What Makes Adventitious Roots?

Seasonal Coloration and Ecological Adaptations of Adventitious Roots of Four Salicaceous Species in Jiuzhaigou World Natural Heritage Site, Southwestern China

Jiuzhaigou is a world natural heritage with extraordinary beauty of wetlands largely developed on tufa landforms. The wetlands are dominated by shrubs and trees. A striking feature of dense and plentiful adventitious roots is found during summer, and the color changes to unnoticeable during winter. Despite the visual prominence of this phenomenon, its biochemical mechanisms and ecological significance remain unexplored. Integrating field surveys, anatomical analyses, and biochemical profiling to decipher coloration dynamics and their potential as environmental bioindicators, results indicate that dense adventitious roots were found only with willow and poplar species in the tufa wetlands in Shuzheng and Rize valleys. Adventitious roots displayed specialized adaptations, including well-developed aerenchyma, degenerated mechanical tissue and xylem, and a floating habit on the water surface, which enhances oxygen uptake in aquatic habitats. Seasonal color variations followed a distinct temporal pattern, transitioning from red or pink hues in summer to reddish-brown in spring and autumn, and maroon or gray in winter. Proanthocyanidins were identified as principal pigments, with their oxidation into quinones under the influence of temperature and light driving the observed color transitions. The proanthocyanidins redox dynamics reflect seasonal fluctuations in air temperature and solar irradiance, providing a novel biomarker for assessing climate impacts on wetland ecosystems. The close link between seasonal color change of adventitious roots and the aquatic environment sheds new light on effective ecosystem management in karst areas.

MDF Regulates a Network of Auxin-Dependent and Auxin-Independent Pathways of Adventitious Root Regeneration in Arabidopsis

Plants exhibit strong plasticity in growth and development, seen clearly in lateral and adventitious root development from differentiated tissues in response to environmental stresses. Previous studies have demonstrated the role of both auxin-dependent and auxin-independent signaling pathways in regulating the de novo formation of adventitious roots (ARs) from differentiated tissues, such as leaf petiole in Arabidopsis. One important question is how the auxin-dependent and auxin-independent pathways are coordinated. To investigate this question, we used a combined approach of inducible gene expression, mutant, and signaling reporter gene analysis during AR regeneration in the Arabidopsis petiole to understand regulatory relationships. Auxin signaling components AXR1 and AXR3 are each required for both AR and subsequent lateral root (LR) initiation, as is the ethylene signaling repressor POLARIS, but not EIN2. The PIN trafficking SNARE protein VAMP714 is required for LR rather than AR formation, through effects on auxin-induced gene expression. We identify the RNA splicing regulator MDF and the transcription factor RAP2.7 as new positive regulators of both the auxin-independent and auxin-dependent pathways, and show that MDF regulates RAP2.7, WOX5, and NAC1 while RAP2.7 regulates WOX5 but not NAC1 or YUC1. NAC1 is required for de novo root formation in a pathway independent of YUC1, WOX5, or RAP2.7. We propose a model in which MDF represents a point of molecular crosstalk between auxin-dependent and auxin-independent regeneration processes.

DNA Hypomethylation Activates the RpMYB2-Centred Gene Network to Enhance Regeneration of Adventitious Roots

Plants, being immobile, are exposed to environmental adversities such as wind, snow and animals that damage their structure, making regeneration essential for their survival. The adventitious roots (ARs) primarily emerge from a detached explant to uptake nutrients; therefore, the molecular network involved in their regeneration needs to be explored. DNA methylation, a key epigenetic mark, influences molecular pathways, and recent studies suggested its role in regeneration. In our research, the application of 5-azacytidine (5-azaC), an inhibitor of DNA methylation, caused the earlier initiation and development of root primordia and consequently enhanced the AR regeneration rate in Robinia psuedoacacia L (black locust). The whole-genome bisulfite sequencing (WGBS) revealed a decrease in global methylation and an increase in hypomethylated cytosine sites and regions across all contexts including CHH, CHG and mergedCG caused transcriptional variations in 5-azaC-treated sample. The yeast two-hybrid (Y2H) assay revealed a RpMYB2-centred network of transcriptionally activated transcription factors (TFs) including RpWRKY23, RpGATA23, RpSPL16 and other genes like RpSDP, RpSS1, RpBEN1, RpGULL05 and RpCUV with nuclear localization suggesting their potential co-localization. Additionally, yeast one-hybrid (Y1H) assay showed the interaction of RpMYB2 interactors, RpGATA23 and RpWRKY23, with promoters of RpSK6 and RpCDC48, and luciferase reporting assay (LRA) validated their binding with RpSK6. Our results revealed that hypomethylation-mediated transcriptomic modifications activated the RpMYB2-centred gene network to enhance AR regeneration in black locust hypocotyl cuttings. These findings pave the way for genetic modification to improve plant regeneration ability and increase wood production while withstanding environmental damage.

Spatial-Temporal Dynamics of Adventitious Roots of Typha domingensis Pers. Seedlings Grown with Auxin/Cytokinin

The spatial-temporal dynamics of an in vitro radicular system of Typha domingensis for the development of rhizofiltration technologies, with the potential for use as a phytotreatment of eutrophicated water, were studied for the first time in the roots of seedlings and in rhizotron systems. The effect of indole-3-acetic acid (AIA) in combination with kinetin (CIN) or 6-benzylaminopurine (BAP) on seedlings cultivated in the light and dark in three radicular systems and in a rhizotrophic regime for the screening of dynamic rhizogenic lines, by weekly allometric measurements of the length and number of roots, were studied. Inhibition of the elongation and branching velocities of roots by BAP and light was observed but CIN increased elongation and branching. In rhizotrons cultivated in light and dark conditions with different AIA/CIN ratios, isolated root explants remained inactive; however, roots attached to a meristematic base presented a significant increase in growth development, with values comparable to those of roots attached to seedlings cultivated in light without hormones. The results revealed that six adventitious rhizogenic root lines with basal meristems have the potential for use in a wide range of environmental and innovative applications in phytotreatment technologies involving eutrophicated water.

De novo root regeneration from leaf explant: a mechanistic review of key factors behind cell fate transition

MAIN CONCLUSION

De novo root regeneration (DNRR) involves activation of special cells after wounding, along with the converter cells, reactive oxygen species, ethylene, and jasmonic acid, also playing key roles. An updated DNRR model is presented here with gene regulatory networks. Root formation after tissue injury is a type of plant regeneration known as de novo root regeneration (DNRR). DNRR system has wide applications in agriculture and tissue culture biotechnology. This review summarizes the recent advancements in the DNRR model for the cellular and molecular framework, targeting leaf explant of Arabidopsis and highlighting differences among direct and indirect pathways. Key findings highlight the presence of special cells in leaf explants after wounding, under different time lapses, through single-cell sequencing of the transcriptional landscape. The possible roles of reactive oxygen species (ROS), ethylene, and jasmonic acid are explored in the early establishment of wounding signals (short/long) for auxin biosynthesis, ultimately leading to adventitious root formation. The synergistic manner of 3rd type of special cells along converter and regeneration-competent cells automatically leads towards cell fate transition for auxin flux in regeneration-competent cells. The signaling mechanisms of these suggested special cells need to be further investigated to understand the DNRR mechanistic story entirely, in addition to root-to-root regeneration and stem-to-root regeneration. Meta-analysis of DNRR is also presented for past and future reference.

