoreceptor cell degeneration in canines. The inheritance pattern of PRA is autosomal recessive and genetically heterogeneous. Here, using targeted sequencing technology, we have performed exome sequencing of 10 PRA-affected (Spitz=7, Cocker Spaniel=1, Lhasa Aphso=1 and Spitz-Labrador cross breed=1) and 6 normal (Spitz=5, Cocker Spaniel=1) dogs. The high-throughput sequencing using 454-Roche Titanium sequencer generated about 2.16 Giga bases of raw data. Initially, we have successfully identified 25,619 single nucleotide polymorphisms (SNPs) that passed the stringent SNP calling parameters. Further, we performed association study on the cohort, and the highly significant (0.001) associations were short-listed and investigated in-depth. Out of the 171 significant SNPs, 113 were previously unreported. Interestingly, six among them were non-synonymous coding (NSC) SNPs, which includes CPPED1 A>G (p.M307V), PITRM1 T>G (p.S715A), APP G>A (p.T266M), RNF213 A>G (p.V1482A), C>A (p.V1456L), and SLC46A3 G>A (p.R168Q). On the other hand, 35 out of 113 unreported SNPs were falling in regulatory regions such as 3'-UTR, 5'-UTR, etc. In-depth bioinformatics analysis revealed that majority of NSC SNPs have damaging effect and alter protein stability. This study highlighted the genetic markers associated with PRA, which will help to develop genetic assay-based screening in effective breeding.