The main goal of this project was to develop genomic resources for the analysis of traits related to ozone response in black cherry (Prunus serotina Ehrh.), an economically and ecologically valuable hardwood tree native to the eastern United States. As a first goal we developed deep, high quality EST databases from black cherry seedlings previously phenotyped for ozone-tolerance/-sensitivity by exposure to ambient like ozone stress under controlled greenhouse conditions. We present the updated cDNA sequencing results, DNA markers and candidate genes discovered with the EST unigene assemblies. The second goal of this project was to provide linkage maps and marker/trait information by developing reference populations segregating for ozone sensitivity. As a first step we identified full-sib progeny from two populations (ozone-tolerant/-sensitive) of 1500 half-sib (open-pollinated) individuals by progeny exclusion using DNA fingerprinting with SSR markers identified from our EST databases for black cherry and SSR markers from several Prunus species found to be polymorphic in black cherry. From app. 500 amplifiable microsatellite markers we identified a set of 50 SSR polymorphic markers that presently form the base of our first linkage maps. In addition, we have identified over a thousand SNPs in the black cherry EST data, from which 384 markers were tested with the Illumina Goldengate system, of which 319 amplified, and 100 SNP were inserted into our linkage maps. We also report mapping of QTL for ozone tolerance in these populations. This project was supported by a grant from the USDA NIFA Plant Genome Program (#2008-35300-19234).