2.2.1 Plant material and growth conditions
The HRR mutant line (hrr mutant), a GT_5_47364 transposon line in Landsberg erecta (Ler) background of A. thaliana, was used to evaluate the effect of HRR (At5g53680) loss-in-function. This line and wild-type Ler were obtained from John Innes Centre (JIC, UK) collection and ordered through NASC center (http://arabidopsis.info/). Plant growth was promoted under a long photoperiod
(16 h light/ 8 h dark), at 23ºC with 80 µE m- 2.s-1 of light intensity (Annex II, sections 1 and 2).
2.2.2 Plasmid construct and plant transformation
For producing over-expression lines, the p35S::HRR-GFP6 construct was obtained through the Gateway system (Invitrogen). RNA from 16-days-old Ler seedlings, subjected to HS for 60 min at 38ºC, was used for the cDNA synthesis and amplification of the HRR coding sequence (510 bp). PCR conditions and specific primers are presented in Annexes III and IV. The amplified sequence was cloned into the Gateway® vector pDONR™201 (Invitrogen) by performing the BP recombination reaction (Annex II, section 12). The resulting pENTR-HRR vector was used to perform the LR recombination reaction with the pDEST vector pMDC83 (Curtis and Grossniklaus 2003), which contained the translational fusion GFP6 (C-terminal GFP6). The Agrobacterium tumefaciens (EHA105 strain) harbouring the resulting p35S::HRR-GFP6 construct was used to transform wild- type (Ler) and hrr mutant Arabidopsis plants by the floral dip method (Clough and Bent 1998). Single genetic transformants were detected in the T2 generation by growing on MS medium supplemented with hygromycin and followed a 3:1 segregation. From the homozygous T3 transgenic lines, five transformed lines were selected: L2 and L6 (in Ler genetic background), and JP5, JP6 and JP9 (in
hrr genetic background). Synchronised plants of hrr and HRR over-expression mutant lines (T3), as
well as wild-type Ler, were screened by diagnostic PCR using the conditions and specific primers described in Annexes II (section 8), III and IV.
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2.2.3 Selection of HRR homozygous recessive insertion and over-expression
lines
About 100 plants from the T3 generation of ordered hrr seed stocks were grown for diagnostic PCR and seed harvesting. Genomic DNA from Arabidopsis leaves was extracted (Annex II, section 3) and used for selecting the homozygous hrr mutant lines by diagnostic PCR analysis (Annex II, section 8). For this amplification a multiplex primer system was used: one specific primer for the transposon insertion (prb.ZF_rv primer) and two primers conceived to HRR gene (RB and LB primers). These primers were designed using the Oligo6 software (Primer Analysis Software, version 6.68). Primer sequences and PCR conditions are present in Annexes III and IV, respectively. After gel electrophoresis (Annex II, section 7), the hrr mutant seeds from those plants displaying the proper estimated fragment size were harvested. The diagnostic PCR analysis was repeated for these hrr mutants in the following three generations to guarantee that transposon insertion remained stable. From the selected homozygous T3 HRR over-expression lines, a diagnostic PCR was performed to evaluate the presence of p35S::HRR-GFP6 transgene in the genome of these plants. The genomic DNA was isolated and amplified with diagnostic primers for pMDC 35S and pMDC gfp left borders as referred above.
2.2.4 Expression analysis of HRR homozygous recessive insertion and over-
expression lines
To analyse the HRR expression levels in five-weeks-old plants of wild-type (Ler) and hrr mutant lines, grown under standard conditions, total RNA was isolated from different Arabidopsis organs/tissues with Trizol® reagent (Annex II, section 4). For the cDNA synthesis (SuperScript First- Strand Synthesis System, Invitrogen), it was followed the provider instructions (Annex II, section 9). The resulting cDNA pools were then used for the gene expression analysis by semi-quantitative RT- PCR amplification, which was performed as described in standard protocol for PCR reaction (Annex II, section 8). The same procedure was followed for confirming the over-expression of HRR transcripts in HRR over-expression seedlings (16-days-old), grown under standard conditions. The gene-specific primer pairs used for this analysis, HRRcDNA_fw/HRRcDNA_rv for wild-type Ler and
hrr mutant sample and HRR_RT_fw/HRR_RT_rv for HRR over-expression lines, and corresponding
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expression levels were simultaneously analysed as internal control for RNA amount normalisation of each RNA sample (gene-specific primers and PCR conditions are presented in Annexes III and IV).
2.2.5 Thermotolerance germination assays
All seed germination assays were performed with synchronised seeds (seed pools from lines simultaneously grown in the same conditions). Seeds were stratified (4ºC, 2 days) in the dark, and subsequently surface sterilised (Annex II, section 1). For HS treatments, sterilised seeds were heat- stressed by immersion of respective microtubes into a water bath under a constant temperature of 50°C, for different periods (15-300 min), or at different temperatures (38-56°C) for 60 minutes. Immediately after HS, seeds were resuspended in sterile 0.25% (w/v) agarose solution and sown
onto MS-agar medium. The plates were incubated under 16h light/8h dark photoperiod (80 µE.m- 2.s-
1 light intensity) at 23ºC. The emergence of radicle was followed every day, from second to tenth day
after stress imposition. Germination rate (as percentage, %) was normalised with corresponding germinated seeds in control conditions (23ºC). Mean and SEM were determined based on results from four replicates for each seed line, all containing 30 seeds. Results were submitted to statistical analysis using t-test, one-way or two-way analysis of variances (ANOVA) tests (GraphPad Prism v.5 program), considering statistically significant differences those that exhibit p-values of <0.001, <0.01 or <0.05. All experiences were repeated with similar results.
2.2.6 Salt, osmotic and oxidative stress assays
Germination of heat stressed seeds in salt, osmotic or oxidative stress conditions was performed as previously referred, but with some modifications. Stratified hrr mutant and wild-type Ler seeds were heat-stressed (47ºC), during for 60 min. Seeds were sown and allowed to germinate onto MS medium supplemented with different concentrations of sodium chloride (NaCl; 0, 75, 100, 150, 200 mM), mannitol [1.5, 3, 5, 7% (w/v)] or paraquat (0.001, 0.01, 0.1, 1 µM). The appearance of
green and fully expanded cotyledons (viable seedlings) was scored at 10th day of assay. The same
assay was simultaneously performed with stratified seeds without HS treatment. Survival seedlings percentage (survival rate) was normalised with corresponding viable seedlings in control conditions (non-HS seeds sown onto MS medium without stressors). Mean and SEM were determined based on results from three replicates for each seed line, all containing 40 seeds. Statistical analysis was performed as described for thermotolerance germination assays.
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2.2.7 Hormonal sensitivity assays with ABA and GA
3Germination of seeds in the presence of exogenous ABA and an active form GA3 was performed as
previously described, with some modifications. Stratified wild-type Ler, hrr and HRR over-expression mutant seeds were sown onto MS medium supplemented with different concentrations of ABA (0.5,
1, 1.5 and 2 µM, Duchefa). For germination assays in the presence of exogenous GA3, stratified hrr
mutant and wild-type Ler seeds were directly sown onto MS-agar medium containing variable GA3
concentrations (25, 50, 75 and 100 µM, Duchefa). Whenever a HS treatment was applied, stratified seeds were previously heat-stressed at 50ºC, during 60 min. The emergence of radicle was scored every day, from the second to the tenth day after sowing. Germination rate (%) was normalised with respective viable seeds in control samples. Mean and SEM were based on results from three replicates for each seed line, all containing 40 seeds. Statistical analysis was performed as described for thermotolerance germination assays.