Root branching is not induced by auxins in Selaginella moellendorffii

Angiosperms develop intensively branched root systems that are accommodated with the high capacity to produce plenty of new lateral roots throughout their life-span. Root branching can be dynamically regulated in response to edaphic conditions and provides the plants with a soil-mining potential. This highly specialized branching capacity has most likely been key in the colonization success of the present flowering plants on our planet. The initiation, formation and outgrowth of branching roots in Angiosperms are dominated by the plant hormone auxin. Upon auxin treatment root branching through the formation of lateral roots can easily be induced. In this study, we questioned whether this strong branching-inducing action of auxin is part of a conserved mechanism that was already active in the earliest diverging lineage of vascular plants with roots. In Selaginella, an extant representative species of this early clade of root forming plants, components of the canonical auxin signaling pathway are retrieved in its genome. Although we observed a clear physiological response and an indirect effect on root branching, we were not able to directly induce root branching in this species by application of different auxins. We conclude that the structural and developmental difference of the Selaginella root, which branches via bifurcation of the root meristem, or the absence of an auxin-mediated root development program, is most likely causative for the absence of an auxin-induced branching mechanism

Exploiting natural variation in root system architecture via genome wide association studies

Root growth and development has become an important research topic for breeders and researchers based on a growing need to adapt plants to changing and more demanding environmental conditions worldwide. Over the last few years, Genome Wide Association Studies (GWASs) became an important tool to identify the link between traits in the field and their genetic background. In this review, we give an overview of the current literature concerning GWASs performed on Root System Architecture (RSA) in plants. We summarize which root traits and approaches have been used for GWAS mentioning their respective success rate towards a successful gene discovery. Furthermore, we zoom in on the current technical hurdles in root phenotyping and GWAS and discuss future possibilities in this field of research

Root Branching Is Not Induced by Auxins in Selaginella moellendorffii

Angiosperms develop intensively branched root systems that are accommodated with the high capacity to produce plenty of new lateral roots throughout their life-span. Root branching can be dynamically regulated in response to edaphic conditions and provides the plants with a soil-mining potential. This highly specialized branching capacity has most likely been key in the colonization success of the present flowering plants on our planet. The initiation, formation and outgrowth of branching roots in Angiosperms are dominated by the plant hormone auxin. Upon auxin treatment root branching through the formation of lateral roots can easily be induced. In this study, we questioned whether this strong branching-inducing action of auxin is part of a conserved mechanism that was already active in the earliest diverging lineage of vascular plants with roots. In Selaginella, an extant representative species of this early clade of root forming plants, components of the canonical auxin signaling pathway are retrieved in its genome. Although we observed a clear physiological response and an indirect effect on root branching, we were not able to directly induce root branching in this species by application of different auxins. We conclude that the structural and developmental difference of the Selaginella root, which branches via bifurcation of the root meristem, or the absence of an auxin-mediated root development program, is most likely causative for the absence of an auxin-induced branching mechanism

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes

Auxin-dependent cell cycle reactivation through transcriptional regulation of Arabidopsis E2Fa by lateral organ boundary proteins

Multicellular organisms depend on cell production, cell fate specification, and correct patterning to shape their adult body. In plants, auxin plays a prominent role in the timely coordination of these different cellular processes. A well-studied example is lateral root initiation, in which auxin triggers founder cell specification and cell cycle activation of xylem pole-positioned pericycle cells. Here, we report that the E2Fa transcription factor of Arabidopsis thaliana is an essential component that regulates the asymmetric cell division marking lateral root initiation. Moreover, we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis through E2Fa transcriptional activation, whereas E2Fa expression under control of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation, vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected in auxin signaling and lbd mutants, indicating that the transcriptional induction of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle activation. Our data illustrate how a conserved mechanism driving cell cycle entry has been adapted evolutionarily to connect auxin signaling with control of processes determining plant architecture

NAC transcription factors ANAC087 and ANAC046 control distinct aspects of programmed cell death in the Arabidopsis columella and lateral root cap

