Short-Root regulates primary, lateral, and adventitious root development in Arabidopsis

Knockout of endoplasmic reticulum-localized molecular chaperone HSP90.7 impairs seedling development and cellular auxin homeostasis in Arabidopsis

The Arabidopsis endoplasmic reticulum-localized heat shock protein HSP90.7 modulates tissue differentiation and stress responses; however, complete knockout lines have not been previously reported. In this study, we identified and analyzed a mutant allele, hsp90.7-1, which was unable to accumulate the HSP90.7 full-length protein and showed seedling lethality. Microscopic analyses revealed its essential role in male and female fertility, trichomes and root hair development, proper chloroplast function, and apical meristem maintenance and differentiation. Comparative transcriptome and proteome analyses also revealed the role of the protein in a multitude of cellular processes. Particularly, the auxin-responsive pathway was specifically downregulated in the hsp90.7-1 mutant seedlings. We measured a much-reduced auxin content in both root and shoot tissues. Through comprehensive histological and molecular analyses, we confirmed PIN1 and PIN5 accumulations were dependent on the HSP90 function, and the TAA-YUCCA primary auxin biosynthesis pathway was also downregulated in the mutant seedlings. This study therefore not only fulfilled a gap in understanding the essential role of HSP90 paralogs in eukaryotes but also provided a mechanistic insight on the ER-localized chaperone in regulating plant growth and development via modulating cellular auxin homeostasis.

Not so hidden anymore: Advances and challenges in understanding root growth under water deficits

Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.

SPIRO - the automated Petri plate imaging platform designed by biologists, for biologists

Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.

Inhibition of a conserved bacterial dual-specificity phosphatase confers plant tolerance to Candidatus Liberibacter spp

"Candidatus Liberibacter spp." are insect-vectored, fastidious, and vascular-limited phytopathogens. They are the presumptive causal agents of potato zebra chip, tomato vein clearing, and the devastating citrus greening disease worldwide. There is an urgent need to develop new strategies to control them. In this study, we characterized a dual-specificity serine/tyrosine phosphatase (STP) that is well conserved among thirty-three geographically diverse "Candidatus Liberibacter spp." and strains that infect multiple Solanaceaea and citrus spp. The STP is expressed in infected plant tissues, localized at the plant cytosol and plasma membrane, and interferes with plant cell death responses. We employed an in silico target-based molecular modeling and ligand screen to identify two small molecules with high binding affinity to STP. Efficacy studies demonstrated that the two molecules can inhibit "Candidatus Liberibacter spp." but not unrelated pathogens and confer plant disease tolerance. The inhibitors and strategies are promising means to control "Candidatus Liberibacter spp."

Epistatic interaction between CsCEN and CsSHBY in regulating indeterminate/determinate growth of lateral branch in cucumber

KEY MESSAGE

Two genetic loci, det-ma (CsCEN) and det-lb, showed epistatic interaction on indeterminate/determinate growth of LB in cucumber. CsSHBY was identified as the candidate gene for det-lb locus. Plant architecture depends on the spatial regulation of meristems from both main axis (MA) and lateral branches (LBs). Fate (indeterminate or determinate) of these meristems is a crucial source of architectural diversity determining crop productivity and management. CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING (CETS) gene family have been well known as pivotal regulators for indeterminate/determinate growth of MA. Nevertheless, genes that regulate LB indeterminacy/determinacy remained unclear. Cucumber (Cucumis sativus L.) has typical monopodial growth and multiple lateral branches. Both MA and LBs had indeterminate or determinate growth, and indeterminate/determinate growth of LB was controlled by two distinct loci, det-ma (CsCEN) and det-lb. In our study, based on bulked segregant analysis (BSA) method, the det-lb locus was mapped on a 60.6 kb region on chromosome 1 harboring only one gene CsaV3_1G044330, which encoded a putative vacuolar-sorting protein (designated as CsSHBY). Multipoint mutations in CsSHBY were identified in D082 and D226, compared with CCMC, including nonsynonymous SNP mutations and a 6-bp deletion in exons. Further, qPCR showed that CsSHBY was highly expressed in lateral bud of CCMC, suggesting that CsSHBY might play an active role in regulating indeterminate/determinate growth of LB. Genetic analyses showed that det-ma (CsCEN) had an epistatic effect on det-lb (CsSHBY), and CsCEN could activate CsSHBY promoter by Dual luciferase and GUS activity assays. Meanwhile, Cscen or Csshby was found to influence auxin contents and CsYUCs and CsPINs expression levels. These findings provided new insights into precisely optimizing plant architecture for yield improvements.

Folate shapes plant root architecture by affecting auxin distribution

Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.

Genome-wide identification of RsGRAS gene family reveals positive role of RsSHRc gene in chilling stress response in radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is an important worldwide root vegetable crop. Little information of the GRAS gene family was available in radish. Herein, a total of 51 GRAS family members were firstly identified from radish genome, and unevenly located onto nine radish chromosomes. Expression analysis of RsGRAS genes in taproot displayed that RsSCL15a and RsSHRc were highly expressed in the radish cambium, and its expression level was increased with the taproot thickening. Comparative transcriptome analysis revealed that the expression patterns of RsGRAS genes varied upon exposure to different abiotic stresses including heavy metals, salt and heat. The expression level of six RsGRAS genes including RsSHRc was increased under chilling stress in two radish genotypes with different cold tolerance. Further analysis indicated that RsGRAS genes could respond to cold stress rapidly and the expression of RsSHRc was up-regulated at different development stages (cortex splitting and thickening stages) under long-term cold treatment. Transient expression of RsSHRc gene in radish showed that RsSHRc possessed the reliable function of eliminating reactive oxygen species (ROS), inhibiting the formation of malondialdehyde (MDA) and promoting to accumulate proline under cold stress. Together, these findings provided insights into the function of RsGRAS genes in taproot development and chilling stress response in radish.

