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

Plant regeneration in the new era: from molecular mechanisms to biotechnology applications

Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.

Organelle Ca2+/CAM1-SELTP confers somatic cell embryogenic competence acquisition and transformation in plant regeneration

Somatic cell totipotency in plant regeneration represents the forefront of the compelling scientific puzzles and one of the most challenging problems in biology. How somatic embryogenic competence is achieved in regeneration remains elusive. Here, we discover uncharacterized organelle-based embryogenic differentiation processes of intracellular acquisition and intercellular transformation, and demonstrate the underlying regulatory system of somatic embryogenesis-associated lipid transfer protein (SELTP) and its interactor calmodulin1 (CAM1) in cotton as the pioneer crop for biotechnology application. The synergistic CAM1 and SELTP exhibit consistent dynamical amyloplast-plasmodesmata (PD) localization patterns but show opposite functional effects. CAM1 inhibits the effect of SELTP to regulate embryogenic differentiation for plant regeneration. It is noteworthy that callus grafting assay reflects intercellular trafficking of CAM1 through PD for embryogenic transformation. This work originally provides insight into the mechanisms responsible for embryogenic competence acquisition and transformation mediated by the Ca2+/CAM1-SELTP regulatory pathway, suggesting a principle for plant regeneration and cell/genetic engineering.

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.

Insights into the Hormone-Regulating Mechanism of Adventitious Root Formation in Softwood Cuttings of Cyclocarya paliurus and Optimization of the Hormone-Based Formula for Promoting Rooting

Adventitious root (AR) formation is vital for successful cutting propagation in plants, while the dynamic regulation of phytohormones is viewed as one of the most important factors affecting AR formation. Cyclocarya paliurus, a hard-to-root plant, is faced with the bottleneck of cloning its superior varieties in practice. In this study, ten treatments were designed to figure out the best hormone-based formula for promoting AR formation in softwood cuttings and explore their hormone-regulating mechanisms. Both the rooting process and the rooting parameters of the softwood cuttings were significantly affected by different hormone-based formulas (p < 0.05), while the greatest rooting rate (93%) and root quality index were achieved in the H3 formula (SR3:IR3 = 1:1). Significant differences in the measured phytohormone concentrations, as well as in their ratios, were detected among the cuttings sampled at various AR formation stages (p < 0.05), whereas the dynamics for each phytohormone varied greatly during AR formation. The transcriptome analysis showed 12,028 differentially expressed genes (DEGs) identified during the rooting process of C. paliurus cuttings, while the KEGG enrichment analysis indicated that a total of 20 KEGG terms were significantly enriched in all the comparison samples, with 253 DEGs detected in signal transduction. Furthermore, 19 genes with vital functions in regulating the hormone signaling pathway were identified by means of a WGCNA analysis. Our results not only optimize a hormone-based formula for improving the rooting of C. paliurus cuttings but also provide an insight into the hormonal regulatory network during AR formation in softwood C. paliurus cuttings.

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.

Uncovering transcriptional reprogramming during callus development in soybean: insights and implications

Callus, a valuable tool in plant genetic engineering, originates from dedifferentiated cells. While transcriptional reprogramming during callus formation has been extensively studied in Arabidopsis thaliana, our knowledge of this process in other species, such as Glycine max, remains limited. To bridge this gap, our study focused on conducting a time-series transcriptome analysis of soybean callus cultured for various durations (0, 1, 7, 14, 28, and 42 days) on a callus induction medium following wounding with the attempt of identifying genes that play key roles during callus formation. As the result, we detected a total of 27,639 alterations in gene expression during callus formation, which could be categorized into eight distinct clusters. Gene ontology analysis revealed that genes associated with hormones, cell wall modification, and cell cycle underwent transcriptional reprogramming throughout callus formation. Furthermore, by scrutinizing the expression patterns of genes related to hormones, cell cycle, cell wall, and transcription factors, we discovered that auxin, cytokinin, and brassinosteroid signaling pathways activate genes involved in both root and shoot meristem development during callus formation. In summary, our transcriptome analysis provides significant insights into the molecular mechanisms governing callus formation in soybean. The information obtained from this study contributes to a deeper understanding of this intricate process and paves the way for further investigation in the field.

An auxin-mediated ultradian rhythm positively influences root regeneration via EAR1/EUR1 in Arabidopsis

Ultradian rhythms have been proved to be critical for diverse biological processes. However, comprehensive understanding of the short-period rhythms remains limited. Here, we discover that leaf excision triggers a gene expression rhythm with ~3-h periodicity, named as the excision ultradian rhythm (UR), which is regulated by the plant hormone auxin. Promoter-luciferase analyses showed that the spatiotemporal patterns of the excision UR were positively associated with de novo root regeneration (DNRR), a post-embryonic developmental process. Transcriptomic analysis indicated more than 4,000 genes including DNRR-associated genes were reprogramed toward ultradian oscillation. Genetic studies showed that EXCISION ULTRADIAN RHYTHM 1 (EUR1) encoding ENHANCER OF ABSCISIC ACID CO-RECEPTOR1 (EAR1), an abscisic acid signaling regulator, was required to generate the excision ultradian rhythm and enhance root regeneration. The eur1 mutant exhibited the absence of auxin-induced excision UR generation and partial failure during rescuing root regeneration. Our results demonstrate a link between the excision UR and adventitious root formation via EAR1/EUR1, implying an additional regulatory layer in plant regeneration.

