Root branching toward water involves posttranslational modification of transcription factor ARF7

CLE3 and its homologs share overlapping functions in the modulation of lateral root formation through CLV1 and BAM1 in Arabidopsis thaliana

Lateral roots are important for a wide range of processes, including uptake of water and nutrients. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) 1 ~ 7 peptide family and their cognate receptor CLV1 have been shown to negatively regulate lateral root formation under low-nitrate conditions. However, little is known about how CLE signaling regulates lateral root formation. A persistent obstacle in CLE peptide research is their functional redundancies, which makes functional analyses difficult. To address this problem, we generate the cle1 ~ 7 septuple mutant (cle1 ~ 7-cr1, cr stands for mutant allele generated with CRISPR/Cas9). cle1 ~ 7-cr1 exhibits longer lateral roots under normal conditions. Specifically, in cle1 ~ 7-cr1, the lateral root density is increased, and lateral root primordia initiation is found to be accelerated. Further analysis shows that cle3 single mutant exhibits slightly longer lateral roots. On the other hand, plants that overexpress CLE2 and CLE3 exhibit decreased lateral root lengths. To explore cognate receptor(s) of CLE2 and CLE3, we analyze lateral root lengths in clv1 barely any meristem 1(bam1) double mutant. Mutating both the CLV1 and BAM1 causes longer lateral roots, but not in each single mutant. In addition, genetic analysis reveals that CLV1 and BAM1 are epistatic to CLE2 and CLE3. Furthermore, gene expression analysis shows that the LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) genes, which promote lateral root formation, are upregulated in cle1 ~ 7-cr1 and clv1 bam1. We therefore propose that CLE2 and CLE3 peptides are perceived by CLV1 and BAM1 to mediate lateral root formation through LBDs regulation.

ZmBET5L1 inhibits primary root growth and decreases osmotic stress tolerance by mediating vesicle aggregation and tethering in maize

Improving osmotic stress tolerance is critical to help crops to thrive and maintain high yields in adverse environments. Here, we characterized a core subunit of the transport protein particle (TRAPP) complex, ZmBET5L1, in maize using knowledge-driven data mining and genome editing. We found that ZmBET5L1 can interact with TRAPP I complex subunits and act as a tethering factor to mediate vesicle aggregation and targeting from the endoplasmic reticulum to the Golgi apparatus. ZmBET5L1 knock-out increased the primary root elongation rate under 20% polyethylene glycol-simulated osmotic stress and the survival rate under drought stress compared to wild-type seedlings. In addition, we found that ZmBET5L1 moderates PIN1 polar localization and auxin flow to maintain normal root growth. ZmBET5L1 knock-out optimized auxin flow to the lateral side of the root and promoted its growth to generate a robust root, which may be related to improved osmotic stress tolerance. Together, these findings demonstrate that ZmBET5L1 inhibits primary root growth and decreases osmotic stress tolerance by regulating vesicle transport and auxin distribution. This study has improved our understanding of the role of tethering factors in response to abiotic stresses and identified desirable variants for breeding osmotic stress tolerance in maize.

SUMOylation facilitates the assembly of a Nuclear Factor-Y complex to enhance thermotolerance in Arabidopsis

Heat stress (HS) has serious negative effects on plant development and has become a major threat to agriculture. A rapid transcriptional regulatory cascade has evolved in plants in response to HS. Nuclear Factor-Y (NF-Y) complexes are critical for this mechanism, but how NF-Y complexes are regulated remains unclear. In this study, we identified NF-YC10 (NF-Y subunit C10), a central regulator of the HS response in Arabidopsis thaliana, as a substrate of SUMOylation, an important post-translational modification. Biochemical analysis showed that the SUMO ligase SIZ1 (SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1) interacts with NF-YC10 and enhances its SUMOylation during HS. The SUMOylation of NF-YC10 facilitates its interaction with and the nuclear translocation of NF-YB3, in which the SUMO interaction motif (SIM) is essential for its efficient association with NF-YC10. Further functional analysis indicated that the SUMOylation of NF-YC10 and the SIM of NF-YB3 are critical for HS-responsive gene expression and plant thermotolerance. These findings uncover a role for the SIZ1-mediated SUMOylation of NF-YC10 in NF-Y complex assembly under HS, providing new insights into the role of a post-translational modification in regulating transcription during abiotic stress responses in plants.

Using single cell atlas data to reconstruct regulatory networks

Inference of global gene regulatory networks from omics data is a long-term goal of systems biology. Most methods developed for inferring transcription factor (TF)-gene interactions either relied on a small dataset or used snapshot data which is not suitable for inferring a process that is inherently temporal. Here, we developed a new computational method that combines neural networks and multi-task learning to predict RNA velocity rather than gene expression values. This allows our method to overcome many of the problems faced by prior methods leading to more accurate and more comprehensive set of identified regulatory interactions. Application of our method to atlas scale single cell data from 6 HuBMAP tissues led to several validated and novel predictions and greatly improved on prior methods proposed for this task.

Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Expression, Purification, and Enzymatic Analysis of Plant SUMO Proteases

The conjugation of SUMO can profoundly change the behavior of substrate proteins, impacting a wide variety of cellular responses. SUMO proteases are emerging as key regulators of plant adaptation to its environment because of their instrumental role in the SUMO deconjugation process. Here we describe how to express, purify, and determine SUMO deconjugation activity of a plant SUMO protease.