Overexpression of a SHORT-ROOT transcriptional factor enhances the auxin mediated formation of adventitious roots and lateral roots in poplar trees

SHORT-ROOT (SHR) defines root stem cells and maintains radial patterning, but its involvement in adventitious root (AR) formation has not been reported. In this study, we showed that PtSHR2 was transcriptionally upregulated by excision before the formation of AR and responded dynamically to auxin. PtSHR2 overexpression (SHR2B^OE) in hybrid poplars resulted in an increased number of ARs with an initial delay. Despite a lower endogenous content in the stems than in wild-type plants, indole-3-acetic acid (IAA) content at the SHR2B^OE basal stem increased rapidly after cutting and reached a higher maximum than in wild-type plants, which was accompanied by a more sustained and stronger induction of AR formation marker genes. In addition, the higher auxin content in SHR2B^OE ARs resulted in more and longer lateral roots (LRs). Application of auxin abolished the early delay in the formation of AR and largely other AR phenotypes of SHR2B^OE plants, whereas the polar auxin transport inhibitor N-1-naphthylphthalamic acid completely inhibited both AR and LR abnormalities. Since the enhanced rooting ability of SHR2B^OE stem cuttings in hydroponics was clearly confirmed, our results suggest a novel role of poplar SHR2 as a positive regulator during the organogenesis of AR and LR by affecting local auxin homeostasis.

Molecular basis of differential adventitious rooting competence in poplar genotypes

Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.

Recent trends in root phenomics of plant systems with available methods- discrepancies and consonances

The phenotyping of plant roots is a challenging task and poses a major lacuna in plant root research. Roots rhizospheric zone is affected by several environmental cues among which salinity, drought, heavy metal and soil pH are key players. Among biological factors, fungal, nematode and bacterial interactions with roots are vital for improving nutrient uptake efficiency in plants. The subterranean nature of a plant root and the limited number of approaches for root phenotyping offers a great challenge to the plant breeders to select a desirable root trait under different stress conditions. Identification of key root traits can provide a basic understanding for generating crop plants with enhanced ability to withstand various biotic or abiotic stresses. For instance, crops with improved soil exploration potential, phosphate uptake efficiency, water use efficiency and others. Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide precise and desired root quantification attributes. Though 3D imaging by X-ray computed tomography (X-ray-CT) and magnetic resonance imaging techniques are complex, however, it provides the most applicable and practically relevant data for quantifying root system architecture traits. This review outlines the current developments in root studies including recent approaches viz. X-ray-CT, MRI, thermal infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it offers multiple advantages by removing discrepancies and providing the actual practical significance of plant roots for breeding programs.

SHORT-ROOT Controls Cell Elongation in the Etiolated Arabidopsis Hypocotyl

Transcriptional regulation, a core component of gene regulatory networks, plays a key role in controlling individual organism's growth and development. To understand how plants modulate cellular processes for growth and development, the identification and characterization of gene regulatory networks are of importance. The SHORT-ROOT (SHR) transcription factor is known for its role in cell divisions in Arabidopsis (Arabidopsis thaliana). However, whether SHR is involved in hypocotyl cell elongation remains unknown. Here, we reveal that SHR controls hypocotyl cell elongation via the transcriptional regulation of XTH18, XTH22, and XTH24, which encode cell wall remodeling enzymes called xyloglucan endotransglucosylase/hydrolases (XTHs). Interestingly, SHR activates transcription of the XTH genes, independently of its partner SCARECROW (SCR), which is different from the known mode of action. In addition, overexpression of the XTH genes can promote cell elongation in the etiolated hypocotyl. Moreover, confinement of SHR protein in the stele still induces cell elongation, despite the aberrant organization in the hypocotyl ground tissue. Therefore, it is likely that SHR-mediated growth is uncoupled from SHR-mediated radial patterning in the etiolated hypocotyl. Our findings also suggest that intertissue communication between stele and endodermis plays a role in coordinating hypocotyl cell elongation of the Arabidopsis seedling. Taken together, our study identifies SHR as a new crucial regulator that is necessary for cell elongation in the etiolated hypocotyl.

Overexpression of SHORT-ROOT2 transcription factor enhances the outgrowth of mature axillary buds in poplar trees

SHORT-ROOT (SHR) transcription factors play important roles in asymmetric cell division and radial patterning of Arabidopsis roots. In hybrid poplar (P. tremula × P. alba clone INRA 717-1B4), PtaSHR2 was preferentially expressed in axillary buds (AXBs) and transcriptionally up-regulated during AXB maturation and activation. Overexpression of SHR2 (PtSHR2OE) induced an enhanced outgrowth of AXBs below the bud maturation point, with a simultaneous transition of an active shoot apex into an arrested terminal bud. The larger and more mature AXBs of PtSHR2OE trees revealed altered expression of genes involved in axillary meristem initiation and bud activation, as well as a higher ratio of cytokinin to auxin. To elucidate the underlying mechanism of PtSHR2OE-induced high branching, subsequent molecular and biochemical studies showed that compared with wild-type trees, decapitation induced a quicker bud outburst in PtSHR2OE trees, which could be fully inhibited by exogenous application of auxin or cytokinin biosynthesis inhibitor, but not by N-1-naphthylphthalamic acid. Our results indicated that overexpression of PtSHR2B disturbed the internal hormonal balance in AXBs by interfering with the basipetal transport of auxin, rather than causing auxin biosynthesis deficiency or auxin insensitivity, thereby releasing mature AXBs from apical dominance and promoting their outgrowth.

PIN3 from Liriodendron May Function in Inflorescence Development and Root Elongation

Auxin, the first discovered phytohormone, is important for the growth and development of plants through the establishment of homeostasis and asymmetry. Here, we cloned the auxin transporter gene PIN-FORMED3 (PIN3) from the valuable timber tree hybrid Liriodendron (Liriodendron chinense × Liriodendron tulipifera). The gene contained a complete open reading frame of 1917 bp that encoded 638 amino acids. Phylogenetic analysis indicated that LhPIN3 exhibited the highest sequence similarity to the PIN3 of Vitis vinifera. Quantitative real-time PCR analysis showed that LhPIN3 was broadly expressed across different tissues/organs of Liriodendron, with the highest expression level in the roots. Heterologous overexpression of LhPIN3 in Arabidopsis thaliana caused considerable phenotypic changes, such as the root length and number of flowers. Genetic complementation of Arabidopsis pin1 mutants by LhPIN3, driven by the cauliflower mosaic virus 35S promoter, fully restored the root length and number of flowers of the pin1 mutant. Overall, our findings reveal that LhPIN3 has similar capacities to regulate the root length and number of flowers of Arabidopsis with AtPIN1.

