WOX11 and 12 are involved in the first-step cell fate transition during de novo root organogenesis in Arabidopsis

All roads lead to dome: Multicellular dynamics during de novo meristem establishment in shoot regeneration

Shoot apical meristems (SAMs) harbor persistent stem cells and give rise to above-ground organs throughout life. In tissue culture-based shoot regeneration, a subpopulation of pluripotent callus cells is specified into SAMs. How callus cells decide whether or not to become SAMs stands as an important question in developmental biology. Furthermore, the developmental basis underlying the de novo construction of dome-shaped SAMs remained largely unknown. Recent high-resolution analyses have revealed the spatiotemporal dynamics of cell fate determination and meristem establishment during shoot regeneration. Cell fates to become meristem are actively determined through interactions between neighboring cells, rather than by cell-autonomous fate transition. Inter-cell layer communication via mobile signal or mechanical cue may enable meristem construction. By integrating recent insights from the two-step tissue culture system in Arabidopsis together with other shoot regeneration systems, we depict the process of de novo meristem establishment as a dynamic multicellular system.

Regeneration and defense: unveiling the molecular interplay in plants

In both plants and animals, tissue or organ regeneration typically follows wounding, which also activates defense responses against pathogenic microbes and herbivores. Both intrinsic and environmental cues guide the molecular decisions between regeneration and defense. In animal studies, extensive research has highlighted the role of various microbes - including pathogenic, commensal, and beneficial species - in influencing the signaling interplay between immunity and regeneration. Conversely, most plant regeneration studies are conducted under sterile conditions, which leaves a gap in our understanding of how plant innate immunity influences regeneration pathways. Recent findings have begun to elucidate the roles of key defense pathways in modulating plant regeneration and the crosstalk between these two processes. These studies also explore how microbes might influence the molecular choice between defense and regeneration in plants. This review examines the molecular mechanisms governing the balance between plant regeneration and innate immunity, with a focus on the emerging role of aging and microbial interactions in shaping these processes.

Dynamic changes in DNA methylation play a regulatory role in gene expression during the formation of callus from immature barley embryos

BACKGROUND

Inducing embryogenic callus with regenerative potential is a pivotal step in barley transformation. Our previous research suggests that epigenetic regulatory factors might influence barley callus formation and regeneration capacity, though the exact mechanisms remain unclear.

RESULTS

In this study, we utilized RNA sequencing (RNA-seq) and whole-genome bisulfite sequencing (WGBS) to examine transcriptional and DNA methylome alterations during callus induction from immature embryos of the barley cultivar Golden Promise. Our findings revealed a slight decline in overall DNA methylation content and distinct 5-methylcytosine (5mC) enrichment patterns in CG, CHG, and CHH sequence contexts within genes and transposable elements. By integrating DNA methylation and transcriptome data, we identified differentially expressed genes (DEGs) associated with differentially methylated regions (DMRs) in the CG (879 DEGs), CHG (229 DEGs), and CHH (2020 DEGs) contexts. Notably, DMRs linked to 210, 94, and 1,214 DEGs were located in the 2 kb upstream regions in the CG, CHG, and CHH contexts, respectively. A negative correlation was observed between promoter methylation levels and transcript abundances of key regeneration-associated genes, such as HvKRP4, HvCYCD1;1, HvSCR, HvRAP2.6L/ERF113, HvWIND4, HvWOX5, HvE2Fa, HvPHV, and HvLBD16. This indicates a regulatory function of DNA methylation in transcriptional regulation during callus induction. Furthermore, treatment with the DNA methylation inhibitor 5-Aza-2'-deoxycytidine (5-Aza-dC) suppressed callus formation. Comparative RNA sequencing analysis between control and treated groups revealed 2,628 and 1,224 DEGs potentially regulated by DNA methylation, at 2- and 9-days post-induction, respectively. These genes were primarily associated with cell cycle and abscisic acid signalling pathways, influenced directly and indirectly by the global reduction in DNA methylation induced by 5-Aza-dC treatment.

CONCLUSIONS

This study provides insights into the intricate relationship between DNA methylation and gene expression during barley callus formation. It could inform future efforts to enhance regeneration and transformation in this significant crop species.

CLINICAL TRIAL NUMBER

Not applicable.

