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Background  Superficial chronic corneal epithelial defects (SCCEDs) are spontaneous corneal defects in dogs that share many clinical and pathologic characteristics to recurrent corneal erosions (RCE) in humans. Boxer dogs are predisposed to SCCEDs, therefore a search for a genetic defect was performed to explain this susceptibility. DNA was extracted from blood collected from Boxer dogs with and without SCCEDs followed by whole genome sequencing (WGS). RNA sequencing of corneal tissue and immunostaining of corneal sections from affected SCCED Boxer dogs with a deletion in the  NOG  gene and affected non-Boxer dogs without the deletion were performed.    Results  A 30 base pair deletion at a splice site in Noggin ( NOG ) (Chr 9:31453999) was identified by WGS and was significantly associated ( P  < 0.0001) with Boxer SCCEDs compared to unaffected non-Boxer dogs. NOG, BMP4, MMP13, and NCAM1 all had significant fold reductions in expression and SHH was significantly increased in Boxers with the  NOG  deletion as identified by RNA-Seq. Corneal IHC from  NOG  deletion dogs with SCCEDs had lower NOG and significantly higher scores of BMP2.    Conclusions  Many Boxer dogs with SCCED have a genetic defect in  NOG .  NOG  is a constitutive protein in the cornea which is a potent inhibitor of BMP, which likely regulate limbal epithelial progenitor cells (LEPC). Dysregulation of LEPC may play a role in the pathogenesis of RCE.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12917-021-02955-1.

A defect in the NOG gene increases susceptibility to spontaneous superficial chronic corneal epithelial defects (SCCED) in boxer dogs