Answer: Junipers can be badly injured by the rust fungus Gymnoporangium clavarieaeforme which attacks trunks and large branches of established plants. Upon closer inspection you may find long, rough cankers on your juniper. It's a difficult disease to control because it invades healthy tissue in a quick manner. Complicating the problem is that there are alternate hosts so even if you control the rust on your juniper, you may need to control it on other plants (Amelanchier, Crataegus (hawthorn) and Pyrus) so they don't reinfect one another. If your juniper is a prized member of your landscape you can use a fungicide to control the disease and do a little surgery. Otherwise you might consider replacing it with a different plant.
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