Although not always possible, avoid planting in low-lying, flood prone areas. Control weeds around the trunk of apple trees, as many serve as alternate hosts for the crown rot fungus(especially nightshades). Reduce nitrogen application on young trees, and trees with excessive growth as they are more susceptible to crown rot.
As there are different species of Phytophthora (like P. cambivora, P. cryptogea, and P. cactorum, to name a few!) resistance isn’t as straightforward as it might appear (See reference at end of this article). Bud. 9 and Emla provide the most reliable resistance in published studies.
To slow lesion growth (canker) on partially girdled trees, expose the crown, scrape away infected bark and air dry. Remember to replace earth around trunks before winter. Right now, Aliette and phosphorous acid derivatives like Alude or Rampart can be sprayed on the foliage of non-bearing trees at 30 to 60 day intervals beginning at tight cluster. For infected trees, in the fall, Ridomil can be applied as a drench around the trunk (best for preventing crown and collar rot) or as a banded treatment within the drip line (best for root rot). A Ridomil drench can be applied in the early spring before growth begins, or in the fall after harvest but before the ground freezes. Ridomil and Aliette rates can be found in the Midwest Fruit Pest Management Spray Guide.
Stone fruit are susceptible to Phytophthora, as well. For new plantings, make the first application 2 weeks after planting. Additional applications should be made at 2–3 month intervals or to coincide with periods most favorable for root, crown, or collar rot development (like now). For established plantings, the application should be made in spring before the plants start growth. Additional applications should be made at 2–3 month intervals or to coincide with periods most favorable for root, crown, or collar rot development(now).
Note: Do not dip roots of trees in, or spray bare roots with, solutions containing Ridomil. Do not apply to stressed trees.
Phytophthoras are a serious problem with small fruit, as well
References:
Brown, T. and Mircetich, SM. 1993. Relative resistance of thirteen apple rootstocks to three species of Phytophthora. Phytopathology 83:744-749.
http://apsnet.org/publications/phytopathology/backissues/Documents/1993Articles/Phyto83n07_744.PDF