Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture

Transcriptional Dynamics of the Salicylic Acid Response and its Interplay with the Jasmonic Acid Pathway

“…For example, our coexpression clustering analysis identified coherent gene modules, which can be used to associate genes of unknown function with particular biological processes. This guilt-by-association principle is an often used approach that we, and others, have previously demonstrated as a successful way to uncover novel regulators of particular biological processes and pathways in Arabidopsis (Lewis et al, 2013; Song et al, 2016; Hickman et al, 2017; Walker et al, 2017). To identify novel regulators of the SA response, we selected TF-encoding genes with no previously reported roles in the SA response pathway that were present in clusters that are enriched for terms related to defense responses.…”

Cell type identity determines transcriptomic immune responses inArabidopsis thalianaroots

“…For instance, roots showed a transient root growth inhibition phenotype under salt stress that coincided with the cell type-specific rewiring of hormone signalling to reconfigure root growth-regulating networks under this environment (Geng et al, 2013). Such plasticity in root growth and development appears to be fundamental as it has been observed under nitrogen depletion and was shown to drive lateral root development (Gifford et al, 2008; Walker et al, 2017). It further underlines the hierarchy of root (cell) function with the maintenance of growth and development as top priorities under fluctuating environments.…”

“…For FACS experiments, plants were grown for 12 days on squared ATS plates, and then treated with 1 ml per plate of 1 μM solutions of flg22 or Pep1 peptide or H 2 O as control for 1 h. Whole roots were cut into pieces and then incubated in protoplast solution (1.5% cellulase R10 (Duchefa Biochemie), 1.2% cellulase RS (Duchefa Biochemie), 0.2% macerozyme R10 (Duchefa Biochemie), and 0.12% pectinase (Sigma Aldrich), in 600 mM mannitol, 2 mM MES hydrate, 10 mM KCl, 2 mM CaCl 2 , 2 mM MgCl 2 , and 0.1% BSA, pH 5.7) (Walker et al, 2017) for 1 h. Protoplasts were filtered through 70 and then 40 μm cell strainers, centrifuged at 300 g for 3 mins, resuspended in protoplast solution lacking cell wall-degrading enzymes and subjected to FACS. Three independent biological experiments were carried out for each marker line.…”

“…This organisation is implemented by the stem cell niche in the very root tip where cell fate is determined and cell types maintain their given identity throughout their lifetime (van den Berg et al, 1995; Sabatini et al, 2003; Wendrich et al, 2017). Overall, the concerted interplay of different cell type functions ascertain root functionality and plasticity (Brady et al, 2007; Birnbaum, 2003; Walker et al, 2017). Understanding this inter-dependency of cell types and its accurate spatio-temporal regulation is of particular relevance for our efforts to generate crops with improved resilience under stressful environments.…”

“…Studies of cell type-specific transcriptomics based on fluorescence-activated cell sorting have significantly advanced our knowledge of processes regulating root development (Birnbaum, 2003; Birnbaum et al, 2005; Brady et al, 2007; Bargmann et al, 2013; Walker et al, 2017) and furthered our understanding of root adaptation to abiotic stress and nutrient depletion (Dinneny et al, 2008; Gifford et al, 2008; Geng et al, 2013; Gifford et al, 2013). Evidence provided in these studies highlighted the functional individuality of cell types and the significance of a coordinated regulation of cell type-specific gene networks to master root development and secure overall root functionality (e.g.…”