Screen of oligonucleotides for microarray transcriptome analysis of Populus deltoides and P. trichocarpa

The purpose of this study was to evaluate a set of 6-7 long oligonucleotide probes developed based on the sequence of the Populus trichocarpa genome, that are optimal for gene expression analysis of P. deltoides and a hybrid of P. deltoides and P. trichocarpa. To evaluate these probes, multiple tissues (differentiating xyle, leaf and whole-root) of a pure P. deltoides and a hybrid (P. deltoides X P. trichocarpa) were transcript profiled for identification of one or more probes that are not biased towards one or the other genotype. Three vegetative tissues (root, leaf and xylem) harvested from two biological replicates from each genotypes of Populus deltoides (genotype D124) and a Populus hybrid (P. deltoides X P. trichocarpa, genotype 52-225) were hybridized separately to microarrays in a single-dye experiment.