Identification of Potato StPIN Gene Family and Regulation of Root Development by StPIN4

The growth hormone export PIN-FORMED (PIN) is an important carrier for regulating the polar transport of plant growth hormones and plays an important role in plant growth and development. However, little is known about the characteristics and functions of PINs in potatoes. In this study, 10 PIN members were identified from potatoes and named StPIN1, StPIN2, StPIN3, StPIN4, StPIN5, StPIN6, StPIN7, StPIN8, StPIN9, and StPIN10 according to their positions in the potato chromosome In addition, the expression of 10 StPINs was analyzed by qRT-PCR during potato root development. The results showed that the StPIN4 gene plays an important regulatory role in potato root development, and its tissue expression varied greatly. Several cis-regulatory elements related to growth factors were also detected in the promoter region of the StPIN gene. The transgenic overexpressing StPIN4 in potato showed suppressed growth in root length and lateral root number, and StPIN4-interfering plants showed the opposite. These results suggested that StPIN4 plays a key role in the regulation of the potato root architecture.

Transcriptomic profiling and discovery of key transcription factors involved in adventitious roots formation from root cuttings of mulberry

ARs plays a crucial role in plant morphogenesis and development. The limited and inefficient rooting of scions poses a significant challenge to the efficiency and quality of clonal propagation of forest trees in silvicultural practices. Building on previous research conducted by our team, we found that applying IBA at a concentration of 1000 mg/L significantly enhanced mulberry rooting. This study aims to uncover the molecular mechanisms underlying this effect by analyzing RNA sequencing data from mulberry phloem before and after treatment with IBA over time intervals of 10, 20, 30, and 40 days. We identified 5226 DEGs, which were then classified into GO terms and KEGG pathways, showing significant enrichment in hormone signaling processes. Using WGCNA, we identified eight co-expression modules, two of which were significantly correlated with the IBA treatment. Additionally, 18 transcription factors that potentially facilitate ARs formation in mulberry were identified, and an exploratory analysis on the cis-regulatory elements associated with these transcription factors was conducted. The findings of this study provide a comprehensive understanding of the mechanisms of ARs in mulberry and offer theoretical support for the discovery and utilization of exceptional genetic resources within the species.

Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.)

BACKGROUND

Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering.

RESULTS

Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process.

CONCLUSIONS

This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.

Azelaic acid can efficiently compete for the auxin binding site TIR1, altering auxin polar transport, gravitropic response, and root growth and architecture in Arabidopsisthaliana roots

The present study investigates the phytotoxic potential of azelaic acid (AZA) on Arabidopsis thaliana roots. Effects on root morphology, anatomy, auxin content and transport, gravitropic response and molecular docking were analysed. AZA inhibited root growth, stimulated lateral and adventitious roots, and altered the root apical meristem by reducing meristem cell number, length and width. The treatment also slowed down the roots' gravitropic response, likely due to a reduction in statoliths, starch-rich organelles involved in gravity perception. In addition, auxin content, transport and distribution, together with PIN proteins' expression and localisation were altered after AZA treatment, inducing a reduction in auxin transport and its distribution into the meristematic zone. Computational simulations showed that AZA has a high affinity for the auxin receptor TIR1, competing with auxin for the binding site. The AZA binding with TIR1 could interfere with the normal functioning of the TIR1/AFB complex, disrupting the ubiquitin E3 ligase complex and leading to alterations in the response of the plant, which could perceive AZA as an exogenous auxin. Our results suggest that AZA mode of action could involve the modulation of auxin-related processes in Arabidopsis roots. Understanding such mechanisms could lead to find environmentally friendly alternatives to synthetic herbicides.

Transcription factors WOX11 and LBD16 function with histone demethylase JMJ706 to control crown root development in rice

Crown roots are the main components of root systems in cereals. Elucidating the mechanisms of crown root formation is instrumental for improving nutrient absorption, stress tolerance, and yield in cereal crops. Several members of the WUSCHEL-related homeobox (WOX) and lateral organ boundaries domain (LBD) transcription factor families play essential roles in controlling crown root development in rice (Oryza sativa). However, the functional relationships among these transcription factors in regulating genes involved in crown root development remain unclear. Here, we identified LBD16 as an additional regulator of rice crown root development. We showed that LBD16 is a direct downstream target of WOX11, a key crown root development regulator in rice. Our results indicated that WOX11 enhances LBD16 transcription by binding to its promoter and recruiting its interaction partner JMJ706, a demethylase that removes histone H3 lysine 9 dimethylation (H3K9me2) from the LBD16 locus. In addition, we established that LBD16 interacts with WOX11, thereby impairing JMJ706-WOX11 complex formation and repressing its own transcriptional activity. Together, our results reveal a feedback system regulating genes that orchestrate crown root development in rice, in which LBD16 acts as a molecular rheostat.

Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages

Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.

Wounding-Related Signaling Is Integrated within the Auxin-Response Framework to Induce Adventitious Rooting in Chestnut

Wounding and exogenous auxin are needed to induce adventitious roots in chestnut microshoots. However, the specific inductive role of wounding has not been characterized in this species. In the present work, two main goals were established: First, we prompted to optimize exogenous auxin treatments to improve the overall health status of the shoots at the end of the rooting cycle. Second, we developed a time-series transcriptomic analysis to compare gene expression in response to wounding alone and wounding plus auxin, focusing on the early events within the first days after treatments. Results suggest that the expression of many genes involved in the rooting process is under direct or indirect control of both stimuli. However, specific levels of expression of relevant genes are only attained when both treatments are applied simultaneously, leading to the successful development of roots. In this sense, we have identified four transcription factors upregulated by auxin (CsLBD16, CsERF113, Cs22D and CsIAA6), with some of them also being induced by wounding. The highest expression levels of these genes occurred when wounding and auxin treatments were applied simultaneously, correlating with the rooting response of the shoots. The results of this work clarify the genetic nature of the wounding response in chestnut, its relation to adventitious rooting, and might be helpful in the development of more specific protocols for the vegetative propagation of this species.

Transcriptome analysis of waterlogging-induced adventitious root and control taproot of Mentha arvensis

KEY MESSAGE

The present study reports differentially expressed transcripts in the waterlogging-induced adventitious root (AR) of Mentha arvensis; the identified transcripts will help to understand AR development and improve waterlogging stress response. Waterlogging notably hampers plant growth in areas facing waterlogged soil conditions. In our previous findings, Mentha arvensis was shown to adapt better in waterlogging conditions by initiating the early onset of adventitious root development. In the present study, we compared the transcriptome analysis of adventitious root induced after the waterlogging treatment with the control taproot. The biochemical parameters of total carbohydrate, total protein content, nitric oxide (NO) scavenging activity and antioxidant enzymes, such as catalase activity (CAT) and superoxide dismutase (SOD) activity, were enhanced in the adventitious root compared with control taproot. Analysis of differentially expressed genes (DEGs) in adventitious root compared with the control taproot were grouped into four functional categories, i.e., carbohydrate metabolism, antioxidant activity, hormonal regulation, and transcription factors that could be majorly involved in the development of adventitious roots. Differential expression of the upregulated and uniquely expressing thirty-five transcripts in adventitious roots was validated using qRT-PCR. This study has generated the resource of differentially and uniquely expressing transcripts in the waterlogging-induced adventitious roots. Further functional characterization of these transcripts will be helpful to understand the development of adventitious roots, leading to the resistance towards waterlogging stress in Mentha arvensis.

Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant

The use of tomato rootstocks has helped to alleviate the soaring abiotic stresses provoked by the adverse effects of climate change. Lateral and adventitious roots can improve topsoil exploration and nutrient uptake, shoot biomass and resulting overall yield. It is essential to understand the genetic basis of root structure development and how lateral and adventitious roots are produced. Existing mutant lines with specific root phenotypes are an excellent resource to analyse and comprehend the molecular basis of root developmental traits. The tomato aerial roots (aer) mutant exhibits an extreme adventitious rooting phenotype on the primary stem. It is known that this phenotype is associated with restricted polar auxin transport from the juvenile to the more mature stem, but prior to this study, the genetic loci responsible for the aer phenotype were unknown. We used genomic approaches to define the polygenic nature of the aer phenotype and provide evidence that increased expression of specific auxin biosynthesis, transport and signalling genes in different loci causes the initiation of adventitious root primordia in tomato stems. Our results allow the selection of different levels of adventitious rooting using molecular markers, potentially contributing to rootstock breeding strategies in grafted vegetable crops, especially in tomato. In crops vegetatively propagated as cuttings, such as fruit trees and cane fruits, orthologous genes may be useful for the selection of cultivars more amenable to propagation.

Ethylene Action Inhibition Improves Adventitious Root Induction in Adult Chestnut Tissues

Phase change refers to the process of maturation and transition from the juvenile to the adult stage. In response to this shift, certain species like chestnut lose the ability to form adventitious roots, thereby hindering the successful micropropagation of adult plants. While auxin is the main hormone involved in adventitious root formation, other hormones, such as ethylene, are also thought to play a role in its induction and development. In this study, experiments were carried out to determine the effects of ethylene on the induction and growth of adventitious roots. The analysis was performed in two types of chestnut microshoots derived from the same tree, a juvenile-like line with a high rooting ability derived from basal shoots (P2BS) and a line derived from crown branches (P2CR) with low rooting responses. By means of the application of compounds to modify ethylene content or inhibit its signalling, the potential involvement of this hormone in the induction of adventitious roots was analysed. Our results show that ethylene can modify the rooting competence of mature shoots, while the response in juvenile material was barely affected. To further characterise the molecular reasons underlying this maturation-derived shift in behaviour, specific gene expression analyses were developed. The findings suggest that several mechanisms, including ethylene signalling, auxin transport and epigenetic modifications, relate to the modulation of the rooting ability of mature chestnut microshoots and their recalcitrant behaviour.

Advancing Antibiotic Residue Analysis: LC-MS/MS Methodology for Ticarcillin Degradation Products in Tomato Leaves

The indiscriminate use of antibiotics in agriculture has raised concerns about antibiotic residues in food products, necessitating robust analytical methods for detection and quantification. In this study, our primary aim was to develop a robust and advanced liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology specifically designed for the accurate quantification of ticarcillin degradation products in tomato leaves. The choice of ticarcillin as the target analyte stems from its frequent use in agriculture and the potential formation of degradation products, which can pose a threat to food safety. The use of tomatoes as the target sample matrix in this study is justified by their significance in human diets, their widespread cultivation, and their suitability as a model for assessing antibiotic residue dynamics in diverse agricultural environments. By optimizing the MS/MS parameters, the study successfully demonstrates the practicality and reliability of the employed LC-MS/MS method in accurately assessing ticarcillin degradation product (Thiophene-2-Acetic acid and Thiophene-3-Acetic acid) levels. The chromatographic separation was achieved using a specialized column, ensuring high resolution and sensitivity in detecting analytes. Multiple reaction monitoring (MRM) data acquisition was employed to enhance the selectivity and accuracy of the analysis. The developed method exhibited excellent linearity and precision, meeting the stringent requirements for antibiotic residue analysis in complex matrices. Key outcomes of this study include the successful identification and quantification of ticarcillin and its degradation products in tomato leaves, providing crucial insights into the fate of this antibiotic in agricultural settings. The methodology's applicability was further demonstrated by analyzing real-world samples, highlighting its potential for routine monitoring and ensuring food safety compliance. In summary, our study constitutes a noteworthy advancement in the domain of antibiotic residue analysis, offering a reliable method for quantifying ticarcillin degradation products in tomato leaves. The optimized parameters and MRM-based LC-MS/MS approach enhance the precision and sensitivity of the analysis, opening up opportunities for further studies in the assessment of antibiotic residues in agricultural ecosystems.

Cultivating potential: Harnessing plant stem cells for agricultural crop improvement

Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.

New Insights into the Enhancement of Adventitious Root Formation Using N,N'-Bis(2,3-methylenedioxyphenyl)urea

Adventitious rooting is a process of postembryonic organogenesis strongly affected by endogenous and exogenous factors. Although adventitious rooting has been exploited in vegetative propagation programs for many plant species, it is a bottleneck for vegetative multiplication of difficult-to-root species, such as many woody species. The purpose of this research was to understand how N,N'-bis-(2,3-methylenedioxyphenyl)urea could exert its already reported adventitious rooting adjuvant activity, starting from the widely accepted knowledge that adventitious rooting is a hormonally tuned progressive process. Here, by using specific in vitro bioassays, histological analyses, molecular docking simulations and in vitro enzymatic bioassays, we have demonstrated that this urea derivative does not interfere with polar auxin transport; it inhibits cytokinin oxidase/dehydrogenase (CKX); and, possibly, it interacts with the apoplastic portion of the auxin receptor ABP1. As a consequence of this dual binding capacity, the lifespan of endogenous cytokinins could be locally increased and, at the same time, auxin signaling could be favored. This combination of effects could lead to a cell fate transition, which, in turn, could result in increased adventitious rooting.

Expression of CsSCL1 and Rooting Response in Chestnut Leaves Are Dependent on the Auxin Polar Transport and the Ontogenetic Origin of the Tissues

The mechanisms underlying the de novo regeneration of adventitious roots are still poorly understood, particularly in trees. We developed a system for studying adventitious rooting (AR) at physiological and molecular levels using leaves excised from chestnut microshoots of the same genotype but with two distinct ontogenetic origins that differ in rooting competence. Leaves were treated with auxin and N-1-naphthyl-phthalamic acid (NPA), an inhibitor of auxin polar transport (PAT). The physiological effects were investigated by recording rooting rates and the number and quality of the roots. Molecular responses were examined by localizing and monitoring the changes in the expression of CsSCL1, an auxin-inducible gene in juvenile and mature shoots during AR. The rooting response of leaves was ontogenetic-stage dependent and similar to that of the donor microshoots. Initiation of root primordia and root development were inhibited by application of NPA, although its effect depended on the timing of application. CsSCL1 was upregulated by auxin only in rooting-competent leaves during the novo root organogenesis, and the expression was reduced by NPA. The inhibitory effect on gene expression was detected during the reprograming of rooting competent cells towards root initials in response to auxin, indicating that PAT-mediated upregulation of CsSCL1 is required in the initial steps of AR in chestnut leaves. The localized expression of CsSCL1 in the quiescent center (QC) also suggests a role for this gene in the maintenance of meristematic competence and root radial patterning.

Transcriptome analysis reveals that auxin promotes strigolactone-induced adventitious root growth in the hypocotyl of melon seedlings

Introduction

Strigolactone (SL) and auxin are two important phytohormones involved in plant root development, but whether they show synergistic or mutual promotion effects during adventitious root (AR) formation has not been adequately explored.