The UPR regulator IRE1 promotes balanced organ development by restricting TOR-dependent control of cellular differentiation in Arabidopsis

Proteostasis of the endoplasmic reticulum (ER) is controlled by sophisticated signaling pathways that are collectively called the unfolded protein response (UPR) and are initiated by specialized ER membrane-associated sensors. The evidence that complete loss-of-function mutations of the most conserved of the UPR sensors, inositol-requiring enzyme 1 (IRE1), dysregulates tissue growth and development in metazoans and plants raises the fundamental question as to how IRE1 is connected to organismal growth. To address this question, we interrogated the Arabidopsis primary root, an established model for organ development, using the tractable Arabidopsis IRE1 mutant ire1a ire1b, which has marked root development defects in the absence of exogenous stress. We demonstrate that IRE1 is required to reach maximum rates of cell elongation and root growth. We also established that in the actively growing ire1a ire1b mutant root tips the Target of Rapamycin (TOR) kinase, a widely conserved pro-growth regulator, is hyperactive, and that, unlike cell proliferation, the rate of cell differentiation is enhanced in ire1a ire1b in a TOR-dependent manner. By functionally connecting two essential growth regulators, these results underpin a novel and critical role of IRE1 in organ development and indicate that, as cells exit an undifferentiated state, IRE1 is required to monitor TOR activity to balance cell expansion and maturation during organ biogenesis.

Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex

Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT-ROOT, and phytohormone-related transcripts, such as ACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.

The Arabidopsis ATR-SOG1 signaling module regulates pleiotropic developmental adjustments in response to 3'-blocked DNA repair intermediates

Base excision repair and active DNA demethylation produce repair intermediates with DNA molecules blocked at the 3'-OH end by an aldehyde or phosphate group. However, both the physiological consequences of these accumulated single-strand DNAs break with 3'-blocked ends (DNA 3'-blocks) and the signaling pathways responding to unrepaired DNA 3'-blocks remain unclear in plants. Here, we investigated the effects of DNA 3'-blocks on plant development using the zinc finger DNA 3'-phosphoesterase (zdp) AP endonuclease2 (ape2) double mutant, in which 3'-blocking residues are poorly repaired. The accumulation of DNA 3'-blocked triggered diverse developmental defects that were dependent on the ATM and RAD3-related (ATR)-suppressor of gamma response 1 (SOG1) signaling module. SOG1 mutation rescued the developmental defects of zdp ape2 leaves by preventing cell endoreplication and promoting cell proliferation. However, SOG1 mutation caused intensive meristematic cell death in the radicle of zdp ape2 following germination, resulting in rapid termination of radicle growth. Notably, mutating FORMAMIDOPYRIMIDINE DNA GLYCOSYLASE (FPG) in zdp ape2 sog1 partially recovered its radicle growth, demonstrating that DNA 3'-blocks generated by FPG caused the meristematic defects. Surprisingly, despite lacking a functional radicle, zdp ape2 sog1 mutants compensated the lack of root growth by generating anchor roots having low levels of DNA damage response. Our results reveal dual roles of SOG1 in regulating root establishment when seeds germinate with excess DNA 3'-blocks.

Insights Into the Genetic Architecture of Complex Traits in Napier Grass (Cenchrus purpureus) and QTL Regions Governing Forage Biomass Yield, Water Use Efficiency and Feed Quality Traits

Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes (although a small population size, the genotypes were selected to best represent the genetic diversity of the collections) were selected and evaluated for 2 years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a 2-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values >10% and a minor allele frequency (MAF) <5%, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms implemented in the GAPIT R package, identified more than 35 QTL regions and markers associated with agronomic, morphological, and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.

At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia

The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.

Adventitious root primordia formation and development in the stem of Ananas comosus var. bracteatus slip

There are about 4-6 slips on a fruit, and they are good materials for effective regeneration of Ananas comosus var. bracteatus. Adventitious root (AR) induction is essential for the propagation of Ananas comosus var. bracteatus slips. Growth regulator treatment, and culture medium are imperative factors that affect slip growth and rooting. In order to screen the optimal methods for slips rooting and reveal the anatomic procedure of slip rooting, this study induced slip rooting by different treatment of growth regulator, culture medium, observed the slip stem structure, AR origination and formation procedure through paraffin sections. The results showed that, slip cuttings treated with 100 mg/L of Aminobenzotriazole (ABT) for 6 hrs, cultured in river sand: coconut chaff: garden soil 2:2:1 medium is the optimal method for rooting. The proper supplementary of ABT can enhance the soluble sugar content, soluble protein content, polyphenol oxidase (PPO) activity and peroxidase (POD) enzyme activity, which resulted in the improvement of rooting. The slip stem structure is quite different from other monocots, which consists of epidermis, cortex, and stele with vascular tissues distributed in the cortex and stele. The AR primordia originates from the parenchyma cells located on the borderline between the cortex and stele. The vascular tissues in the AR develop and are connected with vascular tissue of the stem before the AR grew out the stem. The number of primary xylem poles in AR is about 30.

Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants

Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.

Nature and Nurture: Genotype-Dependent Differential Responses of Root Architecture to Agar and Soil Environments

Root development is crucial for plant growth and therefore a key factor in plant performance and food production. Arabidopsis thaliana is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function plethora (plt) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that plt3plt7 and plt3plt5plt7 plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, plt3, plt3plt5, and plt5plt7 mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants short-root and scarecrow. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined.

