Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana

Abstract

Molecular data concerning the involvement of roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of the root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutations are reported to alter flowering time are expressed in the roots (i.e. were detected in more than 50% of the microarrays). However, only a few flowering integrator genes passed the analysis cutoff. Comparison of root transcriptome in short days and during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories, and cis-regulatory elements converged towards sugar signaling. We concluded that roots are integrated in systemic signaling, whereby carbon supply coordinates growth at the whole plant level during the induction of flowering. This coordination could involve the root circadian clock and cytokinin biosynthesis as a feed forward loop towards the shoot.Flowering is a crucial step in plant development that must be precisely timed to occur when external conditions are favourable for successful reproduction. Floral induction is therefore controlled by environmental and endogenous cues, whose inputs are integrated into finely-tuned regulatory gene networks. In Arabidopsis thaliana, genetic analyses unveiled several flowering pathways that mediate response to photoperiod, temperature, sugars, hormones, and plant aging 1 . These pathways are not restricted to the shoot apical meristem where flowers are initiated, but also involve the leaves supporting the fact that flowering is a systemic process, as shown previously at the physiological level. The clearest genetic evidence supporting this idea came from the photoperiodic pathway, in which a key component, the transcription factor CONSTANS (CO), is expressed rhythmically but is degraded in the dark 2 . Light must therefore coincide with CO synthesis to stabilize the protein and enable activation of its targets. This occurs during long days in the companion cells of phloem, where CO activates FLOWERING LOCUS T (FT). The FT protein then moves systemically and interacts with the transcription factor FD via 14-3-3 proteins in the shoot apical meristem. This complex activates genes that are responsible for the conversion of the vegetative shoot apical meristem into an inflorescence meristem and for the promotion of floral fate in lateral primordia.The prominent role of the FT protein in the systemic signaling of flowering leads to questions concerning the role of side molecules that are co-transported from leaf sources in the phloem and the pleiotropic effects of these signals in different sinks. Sugar loading is the first step of mass-flow movement in phloem, hence...

Super resolution for root imaging

“…• Arabidopsis thaliana roots (https://zenodo.org/record/50831#.XjIAPVNKhQI): an Arabidopsis thaliana dataset for root phenotyping analysis (Bouché et al 2016).…”