Environmental conditions modulate the effect of epigenetic factors controlling the response of Arabidopsis thaliana to Plasmodiophora brassicae

The resistance of Arabidopsis thaliana to clubroot, a major disease of Brassicaceae caused by the obligate protist Plasmodiophora brassicae, is controlled in part by epigenetic factors. The detection of some of these epigenetic quantitative trait loci (QTLepi) has been shown to depend on experimental conditions. The aim of the present study was to assess whether and how temperature and/or soil water availability influenced both the detection and the extent of the effect of response QTLepi. The epigenetic recombinant inbred line (epiRIL) population, derived from the cross between ddm1-2 and Col-0 (partially resistant and susceptible to clubroot, respectively), was phenotyped for response to P. brassicae under four abiotic conditions including standard conditions, a 5°C temperature increase, drought, and flooding. The abiotic constraints tested had a significant impact on both the leaf growth of the epiRIL population and the outcome of the epiRIL-pathogen interaction. Linkage analysis led to the detection of a total of 31 QTLepi, 18 of which were specific to one abiotic condition and 13 common to at least two environments. EpiRIL showed significant plasticity under epigenetic control, which appeared to be specific to the traits evaluated and to the abiotic conditions. These results highlight that the environment can affect the epigenetic architecture of plant growth and immune responses and advance our understanding of the epigenetic factors underlying plasticity in response to climate change.

Submergence stress-induced hypocotyl elongation through ethylene signaling-mediated regulation of cortical microtubules in Arabidopsis

Plant growth is significantly altered in response to submergence stress. However, the molecular mechanisms used by seedlings in response to this stress, especially for hypocotyl growth, are largely unknown in terrestrial plants such as Arabidopsis thaliana. The microtubule cytoskeleton participates in plant cell growth, but it remains unclear whether submergence-mediated plant growth involves the microtubule cytoskeleton. We demonstrated that in Arabidopsis submergence induced underwater hypocotyl elongation through the activation of ethylene signaling, which modulated cortical microtubule reorganization. Submergence enhanced ethylene signaling, which then activated and stabilized its downstream transcription factor, phytochrome-interacting factor 3 (PIF3), to promote hypocotyl elongation. In particular, the regulation of microtubule organization was important for this physiological process. Microtubule-destabilizing protein 60 (MDP60), which was previously identified as a downstream effector of PIF3, played a positive role in submergence-induced hypocotyl elongation. Submergence induced MDP60 expression through ethylene signaling. The effects of submergence on hypocotyl elongation and cortical microtubule reorganization were suppressed in mdp60 mutants. These data suggest a potential mechanism by which submergence activates ethylene signaling to promote underwater hypocotyl elongation via alteration of the microtubule cytoskeleton in Arabidopsis.

Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects

Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.

Improving Flooding Tolerance of Crop Plants

A major problem of climate change is the increasing duration and frequency of heavy rainfall events. This leads to soil flooding that negatively affects plant growth, eventually leading to death of plants if the flooding persists for several days. Most crop plants are very sensitive to flooding, and dramatic yield losses occur due to flooding each year. This review summarizes recent progress and approaches to enhance crop resistance to flooding. Most experiments have been done on maize, barley, and soybean. Work on other crops such as wheat and rape has only started. The most promising traits that might enhance crop flooding tolerance are anatomical adaptations such as aerenchyma formation, the formation of a barrier against radial oxygen loss, and the growth of adventitious roots. Metabolic adaptations might be able to improve waterlogging tolerance as well, but more studies are needed in this direction. Reasonable approaches for future studies are quantitative trait locus (QTL) analyses or genome-wide association (GWA) studies in combination with specific tolerance traits that can be easily assessed. The usage of flooding-tolerant relatives or ancestral cultivars of the crop of interest in these experiments might enhance the chances of finding useful tolerance traits to be used in breeding.

A stress recovery signaling network for enhanced flooding tolerance in Arabidopsis thaliana

Abiotic stresses in plants are often transient, and the recovery phase following stress removal is critical. Flooding, a major abiotic stress that negatively impacts plant biodiversity and agriculture, is a sequential stress where tolerance is strongly dependent on viability underwater and during the postflooding period. Here we show that in Arabidopsis thaliana accessions (Bay-0 and Lp2-6), different rates of submergence recovery correlate with submergence tolerance and fecundity. A genome-wide assessment of ribosome-associated transcripts in Bay-0 and Lp2-6 revealed a signaling network regulating recovery processes. Differential recovery between the accessions was related to the activity of three genes: RESPIRATORY BURST OXIDASE HOMOLOG D, SENESCENCE-ASSOCIATED GENE113, and ORESARA1, which function in a regulatory network involving a reactive oxygen species (ROS) burst upon desubmergence and the hormones abscisic acid and ethylene. This regulatory module controls ROS homeostasis, stomatal aperture, and chlorophyll degradation during submergence recovery. This work uncovers a signaling network that regulates recovery processes following flooding to hasten the return to prestress homeostasis.