Molecular Bases for the Regulation of Adventitious Root Generation in Plants

The formation of adventitious roots (ARs) is an ecologically and economically important developmental process in plants. The evolution of AR systems is an important way for plants to cope with various environmental stresses. This review focuses on identified genes that have known to regulate the induction and initiation of ARs and offers an analysis of this process at the molecular level. The critical genes involved in adventitious rooting are the auxin signaling-responsive genes, including the AUXIN RESPONSE FACTOR (ARF) and the LATERAL ORGAN BOUNDARIES-DOMAIN (LOB) gene families, and genes associated with auxin transport and homeostasis, the quiescent center (QC) maintenance, and the root apical meristem (RAM) initiation. Several genes involved in cell wall modulation are also known to be involved in the regulation of adventitious rooting. Furthermore, the molecular processes that play roles in the ethylene, cytokinin, and jasmonic acid signaling pathways and their crosstalk modulate the generation of ARs. The crosstalk and interaction among many molecular processes generates complex networks that regulate AR generation.

Plant apocarotenoids: from retrograde signaling to interspecific communication

Carotenoids are isoprenoid compounds synthesized by all photosynthetic and some non-photosynthetic organisms. They are essential for photosynthesis and contribute to many other aspects of a plant's life. The oxidative breakdown of carotenoids gives rise to the formation of a diverse family of essential metabolites called apocarotenoids. This metabolic process either takes place spontaneously through reactive oxygen species or is catalyzed by enzymes generally belonging to the CAROTENOID CLEAVAGE DIOXYGENASE family. Apocarotenoids include the phytohormones abscisic acid and strigolactones (SLs), signaling molecules and growth regulators. Abscisic acid and SLs are vital in regulating plant growth, development and stress response. SLs are also an essential component in plants' rhizospheric communication with symbionts and parasites. Other apocarotenoid small molecules, such as blumenols, mycorradicins, zaxinone, anchorene, β-cyclocitral, β-cyclogeranic acid, β-ionone and loliolide, are involved in plant growth and development, and/or contribute to different processes, including arbuscular mycorrhiza symbiosis, abiotic stress response, plant-plant and plant-herbivore interactions and plastid retrograde signaling. There are also indications for the presence of structurally unidentified linear cis-carotene-derived apocarotenoids, which are presumed to modulate plastid biogenesis and leaf morphology, among other developmental processes. Here, we provide an overview on the biology of old, recently discovered and supposed plant apocarotenoid signaling molecules, describing their biosynthesis, developmental and physiological functions, and role as a messenger in plant communication.

Plant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp

A major bottleneck in identifying therapies to control citrus greening and other devastating plant diseases caused by fastidious pathogens is our inability to culture the pathogens in defined media or axenic cultures. As such, conventional approaches for antimicrobial evaluation (genetic or chemical) rely on time-consuming, low-throughput and inherently variable whole-plant assays. Here, we report that plant hairy roots support the growth of fastidious pathogens like Candidatus Liberibacter spp., the presumptive causal agents of citrus greening, potato zebra chip and tomato vein greening diseases. Importantly, we leverage the microbial hairy roots for rapid, reproducible efficacy screening of multiple therapies. We identify six antimicrobial peptides, two plant immune regulators and eight chemicals which inhibit Candidatus Liberibacter spp. in plant tissues. The antimicrobials, either singly or in combination, can be used as near- and long-term therapies to control citrus greening, potato zebra chip and tomato vein greening diseases.

PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in Populus ussuriensis

Adventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive. Here, we report the identification of a poplar homeobox gene, PuHox52, which was induced rapidly (within 15 min) at the basal ends of stems upon cutting and played a key regulatory role in adventitious rooting. We demonstrated that overexpression of PuHox52 significantly increased the number of ARs while suppression of PuHox52 had the opposite effect. A multilayered hierarchical gene regulatory network (ML-hGRN) mediated by PuHox52 was reverse-engineered and demonstrated to govern AR formation. PuHox52 regulated AR formation through upregulation of nine hub regulators, including a jasmonate signaling pathway gene, PuMYC2, and an auxin signaling pathway gene, PuAGL12. We also identified coherent type 4 feed-forward loops within this ML-hGRN; PuHox52 repressed PuHDA9, which encodes a histone deacetylase, and led to an increase in acetylation and presumably expression of three hub regulators, PuWRKY51, PuLBD21 and PuIAA7. Our results indicate that the ML-hGRN mediated by PuHox52 governs AR formation at the basal ends of stem cuttings from poplar trees.

Exogenous 6-benzyladenine application affects root morphology by altering hormone status and gene expression of developing lateral roots in Malus hupehensis

Malus hupehensis is an extensively used apple rootstock in China. In the current study, M. hupehensis seedlings were treated with exogenous 2.2 µm 6-benzyladenine (6-BA) so as to investigate the mechanism by which 6-BA affects lateral root development. The results indicate that 6-BA treatment promotes elongation and thickening of both root and shoot in M. hupehensis, but reduces the number of lateral roots, as well as reducing the auxin level after 6-BA treatment. Moreover, MhAHK4, MhRR1 and MhRR2 were also significantly up-regulated in response to 6-BA treatment. Expression levels of auxin synthesis- and transport-related genes, such as MhYUCCA6, MhYUCCA10, MhPIN1 and MhPIN2, were down-regulated, which corresponds with lower auxin levels in the 6-BA-treated seedlings. A negative regulator of auxin, MhIAA3, was induced by 6-BA treatment, leading to reduced expression of MhARF7 and MhARF19 in 6-BA-treated seedlings. As a result, expression of MhWOX11, MhWOX5, MhLBD16 and MhLBD29 was blocked, which in turn inhibited lateral root initiation. In addition, a lower auxin level decreased expression of MhRR7 and MhRR15, which repressed expression of key transcription factors associated with root development, thus inhibiting lateral root development. In contrast, 6-BA treatment promoted secondary growth (thickening) of the root by inducing expression of MhCYCD3;1 and MhCYCD3;2. Collectively, the changes in hormone levels and gene expression resulted in a reduced number of lateral roots and thicker roots in 6-BA-treated plants.

Transcriptomic analysis reveals the GRAS family genes respond to gibberellin in Salvia miltiorrhiza hairy roots

BACKGROUND

Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental processes in plants. However, their role on the secondary metabolism regulation has not been investigated.

