In an attempt to identify genes that may be responsible for phenotypic traits conferred by an apple rootstock upon the scion along with desirable rootstockspecific traits, we have used the public expressed sequences (EST and cDNA) to identify genes expressed uniquely in apple rootstocks. A total of 203,221 ESTs and cDNA sequences from apple were downloaded, screened for vector, and separated into 9,228 from root and 193,993 non-root tissues. Each set of sequences was separately clustered (root: 1,868 contigs, 3247 singletons; non-root: 23,340 contigs, 10,668 singletons). Of those, 189 contigs and 955 singletons expressed in root tissue had no matches among the non-root sequences (Blast E-value > 1E-20). These sequences were annotated against SwissProt and the Genbank NR databases. Annotations were used as a basis for selection of 44 genes potentially involved in hormone and other developmental pathways. Unique PCR primers were designed and used to screen a BAC library of the commercial dwarfing apple rootstock 'Geneva 41'. Of these, 35 BAC clones were amplified, and 7 BAC clones polymorphic between parents of the mapping population 'Ottawa 3' × 'Robusta 5'. All seven regions were mapped onto nine linkage groups. These markers have been included into a larger map containing 551 markers total, which is being used to identify QTLs associated with tree architecture and disease resistance. Effort is being made to map monomorphic markers using novel allele discrimination techniques such as High Resolution Melting Curve analysis.