Genetic Suppression of Plant Development and Chloroplast Biogenesis by SCO3 and PhyB Pathways

In this study we used genetic approaches and transcriptome profiling to unravel the complex interaction of different developmental pathways required for chloroplast development in plants. The recently described snowy cotyledon 3 (sco3) mutant as well as the Phytochrome B (phyb) mutant revealed, in the double mutant, a complex suppressive or additive genetically linked regulation of chloroplast development, flowering time and transcription regulation. Transcriptional profilling of mutants with aberrant chloroplast development: sco3, phyb and the double mutant sco3phyb. Analysis of differences in gene expression profiles between Col-0 (reference line), sco3, phyb and sco3phyb was performed using Affymetrix Gene Chip Arabidopsis ATH1 genome arrays in biological triplicate. Total mRNA was collected from 4 day old seedlings, grown on sterile Murashige Skoog media with 0.8% Agar under long day conditions (16hr light/8h dark, 21°C), was isolated and DNAse treated using the Spectrum Total RNA Kit (Sigma, USA). These were sent for sample quality control, labelling, hybridization and scanning at the Ramaciotti Centre (Sydney). Results were received as raw CEL files, which were subsequently analyzed.