Transcription factor WUSCHEL-related homeobox (WOX) underground revelations: Insights into plant root development

Plant roots are essential for nutrient and water uptake and play a crucial role in plant growth and development. The development of roots is a complex process regulated by numerous factors, among which transcription factors (TFs) like WUSCHEL-related homeobox (WOX) have an essential function. The importance of WOXs in root development cannot be overstated. They act as key regulators in maintaining the balance between cell proliferation and differentiation and ensure the proper formation and function of root tissues. This review comprehensively presents the roles of WOXs in various root development aspects across multiple plant species, including primary, lateral, adventitious, and crown root development, as well as root hair, rhizoid formation, de novo root regeneration, and root apical meristem maintenance. We also discuss how WOXs regulate root development through various mechanisms in different plant species. Overall, this review provides comprehensive insights into the complex regulatory networks governing plant root growth and the importance of WOXs therein. Understanding WOXs in root development can help improve crop root architecture and stress tolerance and provide insights into the regulatory networks of plant root growth, contributing to plant breeding and agricultural productivity.

Genome-Wide Identification of WOX Gene Family in Chimonanthus praecox and a Functional Analysis of CpWUS

Chimonanthus praecox, also known as wintersweet, is a traditional ornamental plant in China. It blooms during the cold winter months and emits a long-lasting fragrance. The WUSCHEL-related homeobox (WOX) transcription factor family is a plant-specific family of homeodomain (HD) transcription factors that plays diverse roles in plant development. We identified 13 WOX family genes (CpWOX1-CpWOX12 and CpWUS) and systematically analysed their physicochemical properties, evolutionary relationships, conserved domains, and expression regulation characteristics. The subcellular localization prediction indicates that all CpWOX proteins are localized in the nucleus and contain a conserved homeobox domain, with the WUS clade specifically containing a WUS-box motif. Phylogenetic analysis revealed that these genes are divided into three evolutionary branches: the WUS, ancient, and intermediate clades. Promoter analysis suggests that CpWOX genes may be involved in hormone responses, abiotic stress, developmental regulation, and encodes a nuclear-localised protein with self-activating activity. It is highly expressed in the stamen and root and is induced by low and high temperatures, salt stress, and methyl jasmonate. This study revealed the evolutionary characteristics of the WOX family genes in wintersweet and the function of CpWUS in regulating flowering time and root development, providing a theoretical basis for understanding the developmental regulatory mechanisms in wintersweet.

Super pan-genome-wide analysis of Hordeum WOX genes and identification of key members conferring salt stress tolerance

The WUSCHEL-related homeobox (WOX) is a transcription factor family specific to plants, playing a key role in the initiation and maintenance of meristematic tissue, organ formation and response to abiotic stress. Here we identified 14-15 WOX genes in four Hordeum species, conducted their phylogenetic tree, determined their chromosome locations and gene structures, and analyzed their collinearity and cis-acting elements in promoters. Presence Absence Variation (PAV) analysis revealed that certain WOX genes in the four Hordeum species were lost and expanded. Duplication analysis discovered five types of duplications contributing to the formation of WOX genes, with dispersed duplication (DSD) being the main type in four Hordeum species. WOXs belonging to DSD exhibited a high number of long terminal repeat retrotransposons (LTR-RTs), indicating the potential role of LTR-RTs in the formation of WOX genes of the DSD type. Evaluation of Ka/Ks values showed that all WOX genes have undergone purification selection, with varying degrees among different clades of WOX genes. Furthermore, through pan-transcriptome analysis and quantitative experiments, we identified a common gene clade and the WOX13 co-expression networks responding to saline stress. Survival ratio statistics of Arabidopsis thaliana complementation lines under salt treatment suggested that HvWOX13 may play a crucial role in regulating salt tolerance. These findings provide new insights into evolutionary studies of WOX gene family and offer valuable gene resources for breeding crops with enhanced salt stress resistance.

Cell wall remodeling during plant regeneration

Plant regeneration is the process during which differentiated tissues or cells can reverse or alter their developmental trajectory to repair damaged tissues or form new organs. In the plant regeneration process, the cell wall not only functions as a foundational barrier and scaffold supporting plant cells but also influences cell fates and identities. Cell wall remodeling involves the selective degradation of certain cell wall components or the integration of new components. Recently, accumulating evidence has underscored the importance of cell wall remodeling in plant regeneration. Wounding signals, transmitted by transcription factors, trigger the expressions of genes responsible for cell wall loosening, which is essential for tissue repair. In de novo organ regeneration and somatic embryogenesis, phytohormones orchestrate a transcriptional regulatory network to induce cell wall remodeling, which promotes cell fate reprogramming and organ formation. This review summarizes the effects of cell wall remodeling on various regenerative processes and provides novel insights into the future research of uncharacterized roles of cell wall in plant regeneration.