Methods

In this study, we investigated the mechanisms of GR24 (synthetic SL) and indole-3-acetic acid (IAA; a type of auxin) in the formation of ARs using melon as the study material.

Results

Morphological measurements showed that the AR number, length, superficial area, and volume under the GR24 treatment were 1.60-3.27, 1.58-3.99, 2.06-3.42, and 3.00-6.11 times greater than those of the control group, respectively, at 6-10 days; the GR24+IAA treatment further promoted AR formation in melon seedlings, and the AR number, length, superficial area, and volume under the GR24+IAA treatment were 1.44-1.51, 1.28-1.73, 1.19-1.83, and 1.31-1.87 times greater than those obtained with the GR24 treatment, respectively. Transcriptome analysis revealed 2,742, 3,352, and 2,321 differentially expressed genes (DEGs) identified from the GR24 vs. control, GR24+IAA vs. control, and GR24+IAA vs. GR24 comparisons, respectively. The GR24 treatment and GR24+IAA treatment affected auxin and SL synthesis as well as components of the phytohormone signal transduction pathway, such as auxin, brassinosteroid (BR), ethylene (ETH), cytokinin (CK), gibberellin (GA), and abscisic acid (ABA). The concentrations of auxin, GA, zeatin (ZT), and ABA were evaluated using high-performance liquid chromatography (HPLC). From 6 to 10 days, the auxin, GA, and ZT contents in the GR24 treatment group were increased by 11.48%-15.34%, 11.83%-19.50%, and 22.52%-66.17%, respectively, compared to the control group, and these features were increased by 22.00%-31.20%, 21.29%-25.75%, 51.76%-98.96%, respectively, in the GR24+IAA treatment group compared with the control group. Compared to that in the control, the ABA content decreased by 10.30%-11.83% in the GR24 treatment group and decreased by 18.78%-24.00% in the GR24+IAA treatment group at 6-10 days.

Discussion

Our study revealed an interaction between strigolactone and auxin in the induction of AR formation in melon seedlings by affecting the expression of genes related to plant hormone pathways and contents.

A methane-cGMP module positively influences adventitious rooting

KEY MESSAGE

Endogenous cGMP operates downstream of CH₄ control of adventitious rooting, following by the regulation in the expression of cell cycle regulatory and auxin signaling-related genes. Methane (CH₄) is a natural product from plants and microorganisms. Although exogenously applied CH₄ and cyclic guanosine monophosphate (cGMP) are separately confirmed to be involved in the control of adventitious root (AR) formation, the possible interaction still remains elusive. Here, we observed that exogenous CH₄ not only rapidly promoted cGMP synthesis through increasing the activity of guanosine cyclase (GC), but also induced cucumber AR development. These responses were obviously impaired by the removal of endogenous cGMP with two GC inhibitors. Anatomical evidence showed that the emerged stage (V) among AR primordia development might be the main target of CH₄-cGMP module. Genetic evidence revealed that the transgenic Arabidopsis that overexpressed the methyl-coenzyme M reductase gene (MtMCR) from Methanobacterium thermoautotrophicum not only increased-cGMP production, but also resulted in a pronounced AR development compared to wild-type (WT), especially with the addition of CH₄ or the cell-permeable cGMP derivative 8-Br-cGMP. qPCR analysis confirmed that some marker genes associated with cell cycle regulatory and auxin signaling were closely related to the brand-new CH₄-cGMP module in AR development. Overall, our results clearly revealed an important function of cGMP in CH₄ governing AR formation by modulating auxin-dependent pathway and cell cycle regulation.

Adventitious Root Formation in Plants: The Implication of Hydrogen Peroxide and Nitric Oxide

Adventitious root formation is defined as the formation of new roots on above-ground plant parts and is considered crucial for the survival of a plant under harsh environmental conditions (i.e., flooding, salt stress, and other abiotic stresses) as well as in the nursery industry. Clonal propagation is based on the ability of a plant part to grow and generate a completely new plant, genetically identical to the mother plant, where the plant part came from. Nurseries exploit this potential by multiplying millions of new plants. Most nurseries use cuttings to achieve that, through the induction of adventitious root formation. Many factors have been implicated in the capacity of a cutting to root, with the major role being played by auxins. During the last few decades, intense interest has emerged in the role of other potential rooting co-factors, such as carbohydrates, phenolics, polyamines, and other plant growth regulators, as well as signal molecules, such as reactive oxygen and nitrogen species. Among the latter, hydrogen peroxide and nitric oxide have been found to play significant roles in adventitious root formation. Their production, action, and general implication in rhizogenesis are discussed in this review, in terms of interaction with other molecules and signaling.

Application of Data Modeling, Instrument Engineering and Nanomaterials in Selected Medid the Scientific Recinal Plant Tissue Culture

At present, most precious compounds are still obtained by plant cultivation such as ginsenosides, glycyrrhizic acid, and paclitaxel, which cannot be easily obtained by artificial synthesis. Plant tissue culture technology is the most commonly used biotechnology tool, which can be used for a variety of studies such as the production of natural compounds, functional gene research, plant micropropagation, plant breeding, and crop improvement. Tissue culture material is a basic and important part of this issue. The formation of different plant tissues and natural products is affected by growth conditions and endogenous substances. The accumulation of secondary metabolites are affected by plant tissue type, culture method, and environmental stress. Multi-domain technologies are developing rapidly, and they have made outstanding contributions to the application of plant tissue culture. The modes of action have their own characteristics, covering the whole process of plant tissue from the induction, culture, and production of natural secondary metabolites. This paper reviews the induction mechanism of different plant tissues and the application of multi-domain technologies such as artificial intelligence, biosensors, bioreactors, multi-omics monitoring, and nanomaterials in plant tissue culture and the production of secondary metabolites. This will help to improve the tissue culture technology of medicinal plants and increase the availability and the yield of natural metabolites.

Species-specific transcriptional reprogramming during adventitious root initiation

Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.

Steroidal glycoside profile differences among primary roots system and adventitious roots in Solanum dulcamara

Solanum dulcamara primary and adventitious roots showed qualitative and quantitative differences in their steroidal glycosides profile. This opened new venues to evaluate the bioactivity of these molecules in belowground ecosystems. The Solanum genus is characterized by the presence of steroidal glycosides (SGs) that confer herbivore resistance and serve as drug precursors in the pharmaceutical industry. Solanum dulcamara is a self-compatible, sexually reproducing species that produces seeds after buzz-pollination. In addition, primordia on the stem facilitate clonal propagation via adventitious root (AR) formation. ARs contain aerenchyma being developmentally and morphologically different from primary roots (PRs). Therefore, we hypothesized that ARs and PRs have different SG profiles. Aiming to assess differences in SGs profiles in S. dulcamara roots in relation to their origins and morphologies, we used liquid chromatography coupled to electron spray ionization quadruple time of flight mass spectrometry (LC-ESI-qToF-MS) to profile SGs from PRs and ARs of seven S. dulcamara individuals. Mass fragmentation pattern analysis indicated the presence of 31 SG-type structures, including those with spirostans and furostans moieties. We assigned the 31 structures to 9 classes of steroidal aglycons (SAgls) that differ in hydroxylation and degree of unsaturation. We found that SAgls were conjugated with di-, tri- and tetra saccharides whereby one compound contained a malonylated sugar. Principle component analysis showed that SG profiles of PRs and ARs separated on the first principal component, supporting our hypothesis. Specifically, PRs contain higher number of SGs than ARs with some compounds exclusively present in PRs. Our results reveal a high level of novel chemodiversity in PRs and ARs of Solanum dulcamara. The knowledge gained will deepen our understanding of SGs biosynthesis and their functional role in plant-environment interactions.

