ETHYLENE INSENSITIVE 3 suppresses plant de novo root regeneration from leaf explants and mediates age-regulated regeneration decline

An efficient genetic transformation system mediated by Rhizobium rhizogenes in fruit trees based on the transgenic hairy root to shoot conversion

Genetic transformation is a critical tool for gene editing and genetic improvement of plants. Although many model plants and crops can be genetically manipulated, genetic transformation systems for fruit trees are either lacking or perform poorly. We used Rhizobium rhizogenes to transfer the target gene into the hairy roots of Malus domestica and Actinidia chinensis. Transgenic roots were generated within 3 weeks, with a transgenic efficiency of 78.8%. Root to shoot conversion of transgenic hairy roots was achieved within 11 weeks, with a regeneration efficiency of 3.3%. Finally, the regulatory genes involved in stem cell activity were used to improve shoot regeneration efficiency. MdWOX5 exhibited the most significant effects, as it led to an improved regeneration efficiency of 20.6% and a reduced regeneration time of 9 weeks. Phenotypes of the overexpression of RUBY system mediated red roots and overexpression of MdRGF5 mediated longer root hairs were observed within 3 weeks, suggesting that the method can be used to quickly screen genes that influence root phenotype scores through root performance, such as root colour, root hair, and lateral root. Obtaining whole plants of the RUBY system and MdRGF5 overexpression lines highlights the convenience of this technology for studying gene functions in whole plants. Overall, we developed an optimized method to improve the transformation efficiency and stability of transformants in fruit trees.

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.

A Highly Efficient Agrobacterium rhizogenes-Mediated Hairy Root Transformation Method of Idesia polycarpa and the Generation of Transgenic Plants

Idesia polycarpa is a promising woody oilseed species because of its high oil yield. However, its use is greatly limited due to the lack of varieties with good qualities; additionally, gene function has been less studied in this plant because an efficient transformation method has not been established yet. In this study, we established a rapid and efficient hairy root transformation method by infecting the whole seedling, the rootless seedling, and the leaf petiole with Agrobacterium rhizogenes using different infection methods. Among these transformation methods, a higher transformation efficiency was obtained using the whole seedling, which could reach up to 71.91%. Furthermore, we found that the seedling age significantly affected the transformation efficiency, either using whole or rootless seedlings. Additionally, we found that the transgenic roots could regenerate transgenic shoots. Taken together, our study lays the foundation for future study and for genetically modifying wood traits in the future.

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.

Temporal profiling of physiological, histological, and transcriptomic dissection during auxin-induced adventitious root formation in tetraploid Robinia pseudoacacia micro-cuttings

MAIN CONCLUSION

Optimal levels of indole-3-butyric acid (IBA) applied at the stem base promote adventitious root (AR) initiation and primordia formation, thus promoting the rooting of leafy micro-cuttings of tetraploid Robinia pseudoacacia. Tetraploid Robinia pseudoacacia L. is a widely cultivated tree in most regions of China that has a hard-rooting capability, propagated by stem cuttings. This study utilizes histological, physiological, and transcriptomic approaches to explore how root primordia are induced after indole butyric acid (IBA) treatment of micro-cuttings. IBA application promoted cell divisions in some cells within the vasculature, showing subcellular features associated with adventitious root (AR) founder cells. The anatomical structure explicitly showed that AR initiated from the cambium layer and instigate the inducible development of AR primordia. Meanwhile, the hormone data showed that similar to that of indole-3-acetic acid, the contents of trans-zeatin and abscisic acid peaked at early stages of AR formation and increased gradually in primordia formation across the subsequent stages, suggesting their indispensable roles in AR induction. On the contrary, 24-epibrassinolide roughly maintained at extremely high levels during primordium initiation thoroughly, indicating its presence was involved in cell-specific reorganization during AR development. Furthermore, antioxidant activities transiently increased in the basal region of micro-cuttings and may serve as biochemical indicators for distinct rooting phases, potentially aiding in AR formation. Transcriptomic analysis during the early stages of root formation shows significant downregulation of the abscisic acid and jasmonate signaling pathways, while ethylene and cytokinin signaling seems upregulated. Network analysis of genes involved in carbon metabolism and photosynthesis indicates that the basal region of the micro-cuttings undergoes rapid reprogramming, which results in the breakdown of sugars into pyruvate. This pyruvate is then utilized to fuel the tricarboxylic acid cycle, thereby sustaining growth through aerobic respiration. Collectively, our findings provide a time-course morphophysiological dissection and also suggest the regulatory role of a conserved auxin module in AR development in these species.

