Stem-borne roots as a framework to study trans-organogenesis and uncover fundamental insights in developmental biology.

Plants have a remarkable ability to generate organs with a different identity to the parent organ, called 'trans-organogenesis'. An example of trans-organogenesis is the formation of roots from stems (a type of adventitious root), which is the first type of root that arose during plant evolution. Despite being ancestral, stem-borne roots are often contextualised through lateral root research, implying that lateral roots precede adventitious roots. In this review we challenge that idea, highlight what is known about stem-borne root development across the plant kingdom, the remarkable diversity in form and function, and the many remaining evolutionary questions. Exploring stem-borne root evolutionary development can enhance our understanding of developmental decision making and the processes by which cells acquire their fates.

Quantification of maize brace root formation after vertical stalk displacement.

Maize brace roots develop from aboveground stem nodes in both upright and vertically displaced stalks. The cues that trigger brace root development after displacement are unknown. Possibilities include disturbance of the belowground roots, gravity, moisture, physical interaction, or node anatomical changes. We show that brace root formation occurs at all growth stages, with more nodes producing brace roots when plants are displaced at later growth stages. This occurs with the underground roots intact, without moisture accumulation and without physical interaction. We propose that the formation of brace roots after vertical stalk displacement is most likely due to gravity or anatomical changes at the node.

Graft incompatibility between pepper and tomato can be attributed to genetic incompatibility between diverged immune systems.

Graft compatibility is the capacity of two plants to form cohesive vascular connections. Tomato and pepper are incompatible graft partners; however, the underlying cause of graft rejection between these two species remains unknown.We diagnosed graft incompatibility between tomato and diverse pepper varieties based on weakened biophysical stability, decreased growth, and persistent cell death using trypan blue and TUNEL assays. Transcriptomic analysis of cell death in the junction was performed using RNA-sequencing, and molecular signatures for incompatible graft response were characterized based on meta-transcriptomic comparisons with other biotic processes.We show that tomato is broadly incompatible with diverse pepper cultivars. These incompatible graft partners activate prolonged transcriptional changes that are highly enriched for defense processes. Amongst these processes was broad NLR upregulation and hypersensitive response. Using transcriptomic datasets for a variety of biotic stress treatments, we identified a significant overlap in the genetic profile of incompatible grafting and plant parasitism. In addition, we found over 1000 genes that are uniquely upregulated in incompatible grafts.Based on NLR overactivity, DNA damage, and prolonged cell death we have determined that tomato and pepper graft incompatibility is likely caused by a form of genetic incompatibility, which triggers a hyperimmune-response.

Root responses to abiotic stress: a comparative look at root system architecture in maize and sorghum.

Under all environments, roots are important for plant anchorage and acquiring water and nutrients. However, there is a knowledge gap regarding how root architecture contributes to stress tolerance in a changing climate. Two closely related plant species, maize and sorghum, have distinct root system architectures and different levels of stress tolerance, making comparative analysis between these two species an ideal approach to resolve this knowledge gap. However, current research has focused on shared aspects of the root system that are advantageous under abiotic stress conditions rather than on differences. Here we summarize the current state of knowledge comparing the root system architecture relative to plant performance under water deficit, salt stress, and low phosphorus in maize and sorghum. Under water deficit, steeper root angles and deeper root systems are proposed to be advantageous for both species. In saline soils, a reduction in root length and root number has been described as advantageous, but this work is limited. Under low phosphorus, root systems that are shallow and wider are beneficial for topsoil foraging. Future work investigating the differences between these species will be critical for understanding the role of root system architecture in optimizing plant production for a changing global climate.

Brace roots in C 3 Poaceae: where have they gone?

Brace roots are common in large C 4 Poaceae species, such as maize and sorghum. However, in other species, these roots were either never reported, or the existence of the trait was neglected. Here we report the presence of brace roots in a high-performing Avena sativa L. (oat) line.

2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative.

