What could be the cause of rust spots and holes on the leaves of my Pluot tree? Other trees nearby do not have this. I'm guessing that those rust spots on the left leaf turn into the holes seen on the right leaf.
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Shot hole disease. It's difficult to control but use mancozeb in the early cover sprays followed by thiophanate methyl closer to harvest. It usually doesn't defoliate the tree. Some varieties are more resistant than others. My Methley rarely gets it but my AU Rubrum gets it every year and it's right beside the Methley.