LkARF7 and LkARF19 overexpression promote adventitious root formation in a heterologous poplar model by positively regulating LkBBM1

Cuttage propagation involves adventitious root formation induced by auxin. In our previous study, Larix kaempferi BABY BOOM 1 (LkBBM1), which is known to regulate adventitious root formation, was affected by auxin. However, the relationship between LkBBM1 and auxin remains unclear. Auxin response factors (ARFs) are a class of important transcription factors in the auxin signaling pathway and modulate the expression of early auxin-responsive genes by binding to auxin response elements. In the present study, we identified 14 L. kaempferi ARFs (LkARFs), and found LkARF7 and LkARF19 bound to LkBBM1 promoter and enhanced its transcription using yeast one-hybrid, ChIP-qPCR, and dual-luciferase assays. In addition, the treatment with naphthalene acetic acid promoted the expression of LkARF7 and LkARF19. We also found that overexpression of these two genes in poplar promoted adventitious root formation. Furthermore, LkARF19 interacted with the DEAD-box ATP-dependent RNA helicase 53-like protein to form a heterodimer to regulate adventitious root formation. Altogether, our results reveal an additional regulatory mechanism underlying the control of adventitious root formation by auxin.

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.

Control of lateral root initiation by DA3 in Arabidopsis

Lateral root (LR) initiation is controlled by the pericycle and the neighboring endodermis in Arabidopsis. Here, we demonstrate that UBIQUITIN-SPECIFIC PROTEASE14/DA3 regulates LR initiation by modulating auxin signaling in the pericycle and endodermis. DA3 negatively affects the mRNA and protein levels of AUXIN RESPONSE FACTOR7 (ARF7) and ARF19 in the pericycle and endodermis but positively regulates the protein stability of SHORT HYPOCOTYL 2 (SHY2/IAA3), an auxin signaling repressor, in the endodermis. We show that DA3 interacts with ARF7 and ARF19, inhibiting their binding to the locus of LATERAL ORGAN BOUNDARY DOMAIN16 (LBD16) to repress its expression in the pericycle. SHY2 also interacts with ARF7 and ARF19 in the endodermis and enhances the DA3 repressive effect on ARF7 and ARF19, thus modulating LBD16 expression in the pericycle. Overall, our findings show that DA3 acts with SHY2, ARF7, and ARF19 to coordinate auxin signaling in the pericycle and endodermis to control LR initiation in Arabidopsis.

The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI regulates primary root growth and lateral root elongation

Roots are the main organs through which plants absorb water and nutrients. As the key phytohormone involved in root growth, auxin functions in plant environmental responses by modulating auxin synthesis, distribution and polar transport. The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI can improve root architecture, and tppi1 mutants have significantly shortened primary roots. However, the mechanism underlying the short roots of the tppi1 mutant and the upstream signaling pathway and downstream genes regulated by AtTPPI are unclear. Here, we demonstrated that the AtTPPI gene could promote auxin accumulation in AtTPPI-overexpressing plants. By comparing the transcriptomic data of tppi1 and wild-type roots, we found several upregulations of auxin-related genes, including GH3.3, GH3.9 and GH3.12, may play an important role in the AtTPPI gene-mediated auxin transport signaling pathway, ultimately leading to changes in auxin content and primary root length. Moreover, increased AtTPPI expression can regulate primary root growth and lateral root elongation under different concentration of nitrate conditions. Overall, constitutive expression of AtTPPI increased auxin contents and improved lateral root elongation, constituting a new method for improving the nitrogen utilization efficiency of plants.

WOX11: the founder of plant organ regeneration

De novo organ regeneration is the process in which adventitious roots or shoots regenerate from detached or wounded organs. De novo organ regeneration can occur either in natural conditions, e.g. adventitious root regeneration from the wounded sites of detached leaves or stems, or in in-vitro tissue culture, e.g. organ regeneration from callus. In this review, we summarize recent advances in research on the molecular mechanism of de novo organ regeneration, focusing on the role of the WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene in the model plant Arabidopsis thaliana. WOX11 is a direct target of the auxin signaling pathway, and it is expressed in, and regulates the establishment of, the founder cell during de novo root regeneration and callus formation. WOX11 activates the expression of its target genes to initiate root and callus primordia. Therefore, WOX11 links upstream auxin signaling to downstream cell fate transition during regeneration. We also discuss the role of WOX11 in diverse species and its evolution in plants.

Systemic control of plant regeneration and wound repair

Plants have a broad capacity to regenerate damaged organs. The study of wounding in multiple developmental systems has uncovered many of the molecular properties underlying plants' competence for regeneration at the local cellular level. However, in nature, wounding is rarely localized to one place, and plants need to coordinate regeneration responses at multiple tissues with environmental conditions and their physiological state. Here, we review the evidence for systemic signals that regulate regeneration on a plant-wide level. We focus on the role of auxin and sugars as short- and long-range signals in natural wounding contexts and discuss the varied origin of these signals in different regeneration scenarios. Together, this evidence calls for a broader, system-wide view of plant regeneration competence.

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.

Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants

Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.

Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses

Detached Arabidopsis thaliana leaves can regenerate adventitious roots, providing a platform for studying de novo root regeneration (DNRR). However, the comprehensive transcriptional framework of DNRR remains elusive. Here, we provide a high-resolution landscape of transcriptome reprogramming from wound response to root organogenesis in DNRR and show key factors involved in DNRR. Time-lapse RNA sequencing (RNA-seq) of the entire leaf within 12 h of leaf detachment revealed rapid activation of jasmonate, ethylene, and reactive oxygen species (ROS) pathways in response to wounding. Genetic analyses confirmed that ethylene and ROS may serve as wound signals to promote DNRR. Next, time-lapse RNA-seq within 5 d of leaf detachment revealed the activation of genes involved in organogenesis, wound-induced regeneration, and resource allocation in the wounded region of detached leaves during adventitious rooting. Genetic studies showed that BLADE-ON-PETIOLE1/2, which control aboveground organs, PLETHORA3/5/7, which control root organogenesis, and ETHYLENE RESPONSE FACTOR115, which controls wound-induced regeneration, are involved in DNRR. Furthermore, single-cell RNA-seq data revealed gene expression patterns in the wounded region of detached leaves during adventitious rooting. Overall, our study not only provides transcriptome tools but also reveals key factors involved in DNRR from detached Arabidopsis leaves.