Responses of root system architecture to water stress at multiple levels: A meta-analysis of trials under controlled conditions

Plants are exposed to increasingly severe drought events and roots play vital roles in maintaining plant survival, growth, and reproduction. A large body of literature has investigated the adaptive responses of root traits in various plants to water stress and these studies have been reviewed in certain groups of plant species at a certain scale. Nevertheless, these responses have not been synthesized at multiple levels. This paper screened over 2000 literatures for studies of typical root traits including root growth angle, root depth, root length, root diameter, root dry weight, root-to-shoot ratio, root hair length and density and integrates their drought responses at genetic and morphological scales. The genes, quantitative trait loci (QTLs) and hormones that are involved in the regulation of drought response of the root traits were summarized. We then statistically analyzed the drought responses of root traits and discussed the underlying mechanisms. Moreover, we highlighted the drought response of 1-D and 2-D root length density (RLD) distribution in the soil profile. This paper will provide a framework for an integrated understanding of root adaptive responses to water deficit at multiple scales and such insights may provide a basis for selection and breeding of drought tolerant crop lines.

Hydraulic flux-responsive hormone redistribution determines root branching

Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.

Ecological strategy of Phyllostachys heteroclada oliver in the riparian zone based on ecological stoichiometry

The abnormality of seasonal water level fluctuation in the riparian zone causes various ecological and environmental problems, such as vegetation degradation, biodiversity reduction, soil erosion, and landscape transformation, thereby critically modifying the ecosystem structure and functions. This necessitates the development of a dominant vegetation zone with competitive potential. In this study, we investigated the content and distribution pattern of nutrient elements in each organ of the dominant bamboo species, Phyllostachys heteroclada, in the riparian zone. We also analyzed the morphological characteristics, root aeration tissue structure, root oxygen exchange capacity, ATP supply situation, and leaf PSII photosynthetic mechanism of two bamboo species (P. heteroclada and P. nigra) in the riparian zone. Compared with P. nigra, the roots of P. heteroclada formed well-developed oxygen storage and transport structure, i.e., aeration tissue, and exhibited root oxygen secretion in the waterlogging environment of the riparian zone, whereas the roots maintained a high ATP content through energy metabolism, thus benefiting mineral absorption and transport. Moreover, the accumulation of N, P, Ca, Mg, and Fe in the leaves of P. heteroclada was greater under waterlogging conditions than under non-waterlogging conditions, which is the basis for the efficient operation of the photosynthetic mechanism of the leaves. Compared with waterlogged P. nigra, the PSII electron acceptor Q_A of P. heteroclada leaves had a vigorous reducing ability and showed higher efficiency of light uptake energy as well as higher quantum yield indexes ϕ(Eo) and ϕ(Po). This study demonstrates that the ecological adaptive regulation strategies of P. heteroclada in the riparian zone are intrinsic driving factors affecting their stoichiometric characteristics, including changes in the absorption and transport of minerals caused by root aeration structure and energy metabolism. Moreover, carbon production and allocation may be caused by the stable photosynthetic mechanism and source-sink relationship of leaves. Through the synergistic regulation of different organs realizing their roles and functions, P. heteroclada developed ecological stoichiometry characteristics adapted to the riparian zone.

Molecular Mechanisms of Diverse Auxin Responses during Plant Growth and Development

The plant hormone auxin acts as a signaling molecule to regulate numerous developmental processes throughout all stages of plant growth. Understanding how auxin regulates various physiological and developmental processes has been a hot topic and an intriguing field. Recent studies have unveiled more molecular details into how diverse auxin responses function in every aspect of plant growth and development. In this review, we systematically summarized and classified the molecular mechanisms of diverse auxin responses, and comprehensively elaborated the characteristics and multilevel regulation mechanisms of the canonical transcriptional auxin response. On this basis, we described the characteristics and differences between different auxin responses. We also presented some auxin response genes that have been genetically modified in plant species and how their changes impact various traits of interest. Finally, we summarized some important aspects and unsolved questions of auxin responses that need to be focused on or addressed in future research. This review will help to gain an overall understanding of and some insights into the diverse molecular mechanisms of auxin responses in plant growth and development that are instrumental in harnessing genetic resources in molecular breeding of extant plant species.

Root osmotic sensing from local perception to systemic responses

Plants face a constantly changing environment, requiring fine tuning of their growth and development. Plants have therefore developed numerous mechanisms to cope with environmental stress conditions. One striking example is root response to water deficit. Upon drought (which causes osmotic stress to cells), plants can among other responses alter locally their root system architecture (hydropatterning) or orientate their root growth to optimize water uptake (hydrotropism). They can also modify their hydraulic properties, metabolism and development coordinately at the whole root and plant levels. Upstream of these developmental and physiological changes, plant roots must perceive and transduce signals for water availability. Here, we review current knowledge on plant osmotic perception and discuss how long distance signaling can play a role in signal integration, leading to the great phenotypic plasticity of roots and plant development.

Roots' Drought Adaptive Traits in Crop Improvement

Drought is one of the biggest concerns in agriculture due to the projected reduction of global freshwater supply with a concurrent increase in global food demand. Roots can significantly contribute to improving drought adaptation and productivity. Plants increase water uptake by adjusting root architecture and cooperating with symbiotic soil microbes. Thus, emphasis has been given to root architectural responses and root-microbe relationships in drought-resilient crop development. However, root responses to drought adaptation are continuous and complex processes and involve additional root traits and interactions among themselves. This review comprehensively compiles and discusses several of these root traits such as structural, physiological, molecular, hydraulic, anatomical, and plasticity, which are important to consider together, with architectural changes, when developing drought resilient crop varieties. In addition, it describes the significance of root contribution in improving soil structure and water holding capacity and its implication on long-term resilience to drought. In addition, various drought adaptive root ideotypes of monocot and dicot crops are compared and proposed for given agroclimatic conditions. Overall, this review provides a broader perspective of understanding root structural, physiological, and molecular regulators, and describes the considerations for simultaneously integrating multiple traits for drought tolerance and crop improvement, under specific growing environments.

