RNA extraction, cDNA synthesis, and quantitative RT-PCR and analysis

RNA extraction, cDNA synthesis, and quantitative (q)RT-PCR were done as described [37]. Selected candidate gene transcript levels were quantified with qRT-PCR with specific primer pairs, designed with Primer-BLAST (http://www.ncbi.nlm.nih.gov/tools/primer-blast/). Transcript levels were normalized to GAMMA-TUBULIN 2 (TUB2; AT5G05620), which was constitutively expressed and auxin independent across samples. All PCRs were run in three biological replicates per three technical repeats. The data were processed with a qRT-PCR analysis software (Frederik Coppens, Ghent University-VIB, Ghent, Belgium). Primers used in this study are listed in the S3 Table.