Prevent blossom-end rot on tomato plants. In the rainy Pacific Northwest, blossom-end rot is a common issue that causes partly grown tomatoes to develop a dark brown spot on the bottom of the fruit. The spot enlarges and eventually causes the entire tomato to rot and develop a leathery skin.The problem is caused by calcium deficiency. It's most common in areas where the growing season starts out wet and then dries out over the summer.Prevent this issue by watering deeply on a regular schedule. Soaker hoses are best because sprinklers that water tomato foliage can cause another disease, called late blight.You can also treat the plants with calcium to prevent or manage blossom-end rot. Eggshells and bone meal are natural sources that can be incorporated into the soil around each tomato plant. There are also commercially available sprays that contain calcium chloride or calcium carbonate to solve this issue. The plant can soak up the nutrient through its foliage for an instant boost.