RESULTS

In this study, we found that gibberellic acid (GA) can promote hairy roots growth and increase the contents of tanshinones and phenolic acids. Transcriptomic sequencing revealed that many genes involved in the secondary metabolism pathway were the GA-responsive. After further analysis of GA signaling pathway genes, which their expression profiles have significantly changed, it was found that the GRAS transcription factor family had a significant response to GA. We identified 35 SmGRAS genes in S. miltiorrhiza, which can be divided into 10 subfamilies. Thereafter, members of the same subfamily showed similar conserved motifs and gene structures, suggesting possible conserved functions.

CONCLUSIONS

Most SmGRAS genes were significantly responsive to GA, indicating that they may play an important role in the GA signaling pathway, also participating in the GA regulation of root growth and secondary metabolism in S. miltiorrhiza.

Genetic control of root architectural plasticity in maize

Root phenotypes regulate soil resource acquisition; however, their genetic control and phenotypic plasticity are poorly understood. We hypothesized that the responses of root architectural phenes to water deficit (stress plasticity) and different environments (environmental plasticity) are under genetic control and that these loci are distinct. Root architectural phenes were phenotyped in the field using a large maize association panel with and without water deficit stress for three seasons in Arizona and without water deficit stress for four seasons in South Africa. All root phenes were plastic and varied in their plastic response. We identified candidate genes associated with stress and environmental plasticity and candidate genes associated with phenes in well-watered conditions in South Africa and in well-watered and water-stress conditions in Arizona. Few candidate genes for plasticity overlapped with those for phenes expressed under each condition. Our results suggest that phenotypic plasticity is highly quantitative, and plasticity loci are distinct from loci that control phene expression in stress and non-stress, which poses a challenge for breeding programs. To make these loci more accessible to the wider research community, we developed a public online resource that will allow for further experimental validation towards understanding the genetic control underlying phenotypic plasticity.

Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation

BACKGROUND

Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear.

OBJECTIVE

To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato.

METHODS

RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression.

RESULTS

42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation.

CONCLUSIONS

The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.

Alternative Polyadenylation and Salicylic Acid Modulate Root Responses to Low Nitrogen Availability

Nitrogen (N) is probably the most important macronutrient and its scarcity limits plant growth, development and fitness. N starvation response has been largely studied by transcriptomic analyses, but little is known about the role of alternative polyadenylation (APA) in such response. In this work, we show that N starvation modifies poly(A) usage in a large number of transcripts, some of them mediated by FIP1, a component of the polyadenylation machinery. Interestingly, the number of mRNAs isoforms with poly(A) tags located in protein-coding regions or 5'-UTRs significantly increases in response to N starvation. The set of genes affected by APA in response to N deficiency is enriched in N-metabolism, oxidation-reduction processes, response to stresses, and hormone responses, among others. A hormone profile analysis shows that the levels of salicylic acid (SA), a phytohormone that reduces nitrate accumulation and root growth, increase significantly upon N starvation. Meta-analyses of APA-affected and fip1-2-deregulated genes indicate a connection between the nitrogen starvation response and salicylic acid (SA) signaling. Genetic analyses show that SA may be important for preventing the overgrowth of the root system in low N environments. This work provides new insights on how plants interconnect different pathways, such as defense-related hormonal signaling and the regulation of genomic information by APA, to fine-tune the response to low N availability.

Reprogramming of Cell Fate During Root Regeneration by Transcriptional and Epigenetic Networks

Many plant species are able to regenerate adventitious roots either directly from aerial organs such as leaves or stems, in particularly after detachment (cutting), or indirectly, from over-proliferating tissue termed callus. In agriculture, this capacity of de novo root formation from cuttings can be used to clonally propagate several important crop plants including cassava, potato, sugar cane, banana and various fruit or timber trees. Direct and indirect de novo root regeneration (DNRR) originates from pluripotent cells of the pericycle tissue, from other root-competent cells or from non-root-competent cells that first dedifferentiate. Independently of their origin, the cells convert into root founder cells, which go through proliferation and differentiation subsequently forming functional root meristems, root primordia and the complete root. Recent studies in the model plants Arabidopsis thaliana and rice have identified several key regulators building in response to the phytohormone auxin transcriptional networks that are involved in both callus formation and DNRR. In both cases, epigenetic regulation seems essential for the dynamic reprogramming of cell fate, which is correlated with local and global changes of the chromatin states that might ensure the correct spatiotemporal expression pattern of the key regulators. Future approaches might investigate in greater detail whether and how the transcriptional key regulators and the writers, erasers, and readers of epigenetic modifications interact to control DNRR.

Determinate root development in the halted primary root1 mutant of Arabidopsis correlates with death of root initial cells and an enhanced auxin response

The transit from indeterminate to determinate root developmental program compromises growth and causes the differentiation of the meristem, but a direct link between this process with auxin signaling and/or viability of initial cells remains untested. Here, through the isolation and characterization of the halted primary root1 (hpr1) mutant of Arabidopsis, which develops primary and lateral roots with genetically stable determinate growth after germination, we show that the differentiation of the root meristem correlates with enhanced auxin responsiveness and is preceded by the death of provasculature initial cells in both primary and lateral roots. Supplementation of indole-3-acetic acid causes both a dose-dependent repression of primary root growth and an induction of DR5:uidA expression in wild-type seedlings, and these effects were exacerbated in hpr1 mutants. The damage of provasculature initial cells in the root of hpr1 mutants occurred at earlier times than the full differentiation of the meristem, and correlates with a reduced expression domain of CycB1:uidA and PRZ:uidA. Thus, HPR1 plays critical functions for stem cell maintenance, auxin homeostasis, cell division in the meristem, and indeterminate root growth.

Anchorene is a carotenoid-derived regulatory metabolite required for anchor root formation in Arabidopsis

Anchor roots (ANRs) arise at the root-shoot junction and are the least investigated type of Arabidopsis root. Here, we show that ANRs originate from pericycle cells in an auxin-dependent manner and a carotenogenic signal to emerge. By screening known and assumed carotenoid derivatives, we identified anchorene, a presumed carotenoid-derived dialdehyde (diapocarotenoid), as the specific signal needed for ANR formation. We demonstrate that anchorene is an Arabidopsis metabolite and that its exogenous application rescues the ANR phenotype in carotenoid-deficient plants and promotes the growth of normal seedlings. Nitrogen deficiency resulted in enhanced anchorene content and an increased number of ANRs, suggesting a role of this nutrient in determining anchorene content and ANR formation. Transcriptome analysis and treatment of auxin reporter lines indicate that anchorene triggers ANR formation by modulating auxin homeostasis. Together, our work reveals a growth regulator with potential application to agriculture and a new carotenoid-derived signaling molecule.

