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

ABSTRACT: The phytohormone abscisic acid (ABA) regulates major aspects of plant growth and development. ABA is involved in diverse key processes, such as germination, root growth, bud bursts or stomata opening. ABA acts as a key signalling molecule that mediates plant response to environmental cues. Changes in endogenous ABA level triggered rapidly transcriptional and post-transcriptional events. The core ABA signalling cascade consisted in a three-step regulatory processes in which ABA receptor complex activated protein kinases which in turn mediated ABA signal towards specific targets such transcription factors or channels. While the core ABA signalling cascade has been established mainly using mutagenesis on the model plant Arabidopsis, it appeared highly conserved across plant genomes. 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.

ORGANISM(S): Populus nigra

PROVIDER: GSE183780 | GEO | 2026/07/21

REPOSITORIES: GEO