Phenotypes were determined for 514 individuals through field assessment of all trees at the time of tissue collection. Trees exempt of beech scale insects and any apparent signs of fungal infection were classified as resistant. A subset of trees was artificially inoculated with scale eggs to confirm resistance either in the field or on grafted ramets of the original trees [16, 17, 25]. A complete description of sampled trees and their phenotypes is included in Additional file 1.