Histone Acetyltransferase GCN5 Affects Auxin Transport during Root Growth by Modulating Histone Acetylation and Gene Expression of PINs

General Control Non-Derepressible 5 (GCN5) is a histone acetyltransferase that targets multiple genes and is essential for the acetylation of Lysine residues in the N-terminal tail of histone H3 in Arabidopsis. GCN5 interacts with the transcriptional coactivator Alteration/Deficiency in Activation 2b (ADA2b), which enhances its activity functioning in multiprotein complexes, such as the Spt-Ada-Gcn5-Acetyltransferase complex (SAGA). Mutations in GCN5 and ADA2b result in pleiotropic phenotypes, including alterations in the growth of roots. Auxin is known to regulate root development by modulating gene expression patterns. Auxin moves polarly during plant growth via the Pin-formed (PIN) auxin efflux transport proteins. The effect of GCN5 and ADA2b on auxin distribution at different stages of early root growth (4 to 7 days post-germination) was studied using the reporter lines DR5rev::GFP and PIN1::PIN1-GFP. In wild-type plants, auxin efflux transporter PIN1 expression increases from the fourth to the seventh day of root growth. The PIN1 expression was reduced in the roots of gcn5-1 and ada2b-1 compared to the wild type. The expression of PIN1 in ada2b-1 mutants is confined only to the meristematic zone, specifically in the stele cells, whereas it is almost abolished in the elongation zone. Gene expression analysis showed that genes associated with auxin transport, PIN1, PIN3 and PIN4, are downregulated in gcn5-1 and ada2b-1 mutants relative to the wild type. As a result, auxin accumulation was also reduced in gcn5-1 and ada2b-1 compared to wild-type roots. Furthermore, acetylation of Lysine 14 of histone H3 (H3K14) was also affected in the promoter and coding region of PIN1, PIN3 and PIN4 genes during root growth of Arabidopsis in gcn5 mutants. In conclusion, GCN5 acts as a positive regulator of auxin distribution in early root growth by modulating histone H3 acetylation and the expression of auxin efflux transport genes.

Transcriptomics Analysis Reveals a Putative Role for Hormone Signaling and MADS-Box Genes in Mature Chestnut Shoots Rooting Recalcitrance

Maturation imposes several changes in plants, which are particularly drastic in the case of trees. In recalcitrant woody species, such as chestnut (Castanea sativa Mill.), one of the major maturation-related shifts is the loss of the ability to form adventitious roots in response to auxin treatment as the plant ages. To analyze the molecular mechanisms underlying this phenomenon, an in vitro model system of two different lines of microshoots derived from the same field-grown tree was established. While juvenile-like shoots root readily when treated with exogenous auxin, microshoots established from the crown of the tree rarely form roots. In the present study, a transcriptomic analysis was developed to compare the gene expression patterns in both types of shoots 24 h after hormone and wounding treatment, matching the induction phase of the process. Our results support the hypothesis that the inability of adult chestnut tissues to respond to the inductive treatment relies in a deep change of gene expression imposed by maturation that results in a significant transcriptome modification. Differences in phytohormone signaling seem to be the main cause for the recalcitrant behavior of mature shoots, with abscisic acid and ethylene negatively influencing the rooting ability of the chestnut plants. We have identified a set of related MADS-box genes whose expression is modified but not suppressed by the inductive treatment in mature shoots, suggesting a putative link of their activity with the rooting-recalcitrant behavior of this material. Overall, distinct maturation-derived auxin sensibility and homeostasis, and the related modifications in the balance with other phytohormones, seem to govern the outcome of the process in each type of shoots.

Transcriptome Dynamics of Rooting Zone and Leaves during In Vitro Adventitious Root Formation in Eucalyptus nitens

Wood properties and agronomic traits associated with fast growth and frost tolerance make Eucalyptus nitens a valuable forest alternative. However, the rapid age-related decline in the adventitious root (AR) formation (herein, meaning induction, initiation, and expression stages) limits its propagation. We analyzed transcriptomic profile variation in leaves and stem bases during AR induction of microcuttings to elucidate the molecular mechanisms involved in AR formation. In addition, we quantified expressions of candidate genes associated with recalcitrance. We delimited the ontogenic phases of root formation using histological techniques and Scarecrow and Short-Root expression quantification for RNA sequencing sample collection. We quantified the gene expressions associated with root meristem formation, auxin biosynthesis, perception, signaling, conjugation, and cytokinin signaling in shoots harvested from 2- to 36-month-old plants. After IBA treatment, 702 transcripts changed their expressions. Several were involved in hormone homeostasis and the signaling pathways that determine cell dedifferentiation, leading to root meristem formation. In part, the age-related decline in the rooting capacity is attributable to the increase in the ARR1 gene expression, which negatively affects auxin homeostasis. The analysis of the transcriptomic variation in the leaves and rooting zones provided profuse information: (1) To elucidate the auxin metabolism; (2) to understand the hormonal and signaling processes involved; (3) to collect data associated with their recalcitrance.

Characterization of walnut JrWOX11 and its overexpression provide insights into adventitious root formation and development and abiotic stress tolerance

The well-developed root system enables plant survival under various environmental stresses. WUSCHEL-RELATED HOMEOBOX GENE 11 (WOX11) plays a critical role in adventitious root formation and development in rice, Arabidopsis, and easy-to-root tree poplar. However, in difficult-to-root trees, the knowledge of WOX11 during adventitious root formation and development remains scarce. In this study, the JrWOX11 gene was isolated from a difficult-to-root tree walnut and heterologously expressed in the "84K" poplar. The results showed that JrWOX11 contained a similar structure and sequence to the homologous genes in rice, Arabidopsis, and poplar, but had different numbers and types of motifs and cis-elements. JrWOX11 lacked the motif GGAIQY compared to that in easy-to-root trees. In addition, JrWOX11 expression was induced by ABA, PEG, and NaCl treatments. Overexpression of JrWOX11 in poplar promoted root initiation and significantly increased adventitious root (ARs) number, lateral roots (LRs) number, and root hair (RH) length. Furthermore, the aboveground biomass was notably increased under NaCl and PEG treatments in transgenic plants. When NaCl and PEG were removed, the survival rate, aerial shoot development, and de novo root organogenesis were also markedly enhanced in transgenic shoot cuttings. The study provides valuable information on the differences between JrWOX11 and the homologous genes in rice, Arabidopsis, and poplar, and supports the critical role of JrWOX11 in the formation of AR and tolerance to salt and osmotic stresses.

Comprehensive transcriptome analysis unravels the crucial genes during adventitious root development induced by carbon monoxide in Cucumis sativus L

BACKGROUND

Carbon monoxide (CO) has been reported to be participated in adventitious rooting. However, knowledge about the interrelationship between CO and phytohormones during rooting is obscure. The molecular mechanism of CO-induced rooting is currently unclear.

