Populus tissue analysis. Populus tissue analysis

We analyzed the transcriptome in roots, young and mature leaves, nodes and internodes in the reference genotype Nisqually-1 and identified a core set of approximately 10,000 genes expressed in common among vegetative organs. Quantitative contrasts of transcript levels among organs identified expected patterns of expression associated with organ-specific physiological processes, although a surprisingly high number of defense-related genes were preferentially expressed in young leaves and nodes. Application of a novel runs test established an objective criterion for the identification of genomic regions in which adjacent genes were expressed more frequently than expected by chance, suggesting the presence of chromatin domains. Comparisons between P. trichocarpa Nisqually-1 and the P. tremula X P. alba hybrid INRA 717-1B4 revealed similar expression patterns, particularly in stems. Although a comparison to Arabidopsis thaliana revealed similar proportions of expressed genes in leaves and stems, there was very little conservation between rank correlations of expression patterns. Keywords: gene expression Overall design: Plant material. Branches from the P. trichocarpa reference genotype Nisqually-1 were placed in soil. After budbreak, shoots were rooted in a misthouse for two weeks. Rooted cuttings (cloned biological replicates) were planted in separate pots in a greenhouse equipped with an ebb-and-flow flood bench system with daily supply of Peters Professional 20-10-20 water-soluble fertilizer diluted to a final concentration of 4 mM nitrogen. After 45 days, whole-roots (R), young leaves (YL) - leaf plastochrone index (LPI) 0-5, mature leaves (ML) - LPI 6-9, nodes (N) and internodes (IN) were collected and immediately frozen in liquid nitrogen. RNA was extracted using standard methods (Chang et al. 1993), DNAse-treated and purified in RNAeasy Qiagen columns (Valencia, CA). The P. tremula × P. alba hybrid genotype INRA 717-1B4, used for a comparison of transcript abundance between poplar species was grown under the same conditions as those described above. Poplar whole-genome oligonucleotide microarrays. This study was based on hybridizations to whole-genome microarrays containing features representing 42,364 predicted transcriptional units from the P. trichocarpa nuclear genome. All transcriptional units were represented by three 60-mer probes, designed by NimbleGen (Madison, WI) in collaboration with Oak Ridge National Laboratory and were synthesized using maskless lithography. cRNA was synthesized from total RNA extracted from individual plants. Labeling, hybridization and scanning were carried out by NimbleGen (Madison, WI) using standard procedures.