Citation: Bassett, C.L., Glenn, D.M., Wisniewski, M.E., Norelli, J.L., Farrell, Jr., R.E. 2011. Apple root, bark and leaf genes responding to water deficit [abstract]. Plant and Animal Genome Conference. p.65. Technical Abstract: Plants respond to environmental stress conditions by altering the expression of suites of genes, many of which are associated with defense. Perennial plants, including woody shrubs and trees, have to deal with numerous cycles of environmental extremes in order to survive. We are using apple (Malus x domestica Borkh.) as a model system for woody plant stress resistance with focus on ‘Royal Gala’, a cultivar of commercial importance. Since most critical plant processes are limited by inappropriate water status, our initial studies have emphasized water deficit stress to mimic frequently encountered drought conditions (periods). Suppression subtractive hybridization (SSH) was used to isolate genes that were up- or down-regulated in response to a two-week severe drought treatment (40% of water saturation). We identified genes with altered expression in roots, bark and leaf compared to water-saturated control plants. Several novel genes were observed in the subtraction representing up-regulated water deficit-responsive root genes; these included BYPASS1 (associated with aerial architecture), a putative leucine zipper homeobox gene of unknown function, and a mitochondrial import receptor subunit. There was little overlap between water-deficit responsive genes from the three tissues and as expected, a number of photosynthetic genes were down-regulated in leaves. The data are discussed in comparison to other plant systems undergoing water restrictions and other stress treatments.