SmGRAS1 and SmGRAS2 Regulate the Biosynthesis of Tanshinones and Phenolic Acids in Salvia miltiorrhiza

Salvia miltiorrhiza is one of the most widely used traditional Chinese medicinal plants because of its excellent performance in treating heart diseases. Tanshinones and phenolic acids are two important classes of effective metabolites, and their biosynthesis has attracted widespread interest. Here, we functionally characterized SmGRAS1 and SmGRAS2, two GRAS family transcription factors from S. miltiorrhiza. SmGRAS1/2 were highly expressed in the root periderm, where tanshinones mainly accumulated in S. miltiorrhiza. Overexpression of SmGRAS1/2 upregulated tanshinones accumulation and downregulated GA, phenolic acids contents, and root biomass. However, antisense expression of SmGRAS1/2 reduced the tanshinones accumulation and increased the GA, phenolic acids contents, and root biomass. The expression patterns of biosynthesis genes were consistent with the changes in compounds accumulation. GA treatment increased tanshinones, phenolic acids, and GA contents in the overexpression lines, and restored the root growth inhibited by overexpressing SmGRAS1/2. Subsequently, yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays (EMSA) showed SmGRAS1 promoted tanshinones biosynthesis by directly binding to the GARE motif in the SmKSL1 promoter and activating its expression. Yeast two-hybrid assays showed SmGRAS1 interacted physically with SmGRAS2. Taken together, the results revealed that SmGRAS1/2 acted as repressors in root growth and phenolic acids biosynthesis but as positive regulators in tanshinones biosynthesis. Overall, our findings revealed the potential value of SmGRAS1/2 in genetically engineering changes in secondary metabolism.

Auxin regulates adventitious root formation in tomato cuttings

BACKGROUND

Adventitious root (AR) formation is a critical developmental process in cutting propagation for the horticultural industry. While auxin has been shown to regulate this process, the exact mechanism and details preceding AR formation remain unclear. Even though AR and lateral root (LR) formation share common developmental processes, there are exist some differences that need to be closely examined at the cytological level. Tomato stem cuttings, which readily form adventitious roots, represent the perfect system to study the influence of auxin on AR formation and to compare AR and LR organogenesis.

RESULTS

Here we show the progression by which AR form from founder cells in the basal pericycle cell layers in tomato stem cuttings. The first disordered clumps of cells assumed a dome shape that later differentiated into functional AR cell layers. Further growth resulted in emergence of mature AR through the epidermis following programmed cell death of epidermal cells. Auxin and ethylene levels increased in the basal stem cutting within 1 h. Tomato lines expressing the auxin response element DR5pro:YFP showed an increase in auxin distribution during the AR initiation phase, and was mainly concentrated in the meristematic cells of the developing AR. Treatment of stem cuttings with auxin, increased the number of AR primordia and the length of AR, while stem cuttings treated with the pre-emergent herbicide/auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) occasionally developed thick, agravitropic AR. Hormone profile analyses showed that auxin positively regulated AR formation, whereas perturbations to zeatin, salicylic acid, and abscisic acid homeostasis suggested minor roles during tomato stem rooting. The gene expression of specific auxin transporters increased during specific developmental phases of AR formation.

CONCLUSION

These data show that AR formation in tomato stems is a complex process. Upon perception of a wounding stimulus, expression of auxin transporter genes and accumulation of auxin at founder cell initiation sites in pericycle cell layers and later in the meristematic cells of the AR primordia were observed. A clear understanding and documentation of these events in tomato is critical to resolve AR formation in recalcitrant species like hardwoods and improve stem cutting propagation efficiency and effectiveness.

Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots

Vascular cambium, a lateral plant meristem, is a central producer of woody biomass. Although a few transcription factors have been shown to regulate cambial activity¹, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we use cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses to identify 62 new transcription factor genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified transcription factors with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the transcription factor network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.

Proteomic profiling of root system development proteins in chrysanthemum overexpressing the CmTCP20 gene

Plant root systems ensure the efficient absorption of water and nutrients and provide anchoring into the soil. Although root systems are a highly plastic set of traits that vary both between and among species, the basic root system morphology is controlled by inherent genetic factors. TCP20 has been identified as a key regulator of root development in plants, and yet its underlying mechanism has not been fully elucidated, especially in chrysanthemum. We found that overexpression of the CmTCP20 gene promoted both adventitious and lateral root development in chrysanthemum. To get further insight into the molecular mechanisms controlling root system development, we conducted a study employing tandem mass tag proteomic to characterize the differential root system development proteomes from CmTCP20-overexpressing and wild-type chrysanthemum root samples. Of the proteins identified, 234 proteins were found to be differentially abundant (>1.5-fold cut off, p < 0.05) in CmTCP20-overexpressing versus wild-type chrysanthemum root samples. Functional enrichment analysis indicated that the CmTCP20 gene may participate in "phytohormone signal transduction". Our findings provide a valuable perspective on the mechanisms of both adventitious and lateral root development via CmTCP20 modulation at the proteome level in chrysanthemum.

Apocarotenoids Involved in Plant Development and Stress Response

Carotenoids are isoprenoid pigments synthesized by all photosynthetic organisms and many heterotrophic microorganisms. They are equipped with a conjugated double-bond system that builds the basis for their role in harvesting light energy and in protecting the cell from photo-oxidation. In addition, the carotenoids polyene makes them susceptible to oxidative cleavage, yielding carbonyl products called apocarotenoids. This oxidation can be catalyzed by carotenoid cleavage dioxygenases or triggered nonenzymatically by reactive oxygen species. The group of plant apocarotenoids includes important phytohormones, such as abscisic acid and strigolactones, and signaling molecules, such as β-cyclocitral. Abscisic acid is a key regulator of plant's response to abiotic stress and is involved in different developmental processes, such as seed dormancy. Strigolactone is a main regulator of plant architecture and an important signaling molecule in the plant-rhizosphere communication. β-Cyclocitral, a volatile derived from β-carotene oxidation, mediates the response of cells to singlet oxygen stress. Besides these well-known examples, recent research unraveled novel apocarotenoid growth regulators and suggests the presence of yet unidentified ones. In this review, we describe the biosynthesis and biological functions of established regulatory apocarotenoids and touch on the recently identified anchorene and zaxinone, with emphasis on their role in plant growth, development, and stress response.