Molecular Determinants of in vitro Plant Regeneration: Prospects for Enhanced Manipulation of Lettuce (Lactuca sativa L.)

In vitro plant regeneration involves dedifferentiation and molecular reprogramming of cells in order to regenerate whole organs. Plant regeneration can occur via two pathways, de novo organogenesis and somatic embryogenesis. Both pathways involve intricate molecular mechanisms and crosstalk between auxin and cytokinin signaling. Molecular determinants of both pathways have been studied in detail in model species, but little is known about the molecular mechanisms controlling de novo shoot organogenesis in lettuce. This review provides a synopsis of our current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis with an emphasis on the former as well as provides insights into applying this information for enhanced in vitro regeneration in non-model species such as lettuce (Lactuca sativa L.).

Pericycle cell division competence underlies various developmental programs

Pericycle cells possess proliferative activity long after leaving the root apical meristem. Depending on the developmental stage and external stimuli, pericycle cell division leads to the production of lateral roots, vascular cambium and periderm, and callus. Therefore, pericycle cell division competence underlies root branching and secondary growth, as well as plant regeneration capacity. In this review, we first briefly present an overview of the molecular pathways of the four developmental programs originated, exclusively or partly, from pericycle cells. Then, we provide a review of up-to-date knowledge in the mechanisms determining pericycle cells' competence to undergo cell division. Furthermore, we discuss directions of future research to further our understanding of the pericycle's characteristics and functions.

Wound-induced signals regulate root organogenesis in Arabidopsis explants

BACKGROUND

Reactive oxygen species (ROS) and calcium ions (Ca²⁺) are representative signals of plant wound responses. Wounding triggers cell fate transition in detached plant tissues and induces de novo root organogenesis. While the hormonal regulation of root organogenesis has been widely studied, the role of early wound signals including ROS and Ca²⁺ remains largely unknown.

RESULTS

We identified that ROS and Ca²⁺ are required for de novo root organogenesis, but have different functions in Arabidopsis explants. The inhibition of the ROS and Ca²⁺ signals delayed root development in detached leaves. Examination of the auxin signaling pathways indicated that ROS and Ca²⁺ did not affect auxin biosynthesis and transport in explants. Additionally, the expression of key genes related to auxin signals during root organogenesis was not significantly affected by the inhibition of ROS and Ca²⁺ signals. The addition of auxin partially restored the suppression of root development by the ROS inhibitor; however, auxin supplementation did not affect root organogenesis in Ca²⁺-depleted explants.

CONCLUSIONS

Our results indicate that, while both ROS and Ca²⁺ are key molecules, at least in part of the auxin signals acts downstream of ROS signaling, and Ca²⁺ acts downstream of auxin during de novo root organogenesis in leaf explants.

Arabidopsis ATXR2 represses de novo shoot organogenesis in the transition from callus to shoot formation

Plants exhibit high regenerative capacity, which is controlled by various genetic factors. Here, we report that ARABIDOPSIS TRITHORAX-RELATED 2 (ATXR2) controls de novo shoot organogenesis by regulating auxin-cytokinin interaction. The auxin-inducible ATXR2 Trithorax Group (TrxG) protein temporally interacts with the cytokinin-responsive type-B ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) at early stages of shoot regeneration. The ATXR2-ARR1 complex binds to and deposits the H3K36me3 mark in the promoters of a subset of type-A ARR genes, ARR5 and ARR7, thus activating their expression. Consequently, the ATXR2/ARR1-type-A ARR module transiently represses cytokinin signaling and thereby de novo shoot regeneration. The atxr2-1 mutant calli exhibit enhanced shoot regeneration with low expression of ARR5 and ARR7, which ultimately upregulates WUSCHEL (WUS) expression. Thus, ATXR2 regulates cytokinin signaling and prevents premature WUS activation to ensure proper cell fate transition, and the auxin-cytokinin interaction underlies the initial specification of shoot meristem in callus.

WIND transcription factors orchestrate wound-induced callus formation, vascular reconnection and defense response in Arabidopsis

Wounding triggers de novo organogenesis, vascular reconnection and defense response but how wound stress evoke such a diverse array of physiological responses remains unknown. We previously identified AP2/ERF transcription factors, WOUND INDUCED DEDIFFERENTIATION1 (WIND1) and its homologs, WIND2, WIND3 and WIND4, as key regulators of wound-induced cellular reprogramming in Arabidopsis. To understand how WIND transcription factors promote downstream events, we performed time-course transcriptome analyses after WIND1 induction. We observed a significant overlap between WIND1-induced genes and genes implicated in cellular reprogramming, vascular formation and pathogen response. We demonstrated that WIND transcription factors induce several reprogramming genes to promote callus formation at wound sites. We, in addition, showed that WIND transcription factors promote tracheary element formation, vascular reconnection and resistance to Pseudomonas syringae pv. tomato DC3000. These results indicate that WIND transcription factors function as key regulators of wound-induced responses by promoting dynamic transcriptional alterations. This study provides deeper mechanistic insights into how plants control multiple physiological responses after wounding.