METHODS AND RESULTS

The roles of CO in adventitious rooting in Cucumis sativus L. at the transcriptional level were investigated. The results show that 10 μM hematin (a CO donor) has a significant positive effect on adventitious rooting in cucumber. A total of 1792 differentially expressed genes (DEGs; 1103 up-regulated and 689 down-regulated) were identified in hematin treatment by RNA sequencing analysis. There were 37, 18 and 19 DEGs significantly enriched in plant hormone signal transduction, sucrose and starch metabolism, and phenylalanine metabolism, respectively. Both transcriptome and real-time quantitative PCR results showed that the expressions of AUX22D, IAA6, SAUR21, SAUR24, GH3.5, CYCD3-3, TIFY10a, TIFY10A and TIF9 promoted the accumulation of IAA, BR, JA and SA in plant hormone signal transduction. The up-regulation of HK3, TPPF, otsB, TPS7, TPS9 and the down-regulation of AGPS1, AGPS3 increased the content of starch and total sugar by mediating the activity of some critical enzymes, including HK, TPS, TPP and AGP. PER47, PER61, PER24, PER66, PER4 and CCR2 increased the lignin content.

CONCLUSION

Our results suggest that CO could promote the accumulation of plant hormones, starch, sugar and lignin during adventitious rooting by regulating the expression of some related genes, including AUX22D, IAA6, SAUR21, SAUR24, GH3.5, CYCD3-3, TIFY10a, TIFY10A, TIF9 HK3, otsB, TPS7, TPS9, AGPS1, AGPS3, PER47, PER61, PER24, PER66, PER4, and CCR2. Thus, we provides an interesting candidate gene list for further studies on the molecular mechanisms of adventitious rooting.

Effective Methods for Adventitious Root Regeneration on Weeping Fig Stems

When transplanting mature Ficus trees, the large root balls are expensive to treat, handle, and move. This study aimed to identify the optimal wounding method and auxin treatment for regenerating adventitious roots (ARs) from weeping fig (Ficus benjamina L.) stems to uptake additional water and to compensate for fewer absorption roots in the smaller root balls at transplantation. We adopted a two-factorial experiment involving the wounding methods (three-line cut (3LC) and rectangular peel (RP)) and auxin treatments (2000 mg·L−1 Indole-3-butyric acid (IBA), 2000 mg·L−1 IBA + 2000 mg·L−1 1-naphthaleneacetic acid (NAA), and 4000 mg·L−1 IBA). The rooting rate of each treatment, the mean root number, the length of the three longest ARs, and the dry weight of ARs in each wound were evaluated. The treatment combination using 4000 mg·L−1 IBA with RP13 (rectangular peel 1/3 the perimeter of the stem) consistently exhibited the best rooting results in 2019 and 2020. It had a 100% rooting rate, a mean of 18.5 roots, a 16.8 cm root length, and a 1640 mg dry weight in the wounds. All auxin treatments demonstrated a superior rooting ability as compared to water treatments. The RP method regenerated more roots than the 3LC method. Doubling the RP length to be 2/3 of the perimeter improved the rooting ability. The locations of ARs varied under different treatment combinations, with 4000 mg·L−1 IBA on RP13 demonstrating the most diversified distribution on four edges of the wounds. Thus, it is recommended to regenerate ARs from stems of F. benjamina trees.

CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice

In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

Ultrastructural and hormonal changes related to harmaline-induced treatment in Arabidopsis thaliana (L.) Heynh. root meristem

Harmaline is an indole alkaloid with demonstrated phytotoxicity and recognized pharmacological applications. However, no information is available concerning its mode of action on plant metabolism. Therefore, the present work evaluated bioherbicide mode of action of harmaline on plant metabolism of Arabidopsis thaliana (L.) Heynh. Harmaline induced a strong inhibitory activity on root growth of treated seedlings, reaching IC₅₀ and IC₈₀ values of 14 and 29 μM, respectively. Treated roots were shorter and thicker than control and were characterized by a shorter root meristem size and an increase of root hairs production. Harmaline induced ultrastructural changes such as increment of cell wall thickness, higher density and condensation of mitochondria and vacuolization, appearance of cell wall deposits, increment of Golgi secretory activity and higher percentage of aberrant nuclei. The ethylene inhibitor AgNO₃ reversed high root hair appearance and increment of root thickness, and pTCSn::GFP transgenic line showed fluorescence cytokinin signal in stele zone after harmaline treatment that was absent in control, whereas the auxin signal in the transgenic line DR5 was significantly reduced by the treatment. All these results suggest that the mode of action of harmaline could be involving auxin, ethylene and cytokinin synergic/antagonistic action.

Enhancing cereal productivity by genetic modification of root architecture

Food security is one of the main topics of today's agriculture, primarily due to increasingly challenging environmental conditions. As most of humankind has a daily intake of cereal grains, current breeding programs focus on these crop plants. Customised endonucleases have been included in the breeders' toolbox after successfully demonstrating their use. Due to technological restrictions, the main focus of the new technology was on above-ground plant organs. In contrast, the essential below ground components were given only limited attention. In the present review, the knowledge of the root system architecture in cereals and the role of phytohormones during their establishment is summarized, and the underlying molecular mechanisms are outlined. The review summarizes how the use of CRISPR-based genome editing methodology can improve the root system architecture to enhance crop production genetically. Finally, future research directions involving this knowledge and technical advances are suggested. This article is protected by copyright. All rights reserved.

Effects of Auxin (Indole-3-butyric Acid) on Adventitious Root Formation in Peach-Based Prunus Rootstocks

Several Prunus species are among the most important cultivated stone fruits in the Mediterranean region, and there is an urgent need to obtain rootstocks with specific adaptations to challenging environmental conditions. The development of adventitious roots (ARs) is an evolutionary mechanism of high relevance for stress tolerance, which has led to the development of environmentally resilient plants. As a first step towards understanding the genetic determinants involved in AR formation in Prunus sp., we evaluated the rooting of hardwood cuttings from five Prunus rootstocks (Adafuel, Adarcias, Cadaman, Garnem, and GF 677) grown in hydroponics. We found that auxin-induced callus and rooting responses were strongly genotype-dependent. To investigate the molecular mechanisms involved in these differential responses, we performed a time-series study of AR formation in two rootstocks with contrasting rooting performance, Garnem and GF 677, by culturing in vitro microcuttings with and without auxin treatment (0.9 mg/L of indole-3-butyric acid [IBA]). Despite showing a similar histological structure, Garnem and GF677 rootstocks displayed dynamic changes in endogenous hormone homeostasis involving metabolites such as indole-3-acetic acid (IAA) conjugated to aspartic acid (IAA-Asp), and these changes could explain the differences observed during rooting.

A conserved superlocus regulates above- and belowground root initiation

Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.