The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses

Root development and its response to environmental changes is crucial for whole plant adaptation. These responses include changes in transcript levels. Here, we show that the alternative polyadenylation (APA) of mRNA is important for root development and responses. Mutations in FIP1, a component of polyadenylation machinery, affects plant development, cell division and elongation, and response to different abiotic stresses. Salt treatment increases the amount of poly(A) site usage within the coding region and 5' untranslated regions (5'-UTRs), and the lack of FIP1 activity reduces the poly(A) site usage within these non-canonical sites. Gene ontology analyses of transcripts displaying APA in response to salt show an enrichment in ABA signaling, and in the response to stresses such as salt or cadmium (Cd), among others. Root growth assays show that fip1-2 is more tolerant to salt but is hypersensitive to ABA or Cd. Our data indicate that FIP1-mediated alternative polyadenylation is important for plant development and stress responses.

Lateral Root Primordium Morphogenesis in Angiosperms

Morphogenetic processes are the basis of new organ formation. Lateral roots (LRs) are the building blocks of the root system. After LR initiation and before LR emergence, a new lateral root primordium (LRP) forms. During this period, the organization and functionality of the prospective LR is defined. Thus, proper LRP morphogenesis is a decisive process during root system formation. Most current studies on LRP morphogenesis have been performed in the model species Arabidopsis thaliana; little is known about this process in other angiosperms. To understand LRP morphogenesis from a wider perspective, we review both contemporary and earlier studies. The latter are largely forgotten, and we attempted to integrate them into present-day research. In particular, we consider in detail the participation of parent root tissue in LRP formation, cell proliferation and timing during LRP morphogenesis, and the hormonal and genetic regulation of LRP morphogenesis. Cell type identity acquisition and new stem cell establishement during LRP morphogenesis are also considered. Within each of these facets, unanswered or poorly understood questions are identified to help define future research in the field. Finally, we discuss emerging research avenues and new technologies that could be used to answer the remaining questions in studies of LRP morphogenesis.

CONSTITUTIVE TRIPLE RESPONSE1 and PIN2 act in a coordinate manner to support the indeterminate root growth and meristem cell proliferating activity in Arabidopsis seedlings

The plant hormone ethylene induces auxin biosynthesis and transport and modulates root growth and branching. However, its function on root stem cells and the identity of interacting factors for the control of meristem activity remains unclear. Genetic analysis for primary root growth in wild-type (WT) Arabidopsis thaliana seedlings and ethylene-related mutants showed that the loss-of-function of CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) inhibits cell division and elongation. This phenotype is associated with an increase in the expression of the auxin transporter PIN2 and a drastic decrease in the expression of key factors for stem cell niche maintenance such as PLETHORA1, SHORT ROOT and SCARECROW. While the root stem cell niche is affected in ctr1 mutants, its maintenance is severely compromised in the ctr1-1eir1-1(pin2) double mutant, in which an evident loss of proliferative capacity of the meristematic cells leads to a fully differentiated root meristem shortly after germination. Root traits affected in ctr1-1 mutants could be restored in ctr1-1ein2-1 double mutants. These results reveal that ethylene perception via CTR1 and EIN2 in the root modulates the proliferative capacity of root stem cells via affecting the expression of genes involved in the two major pathways, AUX-PIN-PLT and SCR-SHR, which are key factors for proper root stem cell niche maintenance.

HY5 Contributes to Light-Regulated Root System Architecture Under a Root-Covered Culture System

Light is essential for plant organogenesis and development. Light-regulated shoot morphogenesis has been extensively studied; however, the mechanisms by which plant roots perceive and respond to aboveground light are largely unknown, particularly because the roots of most terrestrial plants are usually located underground in darkness. To mimic natural root growth conditions, we developed a root-covered system (RCS) in which the shoots were illuminated and the plant roots could be either exposed to light or cultivated in darkness. Using the RCS, we observed that root growth of wild-type plants was significantly promoted when the roots were in darkness, whereas it was inhibited by direct light exposure. This growth change seems to be regulated by ELONGATED HYPOCOTYL 5 (HY5), a master regulator of photomorphogenesis. Light was found to regulate HY5 expression in the roots, while a HY5 deficiency partially abolished the inhibition of growth in roots directly exposed to light, suggesting that HY5 expression is induced by direct light exposure and inhibits root growth. However, no differences in HY5 expression were observed between illuminated and dark-grown cop1 roots, indicating that HY5 may be regulated by COP1-mediated proteasome degradation. We confirmed the crucial role of HY5 in regulating root development in response to light under soil-grown conditions. A transcriptomic analysis revealed that light controls the expression of numerous genes involved in phytohormone signaling, stress adaptation, and metabolic processes in a HY5-dependent manner. In combination with the results of the flavonol quantification and exogenous quercetin application, these findings suggested that HY5 regulates the root response to light through a complex network that integrates flavonol biosynthesis and reactive oxygen species signaling. Collectively, our results indicate that HY5 is a master regulator of root photomorphogenesis.