Crop Root Responses to Drought Stress: Molecular Mechanisms, Nutrient Regulations, and Interactions with Microorganisms in the Rhizosphere

Roots play important roles in determining crop development under drought. Under such conditions, the molecular mechanisms underlying key responses and interactions with the rhizosphere in crop roots remain limited compared with model species such as Arabidopsis. This article reviews the molecular mechanisms of the morphological, physiological, and metabolic responses to drought stress in typical crop roots, along with the regulation of soil nutrients and microorganisms to these responses. Firstly, we summarize how root growth and architecture are regulated by essential genes and metabolic processes under water-deficit conditions. Secondly, the functions of the fundamental plant hormone, abscisic acid, on regulating crop root growth under drought are highlighted. Moreover, we discuss how the responses of crop roots to altered water status are impacted by nutrients, and vice versa. Finally, this article explores current knowledge of the feedback between plant and soil microbial responses to drought and the manipulation of rhizosphere microbes for improving the resilience of crop production to water stress. Through these insights, we conclude that to gain a more comprehensive understanding of drought adaption mechanisms in crop roots, future studies should have a network view, linking key responses of roots with environmental factors.

Understanding SUMO-mediated adaptive responses in plants to improve crop productivity

The response to abiotic and biotic stresses in plants and crops is considered a multifaceted process. Due to their sessile nature, plants have evolved unique mechanisms to ensure that developmental plasticity remains during their life cycle. Among these mechanisms, post-translational modifications (PTMs) are crucial components of adaptive responses in plants and transduce environmental stimuli into cellular signalling through the modulation of proteins. SUMOylation is an emerging PTM that has received recent attention due to its dynamic role in protein modification and has quickly been considered a significant component of adaptive mechanisms in plants during stress with great potential for agricultural improvement programs. In the present review, we outline the concept that small ubiquitin-like modifier (SUMO)-mediated response in plants and crops to abiotic and biotic stresses is a multifaceted process with each component of the SUMO cycle facilitating tolerance to several different environmental stresses. We also highlight the clear increase in SUMO genes in crops when compared with Arabidopsis thaliana. The SUMO system is understudied in crops, given the importance of SUMO for stress responses, and for some SUMO genes, the apparent expansion provides new avenues to discover SUMO-conjugated targets that could regulate beneficial agronomical traits.

The conjugation of SUMO to the transcription factor MYC2 functions in blue light-mediated seedling development in Arabidopsis

A key function of photoreceptor signaling is the coordinated regulation of a large number of genes to optimize plant growth and development. The basic helix loop helix (bHLH) transcription factor MYC2 is crucial for regulating gene expression in Arabidopsis thaliana during development in blue light. Here we demonstrate that blue light induces the SUMOylation of MYC2. Non-SUMOylatable MYC2 is less effective in suppressing blue light-mediated photomorphogenesis than wild-type (WT) MYC2. MYC2 interacts physically with the SUMO proteases SUMO PROTEASE RELATED TO FERTILITY1 (SPF1) and SPF2. Blue light exposure promotes the degradation of SPF1 and SPF2 and enhances the SUMOylation of MYC2. Phenotypic analysis revealed that SPF1/SPF2 function redundantly as positive regulators of blue light-mediated photomorphogenesis. Our data demonstrate that SUMO conjugation does not affect the dimerization of MYC transcription factors but modulates the interaction of MYC2 with its cognate DNA cis-element and with the ubiquitin ligase Plant U-box 10 (PUB10). Finally, we show that non-SUMOylatable MYC2 is less stable and interacts more strongly with PUB10 than the WT. Taken together, we conclude that SUMO functions as a counterpoint to the ubiquitin-mediated degradation of MYC2, thereby enhancing its function in blue light signaling.

Auxin response factors are keys to the many auxin doors

In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.

Signalling mechanisms and cellular functions of SUMO

Sumoylation is an essential post-translational modification that is catalysed by a small number of modifying enzymes but regulates thousands of target proteins in a dynamic manner. Small ubiquitin-like modifiers (SUMOs) can be attached to target proteins as one or more monomers or in the form of polymers of different types. Non-covalent readers recognize SUMO-modified proteins via SUMO interaction motifs. SUMO simultaneously modifies groups of functionally related proteins to regulate predominantly nuclear processes, including gene expression, the DNA damage response, RNA processing, cell cycle progression and proteostasis. Recent progress has increased our understanding of the cellular and pathophysiological roles of SUMO modifications, extending their functions to the regulation of immunity, pluripotency and nuclear body assembly in response to oxidative stress, which partly occurs through the recently characterized mechanism of liquid-liquid phase separation. Such progress in understanding the roles and regulation of sumoylation opens new avenues for the targeting of SUMO to treat disease, and indeed the first drug blocking sumoylation is currently under investigation in clinical trials as a possible anticancer agent.

The role of root hairs in water uptake: recent advances and future perspectives

Sufficient water is essential for plant growth and production. Root hairs connect roots to the soil, extend the effective root radius, and greatly enlarge the absorbing surface area. Although the efficacy of root hairs in nutrient uptake, especially phosphorus, has been well recognized, their role in water uptake remains contentious. Here we review recent advances in this field, discuss the factors affecting the role of root hairs in water uptake, and propose future directions. We argue that root hair length and shrinkage, in response to soil drying, explain the apparently contradictory evidence currently available. Our analysis revealed that shorter and vulnerable root hairs (i.e. rice and maize) made little, if any, contribution to root water uptake. In contrast, relatively longer root hairs (i.e. barley) had a clear influence on root water uptake, transpiration, and hence plant response to soil drying. We conclude that the role of root hairs in water uptake is species (and probably soil) specific. We propose that a holistic understanding of the efficacy of root hairs in water uptake will require detailed studies of root hair length, turnover, and shrinkage in different species and contrasting soil textures.

The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple

Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.