De novo transcriptome analysis provides insights into formation of in vitro adventitious root from leaf explants of Arnebia euchroma

BACKGROUND

Adventitious root formation is considered a major developmental step during the propagation of difficult to root plants, especially in horticultural crops. Recently, adventitious roots induced through plant tissue culture methods have also been used for production of phytochemicals such as flavonoids, anthocyanins and anthraquinones. It is rather well understood which horticultural species will easily form adventitious roots, but the factors affecting this process at molecular level or regulating the induction process in in vitro conditions are far less known. The present study was conducted to identify transcripts involved in in vitro induction and formation of adventitious roots using Arnebia euchroma leaves at different time points (intact leaf (control), 3 h, 12 h, 24 h, 3 d, 7 d, 10 d and 15 d). A. euchroma is an endangered medicinal Himalayan herb whose root contains red naphthoquinone pigments. These phytoconstituents are widely used as an herbal ingredient in Asian traditional medicine as well as natural colouring agent in food and cosmetics.

RESULTS

A total of 137.93 to 293.76 million raw reads were generated and assembled to 54,587 transcripts with average length of 1512.27 bps and N50 of 2193 bps, respectively. In addition, 50,107 differentially expressed genes were identified and found to be involved in plant hormone signal transduction, cell wall modification and wound induced mitogen activated protein kinase signalling. The data exhibited dominance of auxin responsive (AUXIN RESPONSE FACTOR8, IAA13, GRETCHEN HAGEN3.1) and sucrose translocation (BETA-31 FRUCTOFURANOSIDASE and MONOSACCHARIDE-SENSING protein1) genes during induction phase. In the initiation phase, the expression of LATERAL ORGAN BOUNDARIES DOMAIN16, EXPANSIN-B15, ENDOGLUCANASE25 and LEUCINE-rich repeat EXTENSION-like proteins was increased. During the expression phase, the same transcripts, with exception of LATERAL ORGAN BOUNDARIES DOMAIN16 were identified. Overall, the transcriptomic analysis revealed a similar patterns of genes, however, their expression level varied in subsequent phases of in vitro adventitious root formation in A. euchroma.

CONCLUSION

The results presented here will be helpful in understanding key regulators of in vitro adventitious root development in Arnebia species, which may be deployed in the future for phytochemical production at a commercial scale.

An HD-ZIP transcription factor, MxHB13, integrates auxin-regulated and juvenility-determined control of adventitious rooting in Malus xiaojinensis

Adventitious root (AR) formation is a critical factor in the vegetative propagation of forestry and horticultural plants. Competence for AR formation declines in many species during the miR156/SPL-mediated vegetative phase change. Auxin also plays a regulatory role in AR formation. In apple rootstock, both high miR156 expression and exogenous auxin application are prerequisites for AR formation. However, the mechanism by which the miR156/SPL module interacts with auxin in controlling AR formation is unclear. In this paper, leafy cuttings of juvenile (Mx-J) and adult (Mx-A) phase Malus xiaojinensis were used in an RNA-sequencing experiment. The results revealed that numerous genes involved in phytohormone signaling, carbohydrate metabolism, cell dedifferentiation, and reactivation were downregulated in Mx-A cuttings in response to indole butyric acid treatment. Among the differentially expressed genes, an HD-ZIP transcription factor gene, MxHB13, was found to be under negative regulation of MdSPL26 by directly binding to MxHB13 promoter. MxTIFY9 interacts with MxSPL26 and may play a role in co-repressing the expression of MxHB13. The expression of MxTIFY9 was induced by exogenous indole butyric acid. MxHB13 binds to the promoter of MxABCB19-2 and positively affects the expression. A model is proposed in which MxHB13 links juvenility-limited and auxin-limited AR recalcitrance mechanisms in Mx-A.

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.

Model systems for regeneration: Arabidopsis

Plants encompass unparalleled multi-scale regenerative potential. Despite lacking specialized cells that are recruited to injured sites, and despite their cells being encased in rigid cell walls, plants exhibit a variety of regenerative responses ranging from the regeneration of specific cell types, tissues and organs, to the rebuilding of an entire organism. Over the years, extensive studies on embryo, shoot and root development in the model plant species Arabidopsis thaliana have provided insights into the mechanisms underlying plant regeneration. These studies highlight how Arabidopsis, with its wide array of refined molecular, genetic and cell biological tools, provides a perfect model to interrogate the cellular and molecular mechanisms of reprogramming during regeneration.

Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis

BACKGROUND

Barley is known to be recalcitrant to tissue culture, which hinders genetic transformation and its biotechnological application. To date, the ideal explant for transformation remains limited to immature embryos; the mechanism underlying embryonic callus formation is elusive.

RESULTS

This study aimed to uncover the different transcription regulation pathways between calli formed from immature (IME) and mature (ME) embryos through transcriptome sequencing. We showed that incubation of embryos in an auxin-rich medium caused dramatic changes in gene expression profiles within 48 h. Overall, 9330 and 11,318 differentially expressed genes (DEGs) were found in the IME and ME systems, respectively. 3880 DEGs were found to be specific to IME_0h/IME_48h, and protein phosphorylation, regulation of transcription, and oxidative-reduction processes were the most common gene ontology categories of this group. Twenty-three IAA, fourteen ARF, eight SAUR, three YUC, and four PIN genes were found to be differentially expressed during callus formation. The effect of callus-inducing medium (CIM) on IAA genes was broader in the IME system than in the ME system, indicating that auxin response participates in regulating cell reprogramming during callus formation. BBM, LEC1, and PLT2 exhibited a significant increase in expression levels in the IME system but were not activated in the ME system. WUS showed a more substantial growth trend in the IME system than in the ME system, suggesting that these embryonic, shoot, and root meristem genes play crucial roles in determining the acquisition of competency. Moreover, epigenetic regulators, including SUVH3A, SUVH2A, and HDA19B/703, exhibited differential expression patterns between the two induction systems, indicating that epigenetic reprogramming might contribute to gene expression activation/suppression in this process. Furthermore, we examined the effect of ectopic expression of HvBBM and HvWUS on Agrobacterium-mediated barley transformation. The transformation efficiency in the group expressing the PLTPpro:HvBBM + Axig1pro:HvWUS construct was increased by three times that in the control (empty vector) because of enhanced plant regeneration capacity.

