M. Grabowski, UMN Extension Educator
Orange and black elliptical spots on garlic leaves and stems are signs of garlic rust. Cause by the fungus Puccinia allii, garlic rust can infect several members of the allium family including garlic, onion, chives and leeks. Severe infection can result in yellow, withered leaves and reduced bulb size. Not much is known about the biology of the garlic rust fungus. Infection occurs in cool moist conditions and two different types of spores are commonly found on infected plants. The orange spots produce urediniospores. These are easily spread from plant to plant during the growing season resulting in new leaf spots. The black spots produce teliospores. These tough spores survive in plant debris and start new infections the following growing season.
If garlic rust appears in the garden, remove all leaf and stem debris from the garden after harvest. These infected leaves and stems can be burned, buried in an area where no alliums will be grown or composted in a pile that heats up. If backyard composting is not available many areas offer municipal compost drop off sites. Avoid planting garlic, onions, leeks or chives in the same area for the next 2-3 years. It is not known if the garlic rust fungus can move from an infected plant into the garlic cloves used for seed, but disease originating from infected seed has never been reported.