Naturally-occurring canine inherited retinal diseases (IRDs) are true clinical and genetic homologs of human diseases as evidenced by their recent contributions to advancing gene therapies into clinical trials and onto the pharmaceutical market. Nearly 30 different canine IRDs have been characterized at the molecular level with ongoing investigations into the underlying pathogenesis. Cone-rod dystrophy 1 is a form of canine IRD, originally characterized by early-onset blindness, and linked to a genetic variant in the gene RPGRIP1. However, delayed or lack of disease among the RPGRIP1 mutant dogs led us to seek and identify a disease modifier in the gene MAP9. RPGRIP1 has been known to localize at the connecting cilia of photoreceptors with its functions indicated in protein anchoring and trafficking along the cilia. While the role of MAP9 in the retina has not been previously described, we have identified co-localization of MAP9 with RPGRIP1, indicating the involvement of both proteins in the ciliary protein complex. Using the canine model, we aim to elucidate the role of MAP9 in normal photoreceptor connecting cilia and to determine the mechanisms of phenotypic modification in the RPGRIP1 mutants. In parallel, we utilize fibroblasts derived from mutant dogs as well as photoreceptor cell lines to study the effect of normal and abnormal RPGRIP1 and/or MAP9 in ciliogenesis. The large animal, canine model has enabled and facilitated our study into elucidating the role of the ciliary proteins as the driver or the target of pathogenic, and ultimately, therapeutic disease modification.