CONCLUSIONS

We identified some regulatory factors that might contribute to the differential responses of the two explants to callus induction and provide a promising strategy to improve transformation efficiency in barley.

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.

Adventitious Rooting in Populus Species: Update and Perspectives

Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.

Metabolites Secreted by a Plant-Growth-Promoting Pantoea agglomerans Strain Improved Rooting of Pyrus communis L. cv Dar Gazi Cuttings

Strains belonging to Pantoea agglomerans species are known for their ability to produce metabolites that can act in synergy with auxins to induce the adventitious root (AR) formation. The latter is critically important in the agamic propagation of several woody species, including pear (Pyrus communis L.), playing a considerable role in the commercial nursery farms including those using micropropagation techniques. When grown on a medium amended with tryptophan, the plant-growth-promoting (PGP) strain P. agglomerans C1 produces a cocktail of auxin and auxin-like molecules that can be utilized as biostimulants to improve the rooting of vegetable (Solanum lycopersicum L.) and woody crop species (Prunus rootstock GF/677 and hazelnut). In this study, we evaluated the morphological and molecular responses induced by strain C1 exometabolites in microcuttings of P. communis L. cv Dar Gazi and the potential benefits arising from their application. Results showed that exometabolites by P. agglomerans C1 induced a direct and earlier emergence of roots from stem tissues and determined modifications of root morphological parameters and root architecture compared to plants treated with the synthetic hormone indole-3-butyric acid (IBA). Transcription analysis revealed differences in the temporal expression pattern of ARF17 gene when IBA and C1 exometabolites were used alone, while together they also determined changes in the expression pattern of other key auxin-regulated plant genes. These results suggest that the phenotypic and molecular changes triggered by P. agglomerans C1 are dependent on different stimulatory and inhibitory effects that auxin-like molecules and other metabolites secreted by this strain have on the gene regulatory network of the plant. This evidence supports the hypothesis that the strategies used to harness the metabolic potential of PGP bacteria are key factors in obtaining novel biostimulants for sustainable agriculture. Our results demonstrate that metabolites secreted by strain C1 can be successfully used to increase the efficiency of micropropagation of pear through tissue culture techniques.

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.

AUREA maintains the balance between chlorophyll synthesis and adventitious root formation in tomato

Flooding tolerance is an important trait for tomato breeding. In this study, we obtained a recessive mutant exhibiting highly enhanced submergence resistance. Phenotypical analyses showed that this resistant to flooding (rf) mutant displays slightly chlorotic leaves and spontaneous initiation of adventitious roots (ARs) on stems. The mutation was mapped to the phytochromobilin synthase gene AUREA (AU), in which a single amino acid substitution from asparagine to tyrosine occurred. In addition to the classic function of AU in phytochrome and chlorophyll biogenesis in leaves, we uncovered its novel role in mediating AR formation on stems. We further observed temporal coincidence of the two phenotypes in the rf mutant: chlorosis and spontaneous AR formation and revealed that AU functions by maintaining heme homeostasis. Interestingly, our grafting results suggest that heme might play roles in AR initiation via long-distance transport from leaves to stems. Our results present genetic evidence for the involvement of the AU-heme oxygenase-1-heme pathway in AR initiation in tomato. As fruit production and yield in the rf mutant are minimally impacted, the mutation identified in this study may provide a target for biotechnological renovation of tomato germplasm in future breeding.

Adventitious root formation is dynamically regulated by various hormones in leaf-vegetable sweetpotato cuttings

Leaf-vegetable sweetpotato is an important cash crop that is of high nutritional value. Cuttage is the most convenient method for large-scale propagation. However, the rate and number of adventitious roots (ARs) formation vary significantly among different cultivar cuttings. In this study, two varieties, NC1 and FC13-14, were used to compare the rate of ARs formation. The cumulative results of root morphology showed that in NC1 total root length, total root surface area, total root volume, and root tips were 3.7, 3.5, 3.2, and 2.4 times greater, respectively, than those of FC13-14 at 7 d, indicating that the ARs formation and growth were faster in NC1. In addition, the biomass of aboveground and underground parts in NC1 was 3.6 and 1.3 times more, respectively, than that of FC13-14 at 7 d after cutting, suggesting that the rapid ARs formation rate contributed to the growth and yield of stems and leaves. The analysis of plant water potential showed that NC1 exhibiting higher water potential prevented leaf wilting. Gene expression levels of 22 root-related genes revealed differential expression during different developmental periods. Interestingly, YUCCA family genes had elevated transcript abundance at 0, 12, 24, and 36 h. Moreover, analysis of hormones including indole-3-acetic acid (IAA), ethylene (ETH), abscisic acid (ABA), brassinolide (BR), jasmonic acid (JA), gibberellin (GA), and cytokinin (CTK) revealed varied contents during different developmental stages. Cumulative evidence demonstrated that gene expression profiles and hormone content of IAA, ETH, and BR were significantly higher in NC1 roots than in FC13-14 roots following all time periods, while the amount of JA increased and was higher in FC13-14 than in NC1 from 0 to 72 h. This indicates that IAA, BR, and ETH play positive roles and JA has a negative effect on ARs formation. Moreover, ETH takes effect earlier than BR, while IAA and JA have functions throughout the whole process. The findings above were validated by the application of exogenous hormones and hormone synthesis inhibitors. This study reveals the preliminary regulation of ARs formation in leaf-vegetable sweetpotato cuttings and thus contributes to further clarification of the molecular mechanism of multiple hormone interactions.

