Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and two PtaDML10 RNAi lines, KD2 and KD5 transcriptomes

Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between KD transgenic lines and Wild Type Overall design: wild type and two PtaDML10 RNAi lines, KD2 and KD5, were transferred to 3.5 L pots containing blond peat, pH 4.5. Before any photoperiodic treatments, the plants were grown in a chamber under LD controlled conditions (16h light, 21°C, 65% relative humidity and 150 µmol m-2 s-1 light intensity). After 4 weeks the plants were transferred to SD conditions (8h light, 19°C, 65% relative humidity and 150 µmol m-2 s-1 light intensity) for 12 weeks in order to induce apical bud formation. To mimic winter conditions, dormant plants were kept under SD, 100 µmol m-2 s-1 light intensity and 4°C for 4 weeks. Then plants were transferred to LD conditions to promote bud burst. The topmost bud of each plant, so-called apical, was collected when the first visual changes in bud developmental were evident. Buds with morphological changes indicating initial stages of bud break were removed, so all the apical buds were collected in stage 0. We collected 15 apical buds from 15 plants per each WT, KD2 and KD5 genotypes for RNA-seq analyses Results: Using an optimized data analysis workflow, 2151 differentially expressed genes (DEG) were identified in KD lines, among which 764 were found upregulated and 1387 downregulated