Detection of putative polymorphic sites was performed by mapping reads filtered for structural RNAs to the beech reference transcript contigs, using the Newbler’s gsMapper program. Both DNASTAR and Newbler all-library combined contig sets were used, separately, as reference transcriptomes in the SNP discovery. A minimum depth of coverage of 15 reads from each library was required to call putative SNPs. High confidence SNP sites were identified as those with a minimum of 100 bases flanking the SNP site and where the reference nucleotide at the SNP site was non-ambiguous. The stress-response genes and EST-based DNA markers served as a resource (Fagus grandifolia Transcriptome, Hardwood Genomics Project, www.hardwoodgenomics.org) for the construction of linkage maps and a framework for a GWAS study.