Time of In Vitro Anther Culture May Moderate Action of Copper and Silver Ions that Affect the Relationship between DNA Methylation Change and the Yield of Barley Green Regenerants

Plant anther culture allows for the regeneration of uniform and homozygous double haploids. However, off-type regenerants may appear as a result of so-called tissue culture-induced variation (TCIV). In addition, the presence of Cu²⁺ and Ag⁺ ions in the culture medium might influence the number of green plants. The regenerants were obtained via anther cultures of barley under varying Cu²⁺ and Ag⁺ ion concentrations in the induction medium during distinct time conditions. DArTseqMet markers were evaluated based on regenerants and donor plants and delivering data on DNA demethylation (DM) and de novo methylation (DNM) and changes in methylation (Delta). The number of green regenerated plants per 100 anthers (GPs) was evaluated. The Cu²⁺ and Ag⁺ ion concentrations moderated relationships between Delta and the number of green plants conditional on time of tissue cultures. Depending on the ions, moderated moderation is valid within the different time of anther culture. When the highest concentration of copper is analyzed, plant regeneration is possible under short ‘Time’ (21 days) of anther culture wherein Delta is negative or under elongated Time when Delta is positive. Under 21 days of culture, the highest concentration of silver ions and when Delta is negative, some regenerants could be evaluated. However, under high Ag⁺ concentration when Time of culture is long and Delta positive, the highest number of green plants could be obtained.

Local auxin biosynthesis is required for root regeneration after wounding

The root meristem can regenerate following removal of its stem-cell niche by recruitment of remnant cells from the stump. Regeneration is initiated by rapid accumulation of auxin near the injury site but the source of this auxin is unknown. Here, we show that auxin accumulation arises from the activity of multiple auxin biosynthetic sources that are newly specified near the cut site and that their continuous activity is required for the regeneration process. Auxin synthesis is highly localized while PIN-mediated transport is dispensable for auxin accumulation and tip regeneration. Roots lacking the activity of the regeneration competence factor ERF115, or that are dissected at a zone of low regeneration potential, fail to activate local auxin sources. Remarkably, restoring auxin supply is sufficient to confer regeneration capacity to these recalcitrant tissues. We suggest that regeneration competence relies on the ability to specify new local auxin sources in a precise temporal pattern.

Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice

Plant growth and development occurs through meristematic cell activity, and cell fate transition is accompanied by epigenetic modifications. Callus with cell pluripotency exhibits the ability to undergo continued cell division, and is ideal for studying plant meristematic differentiation. By comparing the differential epigenetic modifications between callus and seedling, the changes in chromatin state and effects of various epigenetic modifications on the growth and development of plants can be revealed, and the key genes related to plant growth and development can be identified, providing novel insights into the regulation of plant growth and development. In this study, we performed ChIP assays using various antibodies in rice seed-induced callus and seedlings grown for about 15 days to examine the differential deposition of H3K27me3 and H3K4me3. Furthermore, data for DNase I-hypersensitive sites in the corresponding tissues were downloaded from National Center for Biotechnology Information. We analyzed 4,562 callus H3K27me3-decreased genes especially those encoding transcription factors in callus, and found that most of the transcription factors, including AP2-ERREBP, NAC, and HB gene families, were related to growth and development. Genes related to meristemization, such as OsWOX9, OsWOX11, OsPLT4, OsPLT5, and OsSHR, were also included. In contrast, H3K4me3 positively regulated callus characteristics through its higher deposition in the callus than in the seedling. We further performed transcriptomic analysis on 45 sets of Affymetrix GeneChip arrays and identified 1,565 genes preferentially expressed in the callus. Callus development and root development in rice were found to share a common regulatory mechanism. We found that these genes, which are associated with meristems, require the removal of H3K27me3 and the deposition of H3K4me3, and DNase I-hypersensitive sites to maintain a relatively active state in the callus than in the seedling. The present study provides novel data about the epigenetic mechanisms involved in callus formation and additional resources for the study of cell division and differentiation in plants.

Advances in Plant Regeneration: Shake, Rattle and Roll

Some plant cells are able to rebuild new organs after tissue damage or in response to definite stress treatments and/or exogenous hormone applications. Whole plants can develop through de novo organogenesis or somatic embryogenesis. Recent findings have enlarged our understanding of the molecular and cellular mechanisms required for tissue reprogramming during plant regeneration. Genetic analyses also suggest the key role of epigenetic regulation during de novo plant organogenesis. A deeper understanding of plant regeneration might help us to enhance tissue culture optimization, with multiple applications in plant micropropagation and green biotechnology. In this review, we will provide additional insights into the physiological and molecular framework of plant regeneration, including both direct and indirect de novo organ formation and somatic embryogenesis, and we will discuss the key role of intrinsic and extrinsic constraints for cell reprogramming during plant regeneration.

From Single Cell to Plants: Mesophyll Protoplasts as a Versatile System for Investigating Plant Cell Reprogramming

Plants are sessile organisms that have a remarkable developmental plasticity, which ensures their optimal adaptation to environmental stresses. Plant cell totipotency is an extreme example of such plasticity, whereby somatic cells have the potential to form plants via direct shoot organogenesis or somatic embryogenesis in response to various exogenous and/or endogenous signals. Protoplasts provide one of the most suitable systems for investigating molecular mechanisms of totipotency, because they are effectively single cell populations. In this review, we consider the current state of knowledge of the mechanisms that induce cell proliferation from individual, differentiated somatic plant cells. We highlight initial explant metabolic status, ploidy level and isolation procedure as determinants of successful cell reprogramming. We also discuss the importance of auxin signalling and its interaction with stress-regulated pathways in governing cell cycle induction and further stages of plant cell totipotency.

Gene Regulation via the Combination of Transcription Factors in the INDETERMINATE DOMAIN and GRAS Families

INDETERMINATE DOMAIN (IDD) family proteins are plant-specific transcription factors. Some Arabidopsis IDD (AtIDD) proteins regulate the expression of SCARECROW (SCR) by interacting with GRAS family transcription factors SHORT-ROOT (SHR) and SCR, which are involved in root tissue formation. Some AtIDD proteins regulate genes involved in the synthesis (GA3ox1) or signaling (SCL3) of gibberellic acid (GA) by interacting with DELLA proteins, a subfamily of the GRAS family. We analyzed the DNA binding properties and protein–protein interactions of select AtIDD proteins. We also investigated the transcriptional activity of the combination of AtIDD and GRAS proteins (AtIDD proteins combined with SHR and SCR or with REPRESSOR of ga1-3 (RGA)) on the promoters of SCR,SCL3, and GA3ox1 by conducting a transient assay using Arabidopsis culture cells. Our results showed that the SCR promoter could be activated by the IDD and RGA complexes and that the SCL3 and GA3ox1 promoters could be activated by the IDD, SHR, and SCR complexes, indicating the possibility that these complexes regulate and consequently coordinate the expression of genes involved in GA synthesis (GA3ox1), GA signaling (SCL3), and root formation (SCR).

High frequency in vitro regeneration of adventitious shoots in daylilies (Hemerocallis sp) stem tissue using thidiazuron

BACKGROUND

Daylilies are a lucrative crop used for its floral beauty, medicinal proprieties, landscaping, fire prevention, nutritional value, and research. Despite the importance, daylilies remain extremely challenging for multiplying in vitro. The response difficulty is exacerbated because a few good protocols for daylilies micropropagation are generally difficult to reproduce across genotypes. An efficient strategy, currently applied at Langston University, is to systematically explore individual tissues or organs for their potential to micropropagation. This article is a partial report of the investigation carried out under room environmental conditions and focuses on developing an efficient daylilies in vitro propagation protocol that uses the stem tissue as the principal explant.

RESULTS

In less than three months, using thidiazuron, the use of the stem tissue as the in vitro experimental explant was successful in inducing multiple shoots several folds greater than current daylilies shoot organogenesis protocols. The study showed that tissue culture can be conducted successfully under unrestricted room environmental conditions as well as under the controlled environment of a growth chamber. It also showed that splitting lengthwise stem explants formed multiple shoots several folds greater than cross-sectioned and inverted explants. Shoot conversion rate was mostly independent of the number of shoots formed per explants. The overall response was explant and genotype-dependent. Efficient responses were observed in all thidiazuron treatments.

CONCLUSION

An efficient protocol, which can be applied for mass multiple shoots formation using the daylilies stem tissue as the main explant, was successfully developed. This could lead to a broad and rapid propagation of the crop under an array of environmental conditions to meet the market demand and hasten exogenous gene transfer and breeding selection processes.

Modulatory Role of Reactive Oxygen Species in Root Development in Model Plant of Arabidopsis thaliana

Reactive oxygen species (ROS), a type of oxygen monoelectronic reduction product, have a higher chemical activity than O₂. Although ROS pose potential risks to all organisms via inducing oxidative stress, indispensable role of ROS in individual development cannot be ignored. Among them, the role of ROS in the model plant Arabidopsis thaliana is deeply studied. Mounting evidence suggests that ROS are essential for root and root hair development. In the present review, we provide an updated perspective on the latest research progress pertaining to the role of ROS in the precise regulation of root stem cell maintenance and differentiation, redox regulation of the cell cycle, and root hair initiation during root growth. Among the different types of ROS, O₂ ^•- and H₂O₂ have been extensively investigated, and they exhibit different gradient distributions in the roots. The concentration of O₂ ^•- decreases along a gradient from the meristem to the transition zone and the concentration of H₂O₂ decreases along a gradient from the differentiation zone to the elongation zone. These gradients are regulated by peroxidases, which are modulated by the UPBEAT1 (UPB1) transcription factor. In addition, multiple transcriptional factors, such as APP1, ABO8, PHB3, and RITF1, which are involved in the brassinolide signaling pathway, converge as a ROS signal to regulate root stem cell maintenance. Furthermore, superoxide anions (O₂ ^•-) are generated from the oxidation in mitochondria, ROS produced during plasmid metabolism, H₂O₂ produced in apoplasts, and catalysis of respiratory burst oxidase homolog (RBOH) in the cell membrane. Furthermore, ROS can act as a signal to regulate redox status, which regulates the expression of the cell-cycle components CYC2;3, CYCB1;1, and retinoblastoma-related protein, thereby controlling the cell-cycle progression. In the root maturation zone, the epidermal cells located in the H cell position emerge to form hair cells, and plant hormones, such as auxin and ethylene regulate root hair formation via ROS. Furthermore, ROS accumulation can influence hormone signal transduction and vice versa. Data about the association between nutrient stress and ROS signals in root hair development are scarce. However, the fact that ROBHC/RHD2 or RHD6 is specifically expressed in root hair cells and induced by nutrients, may explain the relationship. Future studies should focus on the regulatory mechanisms underlying root hair development via the interactions of ROS with hormone signals and nutrient components.