Expression Analysis of Phenylpropanoid Pathway Genes and Metabolomic Analysis of Phenylpropanoid Compounds in Adventitious, Hairy, and Seedling Roots of Tartary Buckwheat

Tartary buckwheat (Fagopyrum tataricum) is an important crop that belongs to the Polygonaceae family, whose roots have received considerable attention due to the presence of compounds with high nutritional and medicinal value. In this study, we aimed to develop an efficient protocol for the culture of adventitious (ARs) and hairy (HRs) roots on a half-strength Schenk and Hildebrandt (SH) medium containing different concentrations of the auxins, α-naphthaleneacetic acid (NAA), indole-3-butyric acid (IBA), and indole-3-acetic acid (IAA). The highest percentage of root induction (91.67%) was achieved with 0.5 mg/L IAA, whereas the greatest number of roots was found in 1 mg/L IAA. In contrast, 0.1 mg/L IBA returned the longest roots. As expected, HRs were obtained from in vitro leaf explants infected with Agrobacterium rhizogenes R1000. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of 11 phenolic pathway genes revealed that five genes (FtPAL, FtC3H, FtHQT, FtCHS, and FtANS) were highly expressed in HRs, whereas only four (FtC4H, FtFLS2, FtDFR, and FtANR), and three (Ft4CL, FtCHI, and FtF3H) were recognized in the ARs and seedling roots (SRs), respectively. HPLC analysis of phenolic compounds in different root cultures showed that the majority of the phenolic compounds (both individual and total) were significantly accumulated in the HRs. Principal component analysis (PCA) identified differences among the three root types, whereby HRs were separated from ARs and SRs based on the amount of phenolic compounds present. Analysis of the metabolic pathway revealed that among the identified metabolites, the 3, 2, and 1 pathways were associated with flavonoid, flavone and flavonol, and phenylpropanoid biosynthesis, respectively. Hierarchical clustering analysis and the heat map showed that the different root cultures presented unique metabolites.

Adventitious roots support population expansion of the invasive plant Mikania micrantha Kunth

Mikania micrantha Kunth is a serious invasive alien plant characterized by the formation of an adventitious root system in its prostrate growth form. Unlike the initial roots from seed germination, adventitious roots gradually appear above the stem and branch nodes. Little is known about adventitious roots play on plant growth and population expansion of M. micrantha. We hypothesized that adventitious roots provide an advantage for plant growth and nutrient availability. To test this hypothesis, plant growth, physiology, and nutrition characteristics of M. micrantha were measured under four soil surface conditions allowing various plant parts to touch the soil to stimulate variable adventitious root formation. The results showed that the biomass, stem length, branch number, and adventitious root biomass of M. micrantha were significantly increased (P < 0.05) with increasing nodes bearing adventitious roots. As the number of nodes with adventitious roots increased, the net photosynthetic rate, antioxidant enzyme activities like superoxide dismutase, catalase, peroxidase, and malondialdehyde, chlorophyll content, and plant nutrient contents (N, P, and K) of M. micrantha were increased (P < 0.05), with higher values in main stem leaves than in those of branch leaves. The concentrations of soil organic matter, total N, total P, total K, available N, available P, and available K were greater (P < 0.05) in initial soil (CK) than in treatment soil (with M. micrantha) and were significantly reduced by adventitious roots. Our study was the first to show that plant growth, physiology and nutrition status of M. micrantha were strongly promoted by adventitious roots in the prostrate growth form.

Genome-wide transcriptome signatures of ant-farmed Squamellaria epiphytes reveal key functions in a unique symbiosis

Farming of fungi by ants, termites, or beetles has led to ecologically successful societies fueled by industrial-scale food production. Another type of obligate insect agriculture in Fiji involves the symbiosis between the ant Philidris nagasau and epiphytes in the genus Squamellaria (Rubiaceae) that the ants fertilize, defend, harvest, and depend on for nesting. All farmed Squamellaria form tubers (domatia) with preformed entrance holes and complex cavity networks occupied by P. nagasau. The inner surface of the domatia consists of smooth-surfaced walls where the ants nest and rear their brood, and warty-surfaced walls where they fertilize their crop by defecation. Here, we use RNA sequencing to identify gene expression patterns associated with the smooth versus warty wall types. Since wall differentiation occurred in the most recent common ancestor of all farmed species of Squamellaria, our study also identifies genetic pathways co-opted following the emergence of agriculture. Warty-surfaced walls show many upregulated genes linked to auxin transport, root development, and nitrogen transport consistent with their root-like function; their defense-related genes are also upregulated, probably to protect these permeable areas from pathogen entry. In smooth-surfaced walls, genes functioning in suberin and wax biosynthesis are upregulated, contributing to the formation of an impermeable ant-nesting area in the domatium. This study throws light on a number of functional characteristics of plant farming by ants and illustrates the power of genomic studies of symbiosis.

Shaping the root system: the interplay between miRNA regulatory hubs and phytohormones

The root system commonly lies underground, where it provides anchorage for the aerial organs, as well as nutrients and water. Both endogenous and environmental cues contribute to the establishment of the root system. Among the endogenous cues, microRNAs (miRNAs), transcription factors, and phytohormones modulate root architecture. miRNAs belong to a subset of endogenous hairpin-derived small RNAs that post-transcriptionally control target gene expression, mostly transcription factors, comprising the miRNA regulatory hubs. Phytohormones are signaling molecules involved in most developmental processes. Some miRNAs and targets participate in more than one hormonal pathway, thereby providing new bridges in plant hormonal crosstalk. Unraveling the intricate network of molecular mechanisms underlying the establishment of root systems is a central aspect in the development of novel strategies for plant breeding to increase yield and optimize agricultural land use. In this review, we summarize recent findings describing the molecular mechanisms associated with the interplay between miRNA regulatory hubs and phytohormones to ensure the establishment of a proper root system. We focus on post-embryonic growth and development of primary, lateral, and adventitious roots. In addition, we discuss novel insights for future research on the interaction between miRNAs and phytohormones in root architecture.

Environmental and Cultivation Factors Affect the Morphology, Architecture and Performance of Root Systems in Soilless Grown Plants

Soilless culture systems are currently one of the fastest-growing sectors in horticulture. The plant roots are confined into a specific rootzone and are exposed to environmental changes and cultivation factors. The recent scientific evidence regarding the effects of several environmental and cultivation factors on the morphology, architecture, and performance of the root system of plants grown in SCS are the objectives of this study. The effect of root restriction, nutrient solution, irrigation frequency, rootzone temperature, oxygenation, vapour pressure deficit, lighting, rootzone pH, root exudates, CO2, and beneficiary microorganisms on the functionality and performance of the root system are discussed. Overall, the main results of this review demonstrate that researchers have carried out great efforts in innovation to optimize SCS water and nutrients supply, proper temperature, and oxygen levels at the rootzone and effective plant–beneficiary microorganisms, while contributing to plant yields. Finally, this review analyses the new trends based on emerging technologies and various tools that might be exploited in a smart agriculture approach to improve root management in soilless cropping while procuring a deeper understanding of plant root–shoot communication.

An auxin-mediated regulatory framework for wound-induced adventitious root formation in tomato shoot explants

Adventitious roots (ARs) are produced from non-root tissues in response to different environmental signals, such as abiotic stresses, or after wounding, in a complex developmental process that requires hormonal crosstalk. Here, we characterized AR formation in young seedlings of Solanum lycopersicum cv. 'Micro-Tom' after whole root excision by means of physiological, genetic and molecular approaches. We found that a regulated basipetal auxin transport from the shoot and local auxin biosynthesis triggered by wounding are both required for the re-establishment of internal auxin gradients within the vasculature. This promotes cell proliferation at the distal cambium near the wound in well-defined positions of the basal hypocotyl and during a narrow developmental window. In addition, a pre-established pattern of differential auxin responses along the apical-basal axis of the hypocotyl and an as of yet unknown cell-autonomous inhibitory pathway contribute to the temporal and spatial patterning of the newly formed ARs on isolated hypocotyl explants. Our work provides an experimental outline for the dissection of wound-induced AR formation in tomato, a species that is suitable for molecular identification of gene regulatory networks via forward and reverse genetics approaches.