Differential gene expression in tall fescue tissues in response to water deficit

Tall fescue (Festuca arundinacea Schreb.) is a popular pasture and turf grass particularly known for drought resistance, allowing for its persistence in locations that are unfavorable for other cool-season grasses. Also, its seed-borne fungal symbiont (endophyte) Epichloë coenophiala, which resides in the crown and pseudostem, can be a contributing factor in its drought tolerance. Because it contains the apical meristems, crown survival under drought stress is critical to plant survival as well as the endophyte. In this study, we subjected tall fescue plants with their endophyte to water-deficit stress or, as controls with normal watering, then compared plant transcriptome responses in four vegetative tissues: leaf blades, pseudostem, crown, and roots. A transcript was designated a differentially expressed gene (DEG) if it exhibited at least a twofold expression difference between stress and control samples with an adjusted p value of .001. Pathway analysis of the DEGs across all tissue types included photosynthesis, carbohydrate metabolism, phytohormone biosynthesis and signaling, cellular organization, and a transcriptional regulation. While no specific pathway was observed to be differentially expressed in the crown, genes encoding auxin response factors, nuclear pore anchors, structural maintenance of chromosomes, and class XI myosin proteins were more highly differentially expressed in crown than in the other vegetative tissues, suggesting that regulation in expression of these genes in the crown may aid in survival of the meristems in the crown.

Repressors: the gatekeepers of phytohormone signaling cascades

Coordinated phytohormone signal transduction, in which repressors are the key players, is essential to balance plant development and stress response. In the absence of phytohormones, repressors interplay to terminate the transcription of phytohormone-responsive genes. For phytohormone signal transduction, degradation or inactivation of the repressors is a prerequisite, a process in which proteasomal degradation or protein modifications, such as phosphorylation, are involved. In this review, we summarize the various repressor proteins and their methods of regulation. In addition, we also shed light on other post-transcriptional modifications, including protein sumoylation, acetylation, methylation, and S-nitrosylation, which might be involved in repressor regulation. We conclude that repressors are the gatekeepers of phytohormone signaling, allowing transcription of phytohormone-responsive genes only when required and thus serving as a universal mechanism to conserve energy in plants. Finally, we strongly recommend that plant research should be focused further on elucidating the mechanisms regulating repressor abundance or activity, to improve our understanding of phytohormone signal transduction.

Fourteen Stations of Auxin

Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.

The Root Clock as a Signal Integrator System: Ensuring Balance for Survival

The root system is essential for the survival of terrestrial plants, plant development, and adaptation to changing environments. The development of the root system relies on post-embryonic organogenesis and more specifically on the formation and growth of lateral roots (LR). The spacing of LR along the main root is underpinned by a precise prepatterning mechanism called the Root Clock. In Arabidopsis, the primary output of this mechanism involves the generation of periodic gene expression oscillations in a zone close to the root tip called the Oscillation Zone (OZ). Because of these oscillations, pre-branch sites (PBS) are established in the positions from which LR will emerge, although the oscillations can also possibly regulate the root wavy pattern and growth. Furthermore, we show that the Root Clock is present in LR. In this review, we describe the recent advances unraveling the inner machinery of Root Clock as well as the new tools to track the Root Clock activity. Moreover, we discuss the basis of how Arabidopsis can balance the creation of a repetitive pattern while integrating both endogenous and exogenous signals to adapt to changing environmental conditions. These signals can work as entrainment signals, but in occasions they also affect the periodicity and amplitude of the oscillatory dynamics in gene expression. Finally, we identify similarities with the Segmentation Clock of vertebrates and postulate the existence of a determination front delimiting the end of the oscillations in gene expression and initiating LR organogenesis through the activation of PBS in an ARF7 dependent-manner.

Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology

Auxin response factors (ARFs) play important roles in plant growth and development; however, research in peanut (Arachis hypogaea L.) is still lacking. Here, 63, 30, and 30 AhARF genes were identified from an allotetraploid peanut cultivar and two diploid ancestors (A. duranensis and A. ipaensis). Phylogenetic tree and gene structure analysis showed that most AhARFs were highly similar to those in the ancestors. By scanning the whole-genome for ARF-recognized cis-elements, we obtained a potential target gene pool of AhARFs, and the further cluster analysis and comparative analysis showed that numerous members were closely related to root development. Furthermore, we comprehensively analyzed the relationship between the root morphology and the expression levels of AhARFs in 11 peanut varieties. The results showed that the expression levels of AhARF14/26/45 were positively correlated with root length, root surface area, and root tip number, suggesting an important regulatory role of these genes in root architecture and potential application values in peanut breeding.

Plant hormone regulation of abiotic stress responses

Plant hormones are signalling compounds that regulate crucial aspects of growth, development and environmental stress responses. Abiotic stresses, such as drought, salinity, heat, cold and flooding, have profound effects on plant growth and survival. Adaptation and tolerance to such stresses require sophisticated sensing, signalling and stress response mechanisms. In this Review, we discuss recent advances in understanding how diverse plant hormones control abiotic stress responses in plants and highlight points of hormonal crosstalk during abiotic stress signalling. Control mechanisms and stress responses mediated by plant hormones including abscisic acid, auxin, brassinosteroids, cytokinins, ethylene and gibberellins are discussed. We discuss new insights into osmotic stress sensing and signalling mechanisms, hormonal control of gene regulation and plant development during stress, hormone-regulated submergence tolerance and stomatal movements. We further explore how innovative imaging approaches are providing insights into single-cell and tissue hormone dynamics. Understanding stress tolerance mechanisms opens new opportunities for agricultural applications.

(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants

The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.

Chinese Cherry (Cerasus pseudocerasus Lindl.) ARF7 Participates in Root Development and Responds to Drought and Low Phosphorus

In this paper, an auxin-responsive transcription factor, CpARF7, was isolated from the roots of Chinese cherry (Cerasus pseudocerasus Lindl. Cv. “Manao Hong”). CpARF7 is highly homologous to AtARF7 or AtARF19 in Arabidopsis, and PavARF1 or PavARF14 in sweet cherry. However, in the phenotype of transgenic tomatoes, the root morphology changed, the main root elongated, and the lateral root increased. Both drought treatment and low-phosphorus conditions can elongate the roots of transgenic tomatoes. In addition, the drought resistance and low-phosphorus tolerance of the transgenic lines are improved, and the POD, SOD, and CAT activities under drought and low-phosphorus environments are increased. There is an effect on the tomato somatotropin suppressor gene, SlIAAs, in which SlIAA1/14/19/29 are up-regulated and SlIAA2/11/12/16 are down-regulated. These results indicate that CpARF7 plays an essential regulatory role in root formation and abiotic stress response, and deepens the understanding of auxin-responsive genes in root growth and abiotic stress.

