Heterologous hybridisation to a Pinus microarray: profiling of gene expression in Pinus radiata saplings exposed to ethephon

Background: The design, construction and application of a Pinus microarray platform are described. The oligonucleotide microarray was developed using publicly available Pinus cDNA sequences mostly derived from Pinus taeda to test whether heterologous hybridisation of microarray probes will generate useful data when hybridised with cRNA constructed from the dominant New Zealand forestry species Pinus radiata. Methods: A comprehensive consensus sequence collection of Pinus cDNA sequences was collated into a non-redundant database used for automated design of 60-mer oligonucleotide microarray probes. The microarray slides, manufactured by Agilent Technologies (Palo Alto, California), were used to monitor gene expression in an induction experiment using 2-chloroethylphosphonic acid, common name ethephon and the active ingredient of the plant growth regulator Ethrel (R)(Bayer Crop Science). The transcriptomes from tissues of 2-year old Pinus radiata saplings +/-ethephon treatment were compared by hybridisation onto the Pinus microarray slides. Results: Statistically significant differentially expressed genes identified by heterologous hybridisation to the Pinus microarray following ethephon induction included the up-regulation of genes in the xylem that were related to the metabolism of phenylpropanoids and flavonoids, and also defence responses, specifically against fungal/insect attack and oxidative stress. Bark, mucilaginous xylem and xylem generated largely mutually exclusive cohorts of genes and Gene Ontology (GO) classes. The results are also interpreted in reference to gross and microscopic morphological changes. Samples of gene responses were validated by quantitative RT-PCR. Conclusion: These results confirm the successful development of a Pinus microarray and demonstrate the utility of the microarray for transcriptomic research in Pinus radiata through heterologous hybridisation.