OBJECTIVES: This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scenarios of variable environmental patterns. Hybrids and inbreds are evaluated across multiple environments and phenotypic, genotypic, environmental, and metadata information are made publicly available. DATA DESCRIPTION: The datasets include phenotypic data of the hybrids and inbreds evaluated in 30 locations across the US and one location in Germany in 2020 and 2021, soil and climatic measurements and metadata information for all environments (combination of year and location), ReadMe, and description files for each data type. A set of common hybrids is present in each environment to connect with previous evaluations. Each environment had a collaborator responsible for collecting and submitting the data, the GxE coordination team combined all the collected information and removed obvious erroneous data. Collaborators received the combined data to use, verify and declare that the data generated in their own environments was accurate. Combined data is released to the public with minimal filtering to maintain fidelity to the original data.

Characterization of mechanosensitive MSL gene family expression in Zea mays aerial and subterranean brace roots.

Plants must be able to sense and respond to mechanical stresses encountered throughout their lifespan. The MscS-Like (MSL) family of mechanosensitive ion channels is one mechanism to perceive mechanical stresses. In maize, brace roots emerge from stem nodes above the soil and some remain aerial while some grow into the soil. We tested the hypothesis that MSL gene expression is higher in subterranean brace roots compared to those that remain aerial. However, there was no difference in MSL expression between the two environments. This work sets the foundation for a deeper understanding of MSL gene expression and function in maize.

Genomes to Fields 2022 Maize genotype by Environment Prediction Competition.

OBJECTIVES: The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data. DATA DESCRIPTION: This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.

Image-based assessment of plant disease progression identifies new genetic loci for resistance to Ralstonia solanacearum in tomato.

A major challenge in global crop production is mitigating yield loss due to plant diseases. One of the best strategies to control these losses is through breeding for disease resistance. One barrier to the identification of resistance genes is the quantification of disease severity, which is typically based on the determination of a subjective score by a human observer. We hypothesized that image-based, non-destructive measurements of plant morphology over an extended period after pathogen infection would capture subtle quantitative differences between genotypes, and thus enable identification of new disease resistance loci. To test this, we inoculated a genetically diverse biparental mapping population of tomato (Solanum lycopersicum) with Ralstonia solanacearum, a soilborne pathogen that causes bacterial wilt disease. We acquired over 40 000 time-series images of disease progression in this population, and developed an image analysis pipeline providing a suite of 10 traits to quantify bacterial wilt disease based on plant shape and size. Quantitative trait locus (QTL) analyses using image-based phenotyping for single and multi-traits identified QTLs that were both unique and shared compared with those identified by human assessment of wilting, and could detect QTLs earlier than human assessment. Expanding the phenotypic space of disease with image-based, non-destructive phenotyping both allowed earlier detection and identified new genetic components of resistance.

Maize plants and the brace roots that support them.

Brace roots are a unique but poorly understood set of organs found in some large cereal crops such as maize. These roots develop from aerial stem nodes and can remain aerial or grow into the ground. Despite their name, the function of these roots to brace the plant was only recently shown. In this article, I discuss the current understanding of brace root function and development, as well as the multitude of open questions that remain about these fascinating organs.

Maize brace root mechanics vary by whorl, genotype and reproductive stage.

BACKGROUND AND AIMS: Root lodging is responsible for significant crop losses worldwide. During root lodging, roots fail by breaking, buckling or pulling out of the ground. In maize, above-ground roots, called brace roots, have been shown to reduce susceptibility to root lodging. However, the underlying structural-functional properties of brace roots that prevent root lodging are poorly defined. In this study, we quantified structural mechanical properties, geometry and bending moduli for brace roots from different whorls, genotypes and reproductive stages. METHODS: Using 3-point bend tests, we show that brace root mechanics are variable by whorl, genotype and reproductive stage. KEY RESULTS: Generally, we find that within each genotype and reproductive stage, the brace roots from the first whorl (closest to the ground) had higher structural mechanical properties and a lower bending modulus than brace roots from the second whorl. There was additional variation between genotypes and reproductive stages. Specifically, genotypes with higher structural mechanical properties also had a higher bending modulus, and senesced brace roots had lower structural mechanical properties than hydrated brace roots. CONCLUSIONS: Collectively these results highlight the importance of considering whorl-of-origin, genotype and reproductive stage for the quantification of brace root mechanics, which is important for mitigating crop loss due to root mechanical failure.