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

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

JA and ABA signaling pathways converge to protect plant regeneration in stress conditions

In cuttings, detached leaves or stems are exposed to many stresses during the root regeneration process. Here, we show that the detached Arabidopsis thaliana leaf can tolerate mild osmotic stress and still regenerate roots. Under stress conditions, wounding and stress upregulate the jasmonate (JA) signaling pathway transcription factor gene MYC2 and the abscisic acid (ABA) signaling pathway transcription factor gene ABA INSENSITIVE5 (ABI5). The MYC2-ABI5 complex upregulates the expression of β-GLUCOSIDASE18 (BGLU18), which releases ABA from ABA glucose ester, resulting in ABA accumulation in the detached leaf. Mutations in MYC2, ABI5, and BGLU18 lead to the loss of stress tolerance and defects in root regeneration under osmotic stress. The successive application of JA and ABA can enhance the root regeneration ability in Arabidopsis and poplar cuttings. Overall, the JA-mediated wound signaling pathway and the ABA-mediated stress signaling pathway collaboratively amplify ABA signals to protect root regeneration under stress conditions.

Tracing meristem cell lineages during plant development and regeneration by the all-in-one CRE/LOX system

The root apical meristem (RAM) and the shoot apical meristem (SAM), which contain stem cells and their lineages, are the centers for underground and aboveground organ formation in vascular plants. Accurately tracing stem cell lineage is important to understand how the RAM and SAM are formed and how they give rise to new organs. Here, we introduce the all-in-one CRE/LOX system, which is assembled in a single plasmid and can be used to efficiently trace cell lineage during de novo formation of meristems and cell differentiation within meristems in Arabidopsis thaliana. Using the CRE/LOX-GUS system driven by the WUSCHEL-RELATED HOMEOBOX5 (WOX5) promoter (i.e., WOX5pro-CRE/LOX-GUS), we show that cell division of the quiescent center (QC) within the stem cell niche of the RAM might replenish initial/stem cells in plants grown on mannitol-containing medium or in soil. The results obtained using WOX5pro-CRE/LOX-GUS also show that a group of shoot progenitor cells acts together to initiate the SAM during de novo shoot regeneration from callus in tissue culture. We also demonstrate the use of the CRE/LOX-RUBY system for real-time in vivo tracing of cell lineages in live organs. Overall, this paper not only introduces the all-in-one CRE/LOX tool, but also reveals the cell lineages during meristem development and regeneration.

Investigating the Mechanisms of Adventitious Root Formation in Semi-Tender Cuttings of Prunus mume: Phenotypic, Phytohormone, and Transcriptomic Insights

Mei (Prunus mume Sieb. et Zucc.) is a rare woody species that flowers in winter, yet its large-scale propagation is limited by the variable ability of cuttings to form adventitious roots (ARs). In this study, two cultivars were compared: P. mume 'Xiangxue Gongfen' (GF), which roots readily, and P. mume 'Zhusha Wanzhaoshui' (ZS), which is more recalcitrant. Detailed anatomical observations revealed that following cutting, the basal region expanded within 7 days, callus tissues had appeared by 14 days, and AR primordia emerged between 28 and 35 days. Notably, compared to the recalcitrant cultivar ZS, the experimental cultivar GF exhibited significantly enhanced callus tissue formation and AR primordia differentiation. Physiological analyses showed that the initial IAA concentration was highest at day 0, whereas cytokinin (tZR) and gibberellin (GA1) levels peaked at 14 days, with ABA gradually decreasing over time, resulting in increased IAA/tZR and IAA/GA1 ratios during the rooting process. Transcriptomic profiling across these time points identified significant upregulation of key genes (e.g., PmPIN3, PmLOG2, PmCKX5, PmIAA13, PmLAX2, and PmGA2OX1) and transcription factors (PmWOX4, PmSHR, and PmNAC071) in GF compared to ZS. Moreover, correlation analyses revealed that PmSHR expression is closely associated with IAA and tZR levels. Overexpression of PmSHR in tobacco further validated its role in enhancing lateral root formation. Together, these findings provide comprehensive insights into the temporal, hormonal, and genetic regulation of AR formation in P. mume, offering valuable strategies for improving its propagation.

Integration of Phytomelatonin Signaling With Jasmonic Acid in Wound-induced Adventitious Root Regeneration

Plants exhibit remarkable regenerative abilities under stress conditions like injury, herbivory, and damage from harsh weather, particularly through adventitious root formation. They have sophisticated molecular mechanisms to recognize and respond to wounding. Jasmonic acid (JA), a wound hormone, triggers auxin synthesis to stimulate root regeneration. Melatonin (MT), structurally similar to auxin, also significantly influences root induction, but its specific mechanism is unclear. Phytomelatonin's signal transduction is discovered in wound-induced root formation, identifying SlPMTR1/2 as phytomelatonin receptors, transmitting signals to SHOOT BORNE ROOTLESS 1 (SlSBRL1), a key regulator of wound-induced root regeneration, via the G protein α subunit 1 (SlGPA1). Additionally, SlPMTR1/2 is activated by JA, and targeted by SlMYC2. Overall, the specific mechanisms of phytomelatonin on wound-induced root regeneration is uncovered and revealed a crosstalk between phytomelatonin and JA, offering new insights into plant repair mechanisms.

Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Barley Reveals the Potential Role of HvWOX8 in Salt Tolerance

The WUSCHEL-related homeobox (WOX) belongs to a plant-specific transcription factor gene family that plays crucial roles in plant growth and development. Barley ranks as the fourth global cereal crop and is recognized as a model crop for the study of cereal genetics. However, genome-wide characterization, functional validation, and stress-related studies of the WOX gene family in barley remain limited, hindering efforts to leverage their potential for improving salt tolerance and regeneration efficiency in breeding programs. In this study, we identified 12 HvWOX genes assigned from chromosome 1 to chromosome 5. Phylogenetic analysis revealed that these HvWOX genes can be classified into three clades (WUS, ancient, and intermediate). Gene structure analysis revealed that the exon numbers of HvWOX genes varied in the WUS and intermediate clades but were highly conserved in the ancient clade. Tissue-specific analysis revealed that the most common HvWOX genes were highly expressed in reproductive tissues such as anthers or ovaries. Cis-element analysis suggested that there were multiple stress- and hormone-responsive elements in the HvWOX gene promoters. In addition, overexpression of HvWOX8 in Arabidopsis significantly enhanced root elongation under salt stress (50-100 mM NaCl), suggesting its direct role in salt tolerance. Transcriptomic analysis further revealed that HvWOX8 modulates hormone signaling and electron transfer pathways during ATP synthesis under stress conditions. In conclusion, our results provided a comprehensive understanding of the gene characteristics, expression patterns, and potential roles of barley WOX genes.

Transcriptome-wide identification and characterization of WUSCHEL-related homeobox (WOX) gene family in Pinus yunnanensis

WUSCHEL-related homeobox (WOX), a specific gene family in plants, plays a critical role during stem cell regulation, plant regeneration and upgrowth. However, our understanding of WOX functions in conifers is limited compared to angiosperms. To address this gap, we investigated the presence, expression profiles and protein characteristics of WOX gene in P. yunnanensis. Our findings revealed that 10 PyWOX genes were dispersed across three existing clades, and their expression profiles were presented in specific developmental stages and tissues. The ancient-clade members (PyWOX13, PyWOXG, PyWOXA) exhibited constitutive expressions in most tissues and developmental stages, indicating that they are the oldest and conserved WOX genes. Members of the intermediate-clade (PyWOXB, PyWOXE) were primarily expressed during callus formation and seed germination, suggesting a role in promoting embryogenesis and plant regeneration. Most members of WUS-clade (PyWUS, PyWOX3, PyWOX4, PyWOX5, PyWOXX) showed high transcripts level in cluster buds, which may be related to meristematic development and the formation of axillary meristems. The self-activation assay demonstrated that PyWOX4 has transcriptional activation activity. Our study also suggested that there were highly conserved and clear orthologs of WOX genes present in Pinus. Together, these findings provide a foundation for further clarifying the function and regulatory mechanism of WOX genes in P. yunnanensis growth and development.

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

MAIN CONCLUSION

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

Unlocking regeneration potential: harnessing morphogenic regulators and small peptides for enhanced plant engineering

Plant genetic transformation is essential for understanding gene functions and developing improved crop varieties. Traditional methods, often genotype-dependent, are limited by plants' recalcitrance to gene delivery and low regeneration capacity. To overcome these limitations, new approaches have emerged that greatly improve efficiency and genotype flexibility. This review summarizes key strategies recently developed for plant transformation, focusing on groundbreaking technologies enhancing explant- and genotype flexibility. It covers the use of morphogenic regulators (MRs), stem cell-based methods, and in planta transformation methods. MRs, such as maize Babyboom (BBM) with Wuschel2 (WUS2), and GROWTH-REGULATING FACTORs (GRFs) with their cofactors GRF-interacting factors (GIFs), offer great potential for transforming many monocot species, including major cereal crops. Optimizing BBM/WUS2 expression cassettes has further enabled successful transformation and gene editing using seedling leaves as starting material. This technology lowers the barriers for academic laboratories to adopt monocot transformation systems. For dicot plants, tissue culture-free or in planta transformation methods, with or without the use of MRs, are emerging as more genotype-flexible alternatives to traditional tissue culture-based transformation systems. Additionally, the discovery of the local wound signal peptide Regeneration Factor 1 (REF1) has been shown to enhance transformation efficiency by activating wound-induced regeneration pathways in both monocot and dicot plants. Future research may combine these advances to develop truly genotype-independent transformation methods.

DEMETER DNA demethylase reshapes the global DNA methylation landