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Soil water uptake by roots is central for plant growth and survival. Flooding, as many other environmental constraints such as drought, nutrient deprivation or oxidative stress exerts deep effects on root functions by altering root water permeability (root hydraulic conductivity; Lpr). These effects, which are mediated mainly through the regulation of aquaporins, are fundamental for adaptation of wild plant species to diverse natural habitats and a major target for crop improvement. However, the signaling mechanisms which link soil properties to root hydraulics and aquaporin functions remain largely unknown. We have been investigating the genetic bases of root hydraulics in the model plant, Arabidopsis thaliana. Using quantitative genetics approaches, including linkage mapping and genome-wide association mapping, we have identified several genes controlling Lpr. The signaling pathway for regulation of Lpr by a RAF-like MAP3 kinase named Hydraulic Conductivity of Root 1 (HCR1) will be discussed in details (Shahzad et al (2016) Cell 167: 87-98.e14). This protein kinase delineates a combinatorial signaling pathway integrating two soil signals, K+ and O2 availability, to regulate root hydraulics and hypoxia responsive genes, through the control of RAP2.12, a key transcriptional regulator of the core anaerobic response. In addition, several other candidate genes identified during this study offer interesting perspectives for understanding as yet unknown mechanisms involved in the regulation of root hydraulics.

[i]cis[/i]- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis- acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.