Programmed cell death in plants occurs both during stress responses and as an integral part of regular plant development. Despite the undisputed importance of developmentally controlled cell death processes for plant growth and reproduction, we are only beginning to understand the underlying molecular genetic regulation. Exploiting the Arabidopsis thaliana root cap as a cell death model system, we identified two NAC transcription factors, the little-characterized ANAC087 and the leaf-senescence regulator ANAC046, as being sufficient to activate the expression of cell death-associated genes and to induce ectopic programmed cell death. In the root cap, these transcription factors are involved in the regulation of distinct aspects of programmed cell death. ANAC087 orchestrates postmortem chromatin degradation in the lateral root cap via the nuclease BFN1. In addition, both ANAC087 and ANAC046 redundantly control the onset of cell death execution in the columella root cap during and after its shedding from the root tip. Besides identifying two regulators of developmental programmed cell death, our analyses reveal the existence of an actively controlled cell death program in Arabidopsis columella root cap cells

GOLVEN peptide signalling through RGI receptors and MPK6 restricts asymmetric cell division during lateral root initiation

During lateral root initiation, lateral root founder cells undergo asymmetric cell divisions that generate daughter cells with different sizes and fates, a prerequisite for correct primordium organogenesis. An excess of the GLV6/RGF8 peptide disrupts these initial asymmetric cell divisions, resulting in more symmetric divisions and the failure to achieve lateral root organogenesis. Here, we show that loss-of-function GLV6 and its homologue GLV10 increase asymmetric cell divisions during lateral root initiation, and we identified three members of the RGF1 INSENSITIVE/RGF1 receptor subfamily as likely GLV receptors in this process. Through a suppressor screen, we found that MITOGEN-ACTIVATED PROTEIN KINASE6 is a downstream regulator of the GLV pathway. Our data indicate that GLV6 and GLV10 act as inhibitors of asymmetric cell divisions and signal through RGF1 INSENSITIVE receptors and MITOGEN-ACTIVATED PROTEIN KINASE6 to restrict the number of initial asymmetric cell divisions that take place during lateral root initiation. The authors demonstrate the negative role of GOLVEN peptides during lateral root initiation in Arabidopsis, at the very early stage of the first asymmetric cell division of lateral root founder cells, and identify the receptors for these peptides

Rice plants respond to ammonium‐stress by adopting a helical root growth pattern

High levels of ammonium nutrition reduce plant growth and different plant species have developed distinct strategies to maximize ammonium acquisition while alleviate ammonium toxicity through modulating root growth. Up to now, the mechanism underlying plant tolerance or sensitivity towards ammonium remain unclear. Rice uses ammonium as its main N source. Here we show that ammonium supply restricts rice root elongation and induces a helical growth pattern, which is attributed to root acidification resulting from ammonium uptake. Ammonium-induced low pH triggers asymmetric auxin distribution in rice root tips through changes in auxin signaling, thereby inducing a helical growth response. Blocking auxin signaling completely inhibited this root response. In contrast, this root response is not activated in ammonium-treated Arabidopsis. Acidification of Arabidopsis roots leads to the protonation of IAA, and dampening the intracellular auxin signaling levels that are required for maintaining root growth. Our study suggests a different mode of action by ammonium on the root pattern and auxin response machinery in rice versus Arabidopsis, and the rice-specific helical root response towards ammonium is an expression of the ability of rice in moderating auxin signaling and root growth to utilize ammonium while confronting acidic stress

The xerobranching response represses lateral root formation when roots are not in contact with water

Efficient soil exploration by roots represents an important target for crop improvement and food security [1, 2]. Lateral root (LR) formation is a key trait for optimising soil foraging for crucial resources such as water and nutrients. Here, we report an adaptive response termed xerobranching, exhibited by cereal roots, that represses branching when root tips are not in contact with wet soil. Non-invasive X-ray microCT imaging revealed that cereal roots rapidly repress LR formation as they enter an air space within a soil profile and are no longer in contact with water. Transcript profiling of cereal root tips revealed that transient water deficit triggers the abscisic acid (ABA) response pathway. In agreement with this, exogenous ABA treatment can mimic repression of LR formation under transient water deficit. Genetic analysis in Arabidopsis revealed that ABA repression of LR formation requires the PYR/PYL/RCARdependent signalling pathway. Our findings suggest that ABA acts as the key signal regulating xerobranching. We conclude that this new ABA-dependent adaptive mechanism allows roots to rapidly respond to changes in water availability in their local micro-environment and to use internal resources efficiently