Toward synthetic plant development

The ability to engineer plant form will enable the production of novel agricultural products designed to tolerate extreme stresses, boost yield, reduce waste, and improve manufacturing practices. While historically, plants were altered through breeding to change their size or shape, advances in our understanding of plant development and our ability to genetically engineer complex eukaryotes are leading to the direct engineering of plant structure. In this review, I highlight the central role of auxin in plant development and the synthetic biology approaches that could be used to turn auxin-response regulators into powerful tools for modifying plant form. I hypothesize that recoded, gain-of-function auxin response proteins combined with synthetic regulation could be used to override endogenous auxin signaling and control plant structure. I also argue that auxin-response regulators are key to engineering development in nonmodel plants and that single-cell -omics techniques will be essential for characterizing and modifying auxin response in these plants. Collectively, advances in synthetic biology, single-cell -omics, and our understanding of the molecular mechanisms underpinning development have set the stage for a new era in the engineering of plant structure.

Integration of nutrient and water availabilities via auxin into the root developmental program

In most soils, the spatial distribution of nutrients and water in the rooting zone of plants is heterogeneous and changes over time. To access localized resources more efficiently, plants induce foraging responses by modulating individual morphological root traits, such as the length of the primary root or the number and length of lateral roots. These adaptive responses require the integration of exogenous and endogenous nutrient- or water-related signals into the root developmental program. Recent studies corroborated a central role of auxin in shaping root architectural traits in response to fluctuating nutrient and water availabilities. In this review, we highlight current knowledge on nutrient- and water-related developmental processes that impact root foraging and involve auxin as a central player. A deeper understanding and exploitation of these auxin-related processes and mechanisms promises advances in crop breeding for higher resource efficiency.

Cellular and molecular bases of lateral root initiation and morphogenesis

Lateral root development is essential for the establishment of the plant root system. Lateral root initiation is a multistep process that impacts early primordium morphogenesis and is linked to the formation of a morphogenetic field of pericycle founder cells. Gradual recruitment of founder cells builds this morphogenetic field in an auxin-dependent manner. The complex process of lateral root primordium morphogenesis includes several subprocesses, which are presented in this review. The underlying cellular and molecular mechanisms of these subprocesses are examined.

The hidden half comes into the spotlight: Peeking inside the black box of root developmental phases

Efficient use of natural resources (e.g., light, water, and nutrients) can be improved with a tailored developmental program that maximizes the lifetime and fitness of plants. In plant shoots, a developmental phase represents a time window in which the meristem triggers the development of unique morphological and physiological traits, leading to the emergence of leaves, flowers, and fruits. Whereas developmental phases in plant shoots have been shown to enhance food production in crops, this phenomenon has remained poorly investigated in roots. In light of recent advances, we suggest that root development occurs in three main phases: root apical meristem appearance, foraging, and senescence. We provide compelling evidence suggesting that these phases are regulated by at least four developmental pathways: autonomous, non-autonomous, hormonal, and periodic. Root developmental pathways differentially coordinate organ plasticity, promoting morphological alterations, tissue regeneration, and cell death regulation. Furthermore, we suggest how nutritional checkpoints may allow progression through the developmental phases, thus completing the root life cycle. These insights highlight novel and exciting advances in root biology that may help maximize the productivity of crops through more sustainable agriculture and the reduced use of chemical fertilizers.

WUSCHEL-related homeobox family genes in rice control lateral root primordium size

In recent years, phenotypic plasticity has received attention for improving plant adaptability to variable environments. For more than half a century, it has been known that rice and cereal plants develop different types of lateral roots (LRs), unlike the dicot model plant Arabidopsis. Despite the importance of plastic LR development under variable water conditions, the molecular mechanisms regulating LR types are unknown. Here, we report the regulatory mechanism of LR primordium size in rice, an important determinant of LR type. We identified two WUSCHEL-related homeobox (WOX) transcription factors that opposingly regulate LR primordium size. Our findings form the basis for improving root phenotypic plasticity for sustainable crop production under variable environments.

The development of a plastic root system is essential for stable crop production under variable environments. Rice plants have two types of lateral roots (LRs): S-type (short and thin) and L-type (long, thick, and capable of further branching). LR types are determined at the primordium stage, with a larger primordium size in L-types than S-types. Despite the importance of LR types for rice adaptability to variable water conditions, molecular mechanisms underlying the primordium size control of LRs are unknown. Here, we show that two WUSCHEL-related homeobox (WOX) genes have opposing roles in controlling LR primordium (LRP) size in rice. Root tip excision on seminal roots induced L-type LR formation with wider primordia formed from an early developmental stage. QHB/OsWOX5 was isolated as a causative gene of a mutant that is defective in S-type LR formation but produces more L-type LRs than wild-type (WT) plants following root tip excision. A transcriptome analysis revealed that OsWOX10 is highly up-regulated in L-type LRPs. OsWOX10 overexpression in LRPs increased the LR diameter in an expression-dependent manner. Conversely, the mutation in OsWOX10 decreased the L-type LR diameter under mild drought conditions. The qhb mutants had higher OsWOX10 expression than WT after root tip excision. A yeast one-hybrid assay revealed that the transcriptional repressive activity of QHB was lost in qhb mutants. An electrophoresis mobility shift assay revealed that OsWOX10 is a potential target of QHB. These data suggest that QHB represses LR diameter increase, repressing OsWOX10. Our findings could help improve root system plasticity under variable environments.