Phytochrome B inhibits darkness-induced hypocotyl adventitious root formation by stabilizing IAA14 and suppressing ARF7 and ARF19

Adventitious roots (ARs) are an important root type for plants and display a high phenotypic plasticity in response to different environmental stimuli. Previous studies found that dark-light transition can trigger AR formation from the hypocotyl of etiolated Arabidopsis thaliana, which was used as a model for the identification of regulators of AR biogenesis. However, the central regulatory machinery for darkness-induced hypocotyl AR (HAR) remains elusive. Here, we report that photoreceptors suppress HAR biogenesis through regulating the molecular module essential for lateral roots. We found that hypocotyls embedded in soil or in continuous darkness are able to develop HARs, wherein photoreceptors act as negative regulators. Distinct from wound-induced ARs that require WOX11 and WOX12, darkness-induced HARs are fully dependent on ARF7, ARF19, WOX5/7, and LBD16. Further studies established that PHYB interacts with IAA14, ARF7, and ARF9. The interactions stabilize IAA14 and inhibit the transcriptional activities of ARF7 and ARF19 and thus suppress biogenesis of darkness-induced HARs. This finding not only revealed the central machinery controlling HAR biogenesis but also illustrated that AR formation could be initiated by multiple pathways.

Foliar Application of Different Vegetal-Derived Protein Hydrolysates Distinctively Modulates Tomato Root Development and Metabolism

Despite the scientific evidence supporting their biostimulant activity, the molecular mechanism(s) underlying the activity of protein hydrolysates (PHs) and the specificity among different products are still poorly explored. This work tested five different protein hydrolysates, produced from different plant sources using the same enzymatic approach, for their ability to promote rooting in tomato cuttings following quick dipping. Provided that all the different PHs increased root length (45–93%) and some of them increased root number (37–56%), untargeted metabolomics followed by multivariate statistics and pathway analysis were used to unravel the molecular processes at the basis of the biostimulant activity. Distinct metabolomic signatures could be found in roots following the PHs treatments. In general, PHs shaped the phytohormone profile, modulating the complex interaction between cytokinins and auxins, an interplay playing a pivotal role in root development, and triggered a down accumulation of brassinosteroids. Concerning secondary metabolism, PHs induced the accumulation of aliphatic glucosinolates, alkaloids, and phenylpropanoids, potentially eliciting crop resilience to stress conditions. Here, we confirm that PHs may have a hormone-like activity, and that their application can modulate plant growth, likely interfering with signaling processes. Noteworthy, the heterogenicity of the botanical origin supported the distinctive and peculiar metabolomic responses we observed across the products tested. While supporting their biostimulant activity, these findings suggest that a generalized crop response to PHs cannot be defined and that specific effects are rather to be investigated.

Identifying Molecular Chechkpoints for Adventitious Root Induction: Are We Ready to Fill the Gaps?

The molecular mechanisms underlying de novo root organogenesis have been under intense study for the last decades. As new tools and resources became available, a comprehensive model connecting the processes and factors involved was developed. Separate phases that allow for specific analyses of individual checkpoints were well defined. Physiological approaches provided information on the importance of metabolic processes and long-distance signaling to balance leaf and stem status and activation of stem cell niches to form new root meristems. The study of plant hormones revealed a series of sequential roles for cytokinin and auxin, dynamically interconnected and modulated by jasmonic acid and ethylene. The identification of genes specifying cell identity uncovered a network of sequentially acting transcriptional regulators that link hormonal control to cell fate respecification. Combined results from herbaceous model plants and the study of recalcitrant woody species underscored the need to understand the limiting factors that determine adventitious rooting competence. The relevance of epigenetic control was emphasized by the identification of microRNAs and chromatin remodeling agents involved in the process. As the different players are set in place and missing pieces become apparent, findings in related processes can be used to identify new candidates to complete the picture. Molecular knobs connecting the balance cell proliferation/differentiation to hormone signaling pathways, transcriptional control of cell fate or metabolic modulation of developmental programs can offer clues to unveil new elements in the dynamics of adventitious rooting regulatory networks. Mechanisms for cell non-autonomous signaling that are well characterized in other developmental processes requiring establishment and maintenance of meristems, control of cell proliferation and cell fate specification can be further explored. Here, we discuss possible candidates and approaches to address or elude the limitations that hinder propagation programs requiring adventitious rooting.

Recent Advances in Adventitious Root Formation in Chestnut

The genus Castanea includes several tree species that are relevant because of their geographical extension and their multipurpose character, that includes nut and timber production. However, commercial exploitation of the trees is hindered by several factors, particularly by their limited regeneration ability. Regardless of recent advances, there exists a serious limitation for the propagation of elite genotypes of chestnut due to decline of rooting ability as the tree ages. In the present review, we summarize the research developed in this genus during the last three decades concerning the formation of adventitious roots (ARs). Focusing on cuttings and in vitro microshoots, we gather the information available on several species, particularly C. sativa, C. dentata and the hybrid C.sativa × C. crenata, and analyze the influence of several factors on the achievements of the applied protocols, including genotype, auxin treatment, light regime and rooting media. We also pay attention to the acclimation phase, as well as compile the information available about biochemical and molecular related aspects. Furthermore, we considerate promising biotechnological approaches that might enable the improvement of the current protocols.

Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics?

Adventitious root (AR) formation is a complex developmental process controlled by a plethora of endogenous and environmental factors. Based on fossil evidence and genomic phylogeny, AR formation might be considered the default state of plant roots, which likely evolved independently several times. The application of next-generation sequencing techniques and bioinformatics analyses to non-model plants provide novel approaches to identify genes putatively involved in AR formation in multiple species. Recent results uncovered that the regulation of shoot-borne AR formation in monocots is an adaptive response to nutrient and water deficiency that enhances topsoil foraging and improves plant performance. A hierarchy of transcription factors required for AR initiation has been identified from genetic studies, and recent results highlighted the key involvement of additional regulation through microRNAs. Here, we discuss our current understanding of AR formation in response to specific environmental stresses, such as nutrient deficiency, drought or waterlogging, aimed at providing evidence for the integration of the hormone crosstalk required for the activation of root competent cells within adult tissues from which the ARs develop.

Transcriptome Profiling Provides Molecular Insights into Auxin-Induced Adventitious Root Formation in Sugarcane (Saccharum spp. Interspecific Hybrids) Microshoots

Adventitious root (AR) formation was enhanced following the treatment of sugarcane microshoots with indole-3-butyric acid (IBA) and 1-naphthalene acetic acid (NAA) combined, suggesting that auxin is a positive regulator of sugarcane microshoot AR formation. The transcriptome profile identified 1737 and 1268 differentially expressed genes (DEGs) in the basal tissues (5 mm) of sugarcane microshoots treated with IBA+NAA compared to nontreated control on the 3rd and 7th days post-auxin or water treatment (days post-treatment—dpt), respectively. To understand the molecular changes, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. This analysis showed that DEGs associated with the pathways were associated with plant hormone signaling, flavonoid and phenylpropanoid biosyntheses, cell cycle, and cell wall modification, and transcription factors could be involved in sugarcane microshoot AR formation. Furthermore, qRT–PCR analysis was used to validate the expression patterns of nine genes associated with root formation and growth, and the results were consistent with the RNA-seq results. Finally, a hypothetical hormonal regulatory working model of sugarcane microshoot AR formation is proposed. Our results provide valuable insights into the molecular processes associated with auxin-induced AR formation in sugarcane.