What could cause or be related to holes in the iris of the eye?

Several conditions. True holes in the iris can be created surgically, caused by trauma, or arise from certain congenital or genetic defects. Often, there can be the appearance of a hole caused either by an area of thick iris surrounding a region with less pigment (this really is a "valley" called a crypt), or a dark freckle (nevus) on a lighter iris.
Need more info. I am not sure what "holes" you refer to. If you have in mind black "dots" occasionally seen in one's iris, those are benign lesions that just don't have a normal pigment accumulation. If you do have symptoms or those "holes" are just bothersome in appearance, it won't hurt to consult optometrist or ophthalmologist for an in-depth exam.