Inter-tissue and inter-organ signaling in drought stress response and phenotyping of drought tolerance

Plant response to drought stress includes systems for intracellular regulation of gene expression and signaling, as well as inter-tissue and inter-organ signaling, which helps entire plants acquire stress resistance. Plants sense water-deficit conditions both via the stomata of leaves and roots, and transfer water-deficit signals from roots to shoots via inter-organ signaling. Abscisic acid is an important phytohormone involved in the drought stress response and adaptation, and is synthesized mainly in vascular tissues and guard cells of leaves. In leaves, stress-induced abscisic acid is distributed to various tissues by transporters, which activates stomatal closure and expression of stress-related genes to acquire drought stress resistance. Moreover, the stepwise stress response at the whole-plant level is important for proper understanding of the physiological response to drought conditions. Drought stress is sensed by multiple types of sensors as molecular patterns of abiotic stress signals, which are transmitted via separate parallel signaling networks to induce downstream responses, including stomatal closure and synthesis of stress-related proteins and metabolites. Peptide molecules play important roles in the inter-organ signaling of dehydration from roots to shoots, as well as signaling of osmotic changes and reactive oxygen species/Ca²⁺ . In this review, we have summarized recent advances in research on complex plant drought stress responses, focusing on inter-tissue signaling in leaves and inter-organ signaling from roots to shoots. We have discussed the mechanisms via which drought stress adaptations and resistance are acquired at the whole-plant level, and have proposed the importance of quantitative phenotyping for measuring plant growth under drought conditions.

Phosphorylation of SWEET sucrose transporters regulates plant root:shoot ratio under drought

The root:shoot ratio has long been known to be enhanced in plants under drought stress. Here we discovered that osmotic stress enhances long-distance sucrose transport to increase the root:shoot ratio in an abscisic-acid-dependent manner. The Arabidopsis sucrose transporters SWEET11 and 12, key players in phloem loading, are rapidly phosphorylated upon drought and abscisic acid treatments. The drought- and abscisic-acid-activated SnRK2 protein kinases phosphorylate the carboxy-terminal cytosolic regions of SWEET11 and 12. This phosphorylation enhances the oligomerization and sucrose transport activity of SWEETs, which results in elevated sucrose contents in roots and improved root growth under drought stress, leading to the enhanced root:shoot ratio of biomass and drought resistance. Notably, the expression of phospho-mimic SWEETs led to improved root growth even under non-stressed conditions. The phosphorylation of sucrose transporters provides an explanation for the long-standing observation that drought stress enhances the root:shoot ratio in plants and suggests a strategy for engineering drought-resistant crops.

Hydrogen Sulfide Improves the Cold Stress Resistance through the CsARF5-CsDREB3 Module in Cucumber

As an important gas signaling molecule, hydrogen sulfide (H₂S) plays a crucial role in regulating cold tolerance. H₂S cooperates with phytohormones such as abscisic acid, ethylene, and salicylic acid to regulate the plant stress response. However, the synergistic regulation of H₂S and auxin in the plant response to cold stress has not been reported. This study showed that sodium hydrosulfide (NaHS, an H₂S donor) treatment enhanced the cold stress tolerance of cucumber seedlings and increased the level of auxin. CsARF5, a cucumber auxin response factor (ARF) gene, was isolated, and its role in regulating H₂S-mediated cold stress tolerance was described. Transgenic cucumber leaves overexpressing CsARF5 were obtained. Physiological analysis indicated that overexpression of CsARF5 enhanced the cold stress tolerance of cucumber and the regulation of the cold stress response by CsARF5 depends on H₂S. In addition, molecular assays showed that CsARF5 modulated cold stress response by directly activating the expression of the dehydration-responsive element-binding (DREB)/C-repeat binding factor (CBF) gene CsDREB3, which was identified as a positive regulator of cold stress. Taken together, the above results suggest that CsARF5 plays an important role in H₂S-mediated cold stress in cucumber. These results shed light on the molecular mechanism by which H₂S regulates cold stress response by mediating auxin signaling; this will provide insights for further studies on the molecular mechanism by which H₂S regulates cold stress. The aim of this study was to explore the molecular mechanism of H₂S regulating cold tolerance of cucumber seedlings and provide a theoretical basis for the further study of cucumber cultivation and environmental adaptability technology in winter.

The Adaptation and Tolerance of Major Cereals and Legumes to Important Abiotic Stresses

Abiotic stresses, including drought, extreme temperatures, salinity, and waterlogging, are the major constraints in crop production. These abiotic stresses are likely to be amplified by climate change with varying temporal and spatial dimensions across the globe. The knowledge about the effects of abiotic stressors on major cereal and legume crops is essential for effective management in unfavorable agro-ecologies. These crops are critical components of cropping systems and the daily diets of millions across the globe. Major cereals like rice, wheat, and maize are highly vulnerable to abiotic stresses, while many grain legumes are grown in abiotic stress-prone areas. Despite extensive investigations, abiotic stress tolerance in crop plants is not fully understood. Current insights into the abiotic stress responses of plants have shown the potential to improve crop tolerance to abiotic stresses. Studies aimed at stress tolerance mechanisms have resulted in the elucidation of traits associated with tolerance in plants, in addition to the molecular control of stress-responsive genes. Some of these studies have paved the way for new opportunities to address the molecular basis of stress responses in plants and identify novel traits and associated genes for the genetic improvement of crop plants. The present review examines the responses of crops under abiotic stresses in terms of changes in morphology, physiology, and biochemistry, focusing on major cereals and legume crops. It also explores emerging opportunities to accelerate our efforts to identify desired traits and genes associated with stress tolerance.