Multiple brace root phenotypes promote anchorage and limit root lodging in maize.

Plant mechanical failure (lodging) causes global yield losses of 7%-66% in cereal crops. We have previously shown that the above-ground nodal roots (brace roots) in maize are critical for anchorage. However, it is unknown how brace root phenotypes vary across genotypes and the functional consequence of this variation. This study quantifies the contribution of brace roots to anchorage, brace root traits, plant height, and root lodging susceptibility in 52 maize inbred lines. We show that the contribution of brace roots to anchorage and root lodging susceptibility varies among genotypes and this contribution can be explained by plant architectural variation. Additionally, supervised machine learning models were developed and show that multiple plant architectural phenotypes can predict the contribution of brace roots to anchorage and root lodging susceptibility. Together these data define the plant architectures that are important in lodging resistance and show that the contribution of brace roots to anchorage is a good proxy for root lodging susceptibility.

Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate.

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.

Bracing for sustainable agriculture: the development and function of brace roots in members of Poaceae.

Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, two types of nodal roots-subterranean crown and aerial brace roots function in anchorage and water uptake and preferentially express multiple water and nutrient transporters. Brace root development shares genetic control with juvenile-to-adult phase change and flowering time. We present a comprehensive list of the genes known to alter brace roots and explore these as candidates for QTL studies in maize and sorghum. Brace root development and function may be conserved in other members of Poaceae, however research is limited. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.

Maize brace roots provide stalk anchorage.

Mechanical failure, known as lodging, negatively impacts yield and grain quality in crops. Limiting crop loss from lodging requires an understanding of the plant traits that contribute to lodging-resistance. In maize, specialized aerial brace roots are reported to reduce root lodging. However, their direct contribution to plant biomechanics has not been measured. In this manuscript, we use a non-destructive field-based mechanical test on plants before and after the removal of brace roots. This precisely determines the contribution of brace roots to establish a rigid base (i.e. stalk anchorage) that limits plant deflection in maize. These measurements demonstrate that the more brace root whorls that contact the soil, the greater their overall contribution to anchorage, but that the contributions of each whorl to anchorage were not equal. Previous studies demonstrated that the number of nodes that produce brace roots is correlated with flowering time in maize. To determine if flowering time selection alters the brace root contribution to anchorage, a subset of the Hallauer's Tusón tropical population was analyzed. Despite significant variation in flowering time and anchorage, selection neither altered the number of brace root whorls in the soil nor the overall contribution of brace roots to anchorage. These results demonstrate that brace roots provide a rigid base in maize and that the contribution of brace roots to anchorage was not linearly related to flowering time.

Field-based mechanical phenotyping of cereal crops to assess lodging resistance.

Plant mechanical failure, also known as lodging, is the cause of significant and unpredictable yield losses in cereal crops. Lodging occurs in two distinct failure modes-stalk lodging and root lodging. Despite the prevalence and detrimental impact of lodging on crop yields, there is little consensus on how to phenotype plants in the field for lodging resistance and thus breed for mechanically resilient plants. This review provides an overview of field-based mechanical testing approaches to assess stalk and root lodging resistance. These approaches are placed in the context of future perspectives. Best practices and recommendations for acquiring field-based mechanical phenotypes of plants are also presented.

Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big.

The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.

Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root.

Changes in gene regulation during differentiation are governed by networks of transcription factors. The Arabidopsis root endodermis is a tractable model to address how transcription factors contribute to differentiation. We used a bottom-up approach to understand the extent to which transcription factors that are required for endodermis differentiation can confer endodermis identity to a non-native cell type. Our results show that the transcription factors SHORTROOT and MYB36 alone have limited ability to induce ectopic endodermal features in the absence of additional cues. The stele-derived signalling peptide CIF2 stabilizes SHORTROOT-induced endodermis identity acquisition. The outcome is a partially impermeable barrier deposited in the subepidermal cell layer, which has a transcriptional signature similar to the endodermis. These results demonstrate that other root cell types can be forced to differentiate into the endodermis and highlight a previously unappreciated role for receptor kinase signalling in maintaining endodermis identity.

Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences.

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.