Seedling temperature responses in Arabidopsis RRS-7

Plants have the capacity to sense and respond to even small changes in ambient temperature. Numerous thermomorphogenic responses can be observed in Seedlings including elongation of the hypocotyl, petioles and the primary root while leaf blade areas are reduced. Main objective of the experiment was the assessment of tissue-specific transcriptome responses in Arabidopsis seedlings exposed to elevated ambient temperatures, 5 days old Arabidopsis seedlings grown at 20°C in LD were shifted for 3 or 24h to 28°C. Control plants were kept at 20°C. At time of harvest, cotyledons and roots were dissected and collected separately from the hypocotyl. To minimize circadian effects, plant material was grown in several successive batches and harvested only for a period of 30 min per timepoint on several consecutive days. Shifts and harvest was performed at midday to late afternoon (see ZT in overall design). Seeds of the Arabidopsis accession RRS-7 (CS22688) were surface sterilized, stratified for 4 days in sterile water and subsequently placed on square plates containing ATS medium (Lincoln et al. 1991, The Plant Cell) containing 1.5% Agargel. Seedlings were cultivated for 5d in LD (16h light, 8h dark) at 20°C in walk-in phytochambers with 120 µmol/m2/sec PAR generated from white lite LEDs in approx. 30 cm distance. On day 5, plates were either shifted to 28°C or kept at 20°C as controls. For 3h temperature treatments Seedlings were either shifted at ZT Dissection and harvest of plant material was carried out under the same conditions as cultivation for a total of 30 min for each timepoint. 3 biological replicates for each treatment, timepoint and plant organ were generated by pooling distinct sample sets collected over several successive harvesting sessions. Plant material was homogenized and RNA was extracted using RNeasy Plant Mini Kit (Qiagen) including an on-collumn DNase digestion. Extracted RNA was further processed at the NASC