Genome-Wide Identification of ARF Gene Family Suggests a Functional Expression Pattern during Fruitlet Abscission in Prunus avium L

Auxin response factors (ARFs) play a vital role in plant growth and development. In the current study, 16 ARF members have been identified in the sweet cherry (Prunus avium L.) genome. These genes are all located in the nucleus. Sequence analysis showed that genes in the same subgroup have similar exon-intron structures. A phylogenetic tree has been divided into five groups. The promoter sequence includes six kinds of plant hormone-related elements, as well as abiotic stress response elements such as low temperature or drought. The expression patterns of PavARF in different tissues, fruitlet abscission, cold and drought treatment were comprehensively analyzed. PavARF10/13 was up-regulated and PavARF4/7/11/12/15 was down-regulated in fruitlet abscising. These genes may be involved in the regulation of fruit drop in sweet cherry fruits. This study comprehensively analyzed the bioinformatics and expression pattern of PavARF, which can lay the foundation for further understanding the PavARF family in plant growth development and fruit abscission.

Root plasticity under abiotic stress

Abiotic stresses increasingly threaten existing ecological and agricultural systems across the globe. Plant roots perceive these stresses in the soil and adapt their architecture accordingly. This review provides insights into recent discoveries showing the importance of root system architecture (RSA) and plasticity for the survival and development of plants under heat, cold, drought, salt, and flooding stress. In addition, we review the molecular regulation and hormonal pathways involved in controlling RSA plasticity, main root growth, branching and lateral root growth, root hair development, and formation of adventitious roots. Several stresses affect root anatomy by causing aerenchyma formation, lignin and suberin deposition, and Casparian strip modulation. Roots can also actively grow toward favorable soil conditions and avoid environments detrimental to their development. Recent advances in understanding the cellular mechanisms behind these different root tropisms are discussed. Understanding root plasticity will be instrumental for the development of crops that are resilient in the face of abiotic stress.

The converging path of protein SUMOylation in phytohormone signalling: highlights and new frontiers

The intersection of phytohormone signalling pathways with SUMOylation, a key post-translational modification, offers an additional layer of control to the phytohormone signalling for sophisticated regulation of plant development. Plants live in a constantly changing environment that are often challenging for the growth and development of plants. Phytohormones play a critical role in modulating molecular-level changes for enabling plants to resist climatic aberrations. The orchestration of such effective molecular responses entails rapid regulation of phytohormone signalling at transcriptional, translational and post-translational levels. Post-translational modifications have emerged as a key player in modulating hormonal pathways. The current review lays emphasis on the role of SUMOylation, a key post-translational modification, in manipulating individual hormone signalling pathways for better plant adaptability. Here, we discuss the recent advancement in the field and highlights how SUMO targets key signalling intermediates including transcription factors to provide a quick response to different biotic or abiotic stresses, sometimes even prior to changes in hormone levels. The understanding of the convergence of SUMOylation and hormonal pathways will offer an additional layer of control to the phytohormone signalling for an intricate and sophisticated regulation of plant development and can be utilised as a tool to generate climate-resilient crops.

Casting the Net-Connecting Auxin Signaling to the Plant Genome

Auxin represents one of the most potent and most versatile hormonal signals in the plant kingdom. Built on a simple core of only a few dedicated components, the auxin signaling system plays important roles for diverse aspects of plant development, physiology, and defense. Key to the diversity of context-dependent functional outputs generated by cells in response to this small molecule are gene duplication events and sub-functionalization of signaling components on the one hand, and a deep embedding of the auxin signaling system into complex regulatory networks on the other hand. Together, these evolutionary innovations provide the mechanisms to allow each cell to display a highly specific auxin response that suits its individual requirements. In this review, we discuss the regulatory networks connecting auxin with a large number of diverse pathways at all relevant levels of the signaling system ranging from biosynthesis to transcriptional response.

Uncovering How Auxin Optimizes Root Systems Architecture in Response to Environmental Stresses

Since colonizing land, plants have developed mechanisms to tolerate a broad range of abiotic stresses that include flooding, drought, high salinity, and nutrient limitation. Roots play a key role acclimating plants to these as their developmental plasticity enables them to grow toward more favorable conditions and away from limiting or harmful stresses. The phytohormone auxin plays a key role translating these environmental signals into developmental outputs. This is achieved by modulating auxin levels and/or signaling, often through cross talk with other hormone signals like abscisic acid (ABA) or ethylene. In our review, we discuss how auxin controls root responses to water, osmotic and nutrient-related stresses, and describe how the synthesis, degradation, transport, and response of this key signaling hormone helps optimize root architecture to maximize resource acquisition while limiting the impact of abiotic stresses.

SUMOylation: A critical transcription modulator in plant cells

Gene transcription is critical for various cellular processes and is precisely controlled at multiple levels, and posttranslational modification (PTM) is a fast and powerful way to regulate transcription factors (TFs). SUMOylation, which conjugates small ubiquitin-related modifier (SUMO) molecules to protein substrates, is a crucial PTM that modulates the activity, stability, subcellular localization, and partner interactions of TFs in plant cells. Here, we summarize the mechanisms of SUMOylation in the regulation of transcription in plant development and stress responses. We also discuss the crosstalk between SUMOylation and other PTMs, as well as the potential functions of SUMOylation in the regulation of transcription-associated complexes on plant chromatin. This summary and perspective will improve understanding of the molecular mechanism of PTMs in plant transcription regulation.

Breeding custom-designed crops for improved drought adaptation

The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable, and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high-throughput identification of the genetic architecture of key drought-adaptive traits and explore innovative genomic breeding strategies for designing future crops.