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.

Role of auxin homeostasis and response in nitrogen limitation and dark stimulation of adventitious root formation in petunia cuttings

BACKGROUND AND AIMS

Adventitious root (AR) formation in Petunia hybrida is inhibited by low nitrogen fertilization of stock plants but promoted by dark incubation of cuttings before planting. We investigated whether the plant hormone auxin is involved in nitrogen- and dark-mediated AR formation.

METHODS

Concentrations of indole-3-acetic acid (IAA) and RNA accumulation of genes controlling auxin homeostasis and function were monitored in the stem base in response to high versus low nitrogen supply to stock plants and to temporal dark vs. light exposure of cuttings by use of GC-MS/MS, a petunia-specific microarray and quantitative RT-PCR. Auxin source capacity, polar auxin transport in cuttings and auxin concentration in the rooting zone were manipulated to investigate the functional contribution of auxin homeostasis and response to the effects of nitrogen fertilization and dark exposure on rooting.

KEY RESULTS

The nitrogen content of cuttings had only a marginal effect on IAA concentration in the stem base. Dark incubation enhanced the accumulation of IAA in the stem base during AR induction independent of nitrogen level. Early IAA accumulation in the dark depended on the upper shoot as an auxin source and was enhanced after apical IAA supply. Dark exposure stimulated RNA accumulation of auxin-related genes. In particular, expression of Ph-PIN1 and of genes controlling auxin signalling, including Ph-IAA14, Ph-ARF8, Ph-ARF10 and Ph-SAUR14, was enhanced, while the latter four were repressed in nitrogen-limited cuttings, particularly in the dark. Dark stimulation of rooting depended on polar auxin transport. Basal auxin application partially substituted the effect of dark exposure on rooting, whereas the auxin response of AR formation was strongly depressed by nitrogen limitation.

CONCLUSIONS

Increased auxin delivery from the upper shoot and enhanced auxin signalling in the stem base contribute to dark-stimulated AR formation, while nitrogen limitation inhibits AR formation downstream of the auxin signal.

Topology of regulatory networks that guide plant meristem activity: similarities and differences

Plants adapt their morphology in response to variable environmental conditions such as nitrate availability, drought, and temperature shifts. Three crucial aspects to this developmental plasticity are the control of initiation, identity and activity of meristems. At the cellular level, the activity of meristems is controlled by balancing self-renewal in stem cells, amplifying divisions in their daughter cells, and cell differentiation. Recent studies in plants have uncovered transcription factors regulating meristem activity at cellular resolution, and regulatory networks that couple these factors with phytohormone signalling for global plant growth regulation. Here, we highlight selected recent advances in our understanding of the multidimensional transcriptional networks that regulate meristem activity and discuss emerging insights on how a selection of environmental cues impinges on these networks.

Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants

Horizontal gene transfer (HGT), the movement and genomic integration of DNA across species boundaries, is commonly associated with bacteria and other microorganisms, but functional HGT (fHGT) is increasingly being recognized in heterotrophic parasitic plants that obtain their nutrients and water from their host plants through direct haustorial feeding. Here, in the holoparasitic stem parasite Cuscuta, we identify 108 transcribed and probably functional HGT events in Cuscuta campestris and related species, plus 42 additional regions with host-derived transposon, pseudogene and non-coding sequences. Surprisingly, 18 Cuscuta fHGTs were acquired from the same gene families by independent HGT events in Orobanchaceae parasites, and the majority are highly expressed in the haustorial feeding structures in both lineages. Convergent retention and expression of HGT sequences suggests an adaptive role for specific additional genes in parasite biology. Between 16 and 20 of the transcribed HGT events are inferred as ancestral in Cuscuta based on transcriptome sequences from species across the phylogenetic range of the genus, implicating fHGT in the successful radiation of Cuscuta parasites. Genome sequencing of C. campestris supports transfer of genomic DNA-rather than retroprocessed RNA-as the mechanism of fHGT. Many of the C. campestris genes horizontally acquired are also frequent sources of 24-nucleotide small RNAs that are typically associated with RNA-directed DNA methylation. One HGT encoding a leucine-rich repeat protein kinase overlaps with a microRNA that has been shown to regulate host gene expression, suggesting that HGT-derived parasite small RNAs may function in the parasite-host interaction. This study enriches our understanding of HGT by describing a parasite-host system with unprecedented gene exchange that points to convergent evolution of HGT events and the functional importance of horizontally transferred coding and non-coding sequences.

What Makes Adventitious Roots?

The spermatophyte root system is composed of a primary root that develops from an embryonically formed root meristem, and of different post-embryonic root types: lateral and adventitious roots. Adventitious roots, arising from the stem of the plants, are the main component of the mature root system of many plants. Their development can also be induced in response to adverse environmental conditions or stresses. Here, in this review, we report on the morphological and functional diversity of adventitious roots and their origin. The hormonal and molecular regulation of the constitutive and inducible adventitious root initiation and development is discussed. Recent data confirmed the crucial role of the auxin/cytokinin balance in adventitious rooting. Nevertheless, other hormones must be considered. At the genetic level, adventitious root formation integrates the transduction of external signals, as well as a core auxin-regulated developmental pathway that is shared with lateral root formation. The knowledge acquired from adventitious root development opens new perspectives to improve micropropagation by cutting in recalcitrant species, root system architecture of crops such as cereals, and to understand how plants adapted during evolution to the terrestrial environment by producing different post-embryonic root types.

Plant Genetics: Advances in Regeneration Pathways

Two recent studies highlight the role of stem cell activation as a response to tissue damage and wounding.