Time-resolved transcriptomics and gene networks identify the primary targets for abscisic acid signalling in Populus nigra roots

In the present study, time-resolved transcriptomics and gene co-expression networking were used to decipher the primary ABA targets in the roots of a perennial model. We documented the ABA-triggered transcriptional events in the growing roots of the Populus nigra. Transcriptome was studied throughout two time-series experiments where hydroponically rooted cuttings were exposed to 2 µM ABA treatments.

Controls were treated with ABA-free solution. Hormone profiling not only confirmed that ABA uptake occurred but also highlighted the gradual accumulation of abscissate forms and a rapid rewiring of other hormones. For all time points, transcript abundance was quantified using RNA-Seq technology (Illumina).

Two computational approaches were employed, based either on pairwise differential expression (DESeq2 R package and IDREM) or on co-expression relationships (WGCNA and DGCA R-packages). The ABA targets involved in the poplar root response to osmotic stress were investigated further (DGCA, WGCNA R-packages), as the rapid growth of poplar species required a large water amount to sustain their field productivity. Our study revealed the molecular components of ABA interference and the time-dependant structuration of ABA-responsive-gene expression.