IRR1 contributes to de novo root regeneration from Arabidopsis thaliana leaf explants

Plants are capable of regenerating adventitious roots (ARs), which is important for plant response to stress and survival. Although great advances in understanding AR formation of leaf explants have been made, the regulatory mechanisms of AR formation still need to be investigated. In this study, irr1-1 (impaired root regeneration) was isolated with the inhibition of adventitious rooting from Arabidopsis leaf explants. The β-glucuronidase (GUS) signals of IRR1pro::GUS in detached leaves could be detected at 2-6 days after culture. IRR1 is annotated to encode a Class III peroxidase localized in the cell wall. The total peroxidase (POD) activity of irr1 mutants was significantly lower than that of the wild type. Detached leaves of irr1 mutants showed enhanced reactive oxygen species (ROS) accumulation 4 days after leaves were excised from seedlings. Moreover, thiourea, a ROS scavenger, was able to rescue the adventitious rooting rate in leaf explants of irr1 mutants. Addition of 0.1 μM indole-3-acetic acid (IAA) improved the adventitious rooting from leaf explants of irr1 mutants. Taken together, these results indicated that IRR1 was involved in AR formation of leaf explants, which was associated with ROS homeostasis to some extent.

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.

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.

Integrated multi-omics analysis uncovers roles of mdm-miR164b-MdORE1 in strigolactone-mediated inhibition of adventitious root formation in apple

Apple is one of the most important fruit crops in temperate regions and largely relies on cutting propagation. Adventitious root formation is crucial for the success of cutting propagation. Strigolactones have been reported to function in rooting of woody plants. In this study, we determined that strigolactones have inhibitory effects on adventitious root formation in apple. Transcriptome analysis identified 12 051 differentially expressed genes over the course of adventitious root initiation, with functions related to organogenesis, cell wall biogenesis or plant development. Further analysis indicated that strigolactones might inhibit adventitious root formation through repressing two core hub genes, MdLAC3 and MdORE1. Combining small RNA and degradome sequencing, as well as dual-luciferase sensor assays, we identified and validated three negatively correlated miRNA-mRNA pairs, including mdm-miR397-MdLAC3 and mdm-miR164a/b-MdORE1. Overexpression of mdm-miR164b and silencing MdORE1 exhibited enhanced adventitious root formation in tobacco and apple, respectively. Finally, we verified the role of mdm-miR164b-MdORE1 in strigolactone-mediated repression of rooting ability. Overall, the identified comprehensive regulatory network in apple not only provides insight into strigolactone-mediated adventitious root formation in other woody plants, but also points to a potential strategy for genetic improvement of rooting capacity in woody plants.

The AP2 transcription factors TOE1/TOE2 convey Arabidopsis age information to ethylene signaling in plant de novo root regeneration

We reveal that transcription factors TOE1 and TOE2 directly inhibit the transcription of EIN3. Ethylene triggers leaf abscission and senescence during plant aging. Previous studies have shown that the transcription of ETHYLENE INSENSITIVE 3 (EIN3), which encodes a key transcription factor in ethylene signaling, is gradually upregulated during plant aging. However, it is still unknown how plants transmit their age information to achieve transcriptional control of EIN3. Here, we report that the EAR-like motif-containing transcription factors TARGET OF EAT 1 (TOE1) and its homolog TOE2 directly associated with the EIN3 promoter. The transcription of EIN3 is further enhanced in mutants of toe1 toe2 during plant aging. TOE1/TOE2 are tightly controlled by canonical microRNA 172 (miR172)-mediated plant aging signaling, which result in a decline in TOE1/TOE2 expression during aging. These results illustrate that during plant aging, the reduced expressions of TOE1/TOE2 trigger an upregulation of EIN3. Next, we took advantage of EIN3-regulated de novo root regeneration (DNRR) as an age-controlled phenotype to dissect the biological function of this regulatory circuit. The DNRR rates in toe1 toe2 are more severely decreased with plant aging; however, the simultaneous loss of ein3 and eil1 (toe1 toe2 ein3 eil1 quadruple mutants) almost completely rescued the DNRR defects. Taken together, our findings show that the plant age-regulated TOE transcription factors precisely integrate plant age information and developmental programs through direct protein-DNA interactions.

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.