CaADIP1-dependent CaADIK1-kinase activation is required for abscisic acid signalling and drought stress response in Capsicum annuum

Induction of the abscisic acid (ABA) signalling network is associated with various stress conditions, including cold, high salinity and drought. As core ABA signalling components, group A type 2C protein phosphatases (PP2Cs) interact with and inhibit snf1-related protein kinase2s. Here, we isolated and characterised the pepper mitogen-activated protein kinase kinase kinase CaADIK1, which interacts with the group A PP2C CaADIP1. CaADIK1 transcripts were induced by abiotic stresses, and CaADIK1 localised in the nucleus and cytoplasm. We verified that CaADIP1 inhibits the autokinase activity of CaADIK1; moreover, the kinase activity of CaADIK1 is enhanced by drought stress. We performed genetic analysis using CaADIK1-silenced pepper and CaADIK1-overexpressing (OX) Arabidopsis plants. CaADIK1-silenced pepper plants showed drought-sensitive phenotypes, whereas CaADIK1-OX Arabidopsis plants showed ABA-sensitive and drought-tolerant phenotypes. In CaADIK1^K32N -OX Arabidopsis plants mutated at the ATP-binding site, the ABA-insensitive and drought-sensitive phenotypes were restored. Taken together, our findings show that CaADIK1 positively regulates the ABA-dependent drought stress response and is inhibited by CaADIP1.

SUMO enables substrate selectivity by mitogen-activated protein kinases to regulate immunity in plants

The versatility of mitogen-activated protein kinases (MAPKs) in translating exogenous and endogenous stimuli into appropriate cellular responses depends on its substrate specificity. In animals, several mechanisms have been proposed about how MAPKs maintain specificity to regulate distinct functional pathways. However, little is known of mechanisms that enable substrate selectivity in plant MAPKs. Small ubiquitin-like modifier (SUMO), a posttranslational modification system, plays an important role in plant development and defense by rapid reprogramming of cellular events. In this study we identified a functional SUMO interaction motif (SIM) in Arabidopsis MPK3 and MPK6 that reveals a mechanism for selective interaction of MPK3/6 with SUMO-conjugated WRKY33, during defense. We show that WRKY33 is rapidly SUMOylated in response to Botrytis cinerea infection and flg22 elicitor treatment. SUMOylation mediates WRKY33 phosphorylation by MPKs and consequent transcription factor activity. Disruption of either WRKY33 SUMO or MPK3/6 SIM sites attenuates their interaction and inactivates WRKY33-mediated defense. However, MPK3/6 SIM mutants show normal interaction with a non-SUMOylated form of another transcription factor, SPEECHLESS, unraveling a role for SUMOylation in differential substrate selectivity by MPKs. We reveal that the SUMO proteases, SUMO PROTEASE RELATED TO FERTILITY1 (SPF1) and SPF2 control WRKY33 SUMOylation and demonstrate a role for these SUMO proteases in defense. Our data reveal a mechanism by which MPK3/6 prioritize molecular pathways by differentially selecting substrates using the SUMO-SIM module during defense responses.

A reflux-and-growth mechanism explains oscillatory patterning of lateral root branching sites

Modular, repetitive structures are a key component of complex multicellular body plans across the tree of life. Typically, these structures are prepatterned by temporal oscillations in gene expression or signaling. Although a clock-and-wavefront mechanism was identified and plant leaf phyllotaxis arises from a Turing-type patterning for vertebrate somitogenesis and arthropod segmentation, the mechanism underlying lateral root patterning has remained elusive. To resolve this enigma, we combined computational modeling with in planta experiments. Intriguingly, auxin oscillations automatically emerge in our model from the interplay between a reflux-loop-generated auxin loading zone and stem-cell-driven growth dynamics generating periodic cell-size variations. In contrast to the clock-and-wavefront mechanism and Turing patterning, the uncovered mechanism predicts both frequency and spacing of lateral-root-forming sites to positively correlate with root meristem growth. We validate this prediction experimentally. Combined, our model and experimental results support that a reflux-and-growth patterning mechanism underlies lateral root priming.

Determinants of root system architecture for future-ready, stress-resilient crops

Climate change hampers food safety and food security. Crop breeding has been boosting superior quantity traits such as yield, but roots have often been overlooked in spite of their role in the whole plant physiology. New evidence is emerging on the relevance of root system architecture in coping with the environment. Here, we review determinants of root system architecture, mainly based on studies on Arabidopsis, and we discuss how breeding for appropriate root architecture may help obtain plants that are better adapted or resilient to abiotic and biotic stresses, more productive, and more efficient for soil and water use. We also highlight recent advances in phenotyping high-tech platforms and genotyping techniques that may further help to understand the mechanisms of root development and how roots control relationships between plants and soil. An integrated approach is proposed that combines phenotyping and genotyping information via bioinformatic analyses and reveals genetic control of root system architecture, paving the way for future research on plant breeding.

A SUMO ligase OsMMS21 regulates rice development and auxin response

SUMOylation, which transfers the Small Ubiquitin-related Modifier (SUMO) polypeptides to target proteins, regulates diverse cellular processes in eukaryotes. The SUMO conjugation reaction is usually promoted by SUMO E3 ligases, but the molecular functions of this type of enzymes remain unclear in cereal crops. Here, OsMMS21, a SUMO E3 ligase, was functionally characterized in rice (Oryza sativa). Bioinformatics analysis showed that OsMMS21 harbors a conserved SP-RING domain that is essential for the activity of SUMO ligases. Biochemical data indicated that this protein is auto-SUMOylated. Besides, overexpression of OsMMS21 rescued the developmental defects of the AtMMS21 mutant, supporting that OsMMS21 is a functional homolog of the Arabidopsis SUMO ligase AtMMS21. The OsMMS21 rice T-DNA mutant displays a short-root and dwarfism phenotype. RNA-seq data revealed that the expression levels of many genes involved in signaling transduction of hormones, including auxin, are altered in the OsMMS21 mutant. Further results under the auxin treatment showed that the OsMMS21 mutant is insensitive to auxin. Collectively, our results demonstrated the molecular features of OsMMS21 and uncovered the roles of this SUMO ligase in development and auxin response, providing hints for further studies on protein SUMOylation in rice.