The MADS transcription factor CmANR1 positively modulates root system development by directly regulating CmPIN2 in chrysanthemum

Plant root systems are essential for many physiological processes, including water and nutrient absorption. MADS-box transcription factor (TF) genes have been characterized as the important regulators of root development in plants; however, the underlying mechanism is largely unknown, including chrysanthemum. Here, it was found that the overexpression of CmANR1, a chrysanthemum MADS-box TF gene, promoted both adventitious root (AR) and lateral root (LR) development in chrysanthemum. Whole transcriptome sequencing analysis revealed a series of differentially expressed unigenes (DEGs) in the roots of CmANR1-transgenic chrysanthemum plants compared to wild-type plants. Functional annotation of these DEGs by alignment with Gene Ontology (GO) terms and biochemical pathway Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that CmANR1 TF exhibited "DNA binding" and "catalytic" activity, as well as participated in "phytohormone signal transduction". Both chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) and gel electrophoresis mobility shift assays (EMSA) indicated the direct binding of CmPIN2 to the recognition site CArG-box motif by CmANR1. Finally, a firefly luciferase imaging assay demonstrated the transcriptional activation of CmPIN2 by CmANR1 in vivo. Overall, our results provide novel insights into the mechanisms of MADS-box TF CmANR1 modulation of both AR and LR development, which occurs by directly regulating auxin transport gene CmPIN2 in chrysanthemum.

Manipulation of plant architecture and flowering time by down-regulation of the GRAS transcription factor SlGRAS26 in Solanum lycopersicum

Previous studies suggest that GRAS transcription factors act as essential regulators, not only in plant growth and development but also in response to biotic and abiotic stresses. Recently, 53 GRAS proteins have been identified, but only a few of them have been functionally studied in tomato. Here, we isolated a novel GRAS transcription factor SlGRAS26, its down-regulation generated pleiotropic phenotypes, including reduced plant height with more lateral shoots, internode length, leaf size, even leaflets, accelerated flowering transition and decreased trichome number. Transcription analysis showed that down-regulation of SlGRAS26 altered vegetative growth by suppressing gibberellin (GA) biosynthesis genes and activating the GA inactivating genes, thereby reducing endogenous GA content in transgenic plants. SlGRAS26 may regulate the initiation of lateral buds by regulating the expression of Blind (BL) and BRC1b. The earlier initiation of flower buds in transgenic lines may be controlled by significant up-regulation of SFT, CO1, SBP3, SBP13, and SBP15 genes, related to flowering time. These results demonstrate that SlGRAS26 may play a vital role in the initiation of lateral and inflorescence meristems in tomato.

Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis

Body regeneration through formation of new organs is a major question in developmental biology. We investigated de novo root formation using whole leaves of Arabidopsis (Arabidopsis thaliana). Our results show that local cytokinin biosynthesis and auxin biosynthesis in the leaf blade followed by auxin long-distance transport to the petiole leads to proliferation of J0121-marked xylem-associated tissues and others through signaling of INDOLE-3-ACETIC ACID INDUCIBLE28 (IAA28), CRANE (IAA18), WOODEN LEG, and ARABIDOPSIS RESPONSE REGULATORS1 (ARR1), ARR10, and ARR12. Vasculature proliferation also involves the cell cycle regulator KIP-RELATED PROTEIN2 and ABERRANT LATERAL ROOT FORMATION4, resulting in a mass of cells with rooting competence that resembles callus formation. Endogenous callus formation precedes specification of postembryonic root founder cells, from which roots are initiated through the activity of SHORT-ROOT, PLETHORA1 (PLT1), and PLT2. Primordia initiation is blocked in shr plt1 plt2 mutant. Stem cell regulators SCHIZORIZA, JACKDAW, BLUEJAY, and SCARECROW also participate in root initiation and are required to pattern the new organ, as mutants show disorganized and reduced number of layers and tissue initials resulting in reduced rooting. Our work provides an organ regeneration model through de novo root formation, stating key stages and the primary pathways involved.

KinG Is a Plant-Specific Kinesin That Regulates Both Intra- and Intercellular Movement of SHORT-ROOT

Both endogenous plant proteins and viral movement proteins associate with microtubules to promote their movement through plasmodesmata. The association of viral movement proteins with microtubules facilitates the formation of virus-associated replication complexes, which are required for the amplification and subsequent spread of the virus. However, the role of microtubules in the intercellular movement of plant proteins is less clear. Here we show that the SHORT-ROOT (SHR) protein, which moves between cells in the root to regulate root radial patterning, interacts with a type-14 kinesin, KINESIN G (KinG). KinG is a calponin homology domain kinesin that directly interacts with the SHR-binding protein SIEL (SHR-INTERACING EMBRYONIC LETHAL) and localizes to both microtubules and actin. Since SIEL and SHR associate with endosomes, we suggest that KinG serves as a linker between SIEL, SHR, and the plant cytoskeleton. Loss of KinG function results in a decrease in the intercellular movement of SHR and an increase in the sensitivity of SHR movement to treatment with oryzalin. Examination of SHR and KinG localization and dynamics in live cells suggests that KinG is a nonmotile kinesin that promotes the pausing of SHR-associated endosomes. We suggest a model in which interaction of KinG with SHR allows for the formation of stable movement complexes that facilitate the cell-to-cell transport of SHR.

SHORTROOT-Mediated Increase in Stomatal Density Has No Impact on Photosynthetic Efficiency

The coordinated positioning of veins, mesophyll cells, and stomata across a leaf is crucial for efficient gas exchange and transpiration and, therefore, for overall function. In monocot leaves, stomatal cell files are positioned at the flanks of underlying longitudinal leaf veins, rather than directly above or below. This pattern suggests either that stomatal formation is inhibited in epidermal cells directly in contact with the vein or that specification is induced in cell files beyond the vein. The SHORTROOT pathway specifies distinct cell types around the vasculature in subepidermal layers of both root and shoots, with cell type identity determined by distance from the vein. To test whether the pathway has the potential to similarly pattern epidermal cell types, we expanded the expression domain of the rice (Oryza sativa ssp japonica) OsSHR2 gene, which we show is restricted to developing leaf veins, to include bundle sheath cells encircling the vein. In transgenic lines, which were generated using the orthologous ZmSHR1 gene to avoid potential silencing of OsSHR2, stomatal cell files were observed both in the normal position and in more distant positions from the vein. Contrary to theoretical predictions, and to phenotypes observed in eudicot leaves, the increase in stomatal density did not enhance photosynthetic capacity or increase mesophyll cell density. Collectively, these results suggest that the SHORTROOT pathway may coordinate the positioning of veins and stomata in monocot leaves and that distinct mechanisms may operate in monocot and eudicot leaves to coordinate stomatal patterning with the development of underlying mesophyll cells.