A molecular framework for signaling crosstalk between jasmonate and ethylene in anthocyanin biosynthesis, trichome development, and defenses against insect herbivores in Arabidopsis

The phytohormones ethylene (ET) and jasmonate (JA) regulate plant development, growth, and defense responses; however, the molecular basis for their signaling crosstalk is unclear. Here, we show that JA-ZIM-domain (JAZ) proteins, which repress JA signaling, repress trichome initiation/branching and anthocyanin accumulation, and inhibit the transcriptional activity of the basic helix-loop-helix (bHLH)-MYB members (GLABRA3 (GL3)-GL1 and TRANSPARENT TESTA 8 (TT8)-MYB75) of WD-repeat/bHLH/MYB (WBM) complexes. The ET-stabilized transcription factors ETHYLENE-INSENSITIVE3 (EIN3) and EIN3-LIKE1 (EIL1) were found to bind to several members of WBM complexes, including GL3, ENHANCER OF GLABRA3 (EGL3), TT8, GL1, MYB75, and TRANSPARENT TESTA GLABRA1 (TTG1). This binding repressed the transcriptional activity of the bHLH-MYB proteins and inhibited anthocyanin accumulation, trichome formation, and defenses against insect herbivores while promoting root hair formation. Conversely, the JA-activated bHLH members GL3, EGL3, and TT8 of WBM complexes were able to interact with and attenuate the transcriptional activity of EIN3/EIL1 at the HOOKLESS1 promoter, and their overexpression inhibited apical hook formation. Thus, this study demonstrates a molecular framework for signaling crosstalk between JA and ET in plant development, secondary metabolism, and defense responses.

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.

Genetic Dissection of Light-Regulated Adventitious Root Induction in Arabidopsis thaliana Hypocotyls

Photomorphogenic responses of etiolated seedlings include the inhibition of hypocotyl elongation and opening of the apical hook. In addition, dark-grown seedlings respond to light by the formation of adventitious roots (AR) on the hypocotyl. How light signaling controls adventitious rooting is less well understood. Hereto, we analyzed adventitious rooting under different light conditions in wild type and photomorphogenesis mutants in Arabidopsis thaliana. Etiolation was not essential for AR formation but raised the competence to form AR under white and blue light. The blue light receptors CRY1 and PHOT1/PHOT2 are key elements contributing to the induction of AR formation in response to light. Furthermore, etiolation-controlled competence for AR formation depended on the COP9 signalosome, E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC (COP1), the COP1 interacting SUPPRESSOR OF PHYA-105 (SPA) kinase family members (SPA1,2 and 3) and Phytochrome-Interacting Factors (PIF). In contrast, ELONGATED HYPOCOTYL5 (HY5), suppressed AR formation. These findings provide a genetic framework that explains the high and low AR competence of Arabidopsis thaliana hypocotyls that were treated with dark, and light, respectively. We propose that light-induced auxin signal dissipation generates a transient auxin maximum that explains AR induction by a dark to light switch.

Seedling morphogenesis: when ethylene meets high ambient temperature

Unlike animals, plant development is plastic and sensitive to environmental changes. For example, Arabidopsis thaliana seedlings display distinct growth patterns when they are grown under different light or temperature conditions. Moreover, endogenous plant hormone such as ethylene also impacts seedling morphology. Ethylene induces hypocotyl elongation in light-grown seedlings but strongly inhibits hypocotyl elongation in etiolated (dark-grown) seedlings. Another characteristic ethylene response in etiolated seedlings is the formation of exaggerated apical hooks. Although it is well known that high ambient temperature promotes hypocotyl elongation in light-grown seedlings (thermomorphogenesis), ethylene suppresses thermomorphogenesis. On another side, high ambient temperature also inhibits the ethylene-responsive hypocotyl shortening and exaggerated hook formation in etiolated seedlings. Therefore, the simplest phytohormone ethylene exhibits almost the most complicated responses, depending on temperature and/or light conditions. In this review, we will focus on two topics related to the main theme of this special issue (response to high temperature): (1) how does high temperature suppress ethylene-induced seedling morphology in dark-grown seedlings, and (2) how does ethylene inhibit high temperature-induced seedling growth in light-grown seedlings. Controlling ethylene biosynthesis through antisense technology was the hallmark event in plant genetic engineering in 1990, we assume that manipulations on plant ethylene signaling in agricultural plants may pave the way for coping with climate change in future.

The Molecular Basis of Age-Modulated Plant De Novo Root Regeneration Decline in Arabidopsis thaliana

Plants possess a regeneration capacity that enables them to survive after wounding. For example, detached Arabidopsis thaliana leaves are able to form adventitious roots from their cutting sites even in the absence of exogenous hormone supplements, as process termed de novo root regeneration (DNRR). Wounding rapidly induces auxin biosynthesis at the cutting sites and then elicits a signaling cascade to promote cell fate transitions and finally generate the adventitious roots. However, rooting rates in older plants are much lower than in younger leaf explants. In this review, we highlight the recent breakthroughs in the understanding of DNRR decay in older plants from at least two independent signaling routes: (i) via the accumulation of EIN3 protein in older plants, which directly suppresses expression of WUSCHEL RELATED HOMEOBOX (WOX) genes to inhibit rooting; (ii) the miR156-SPLs-AP2/ERFs pathway, which modulates root regeneration by reducing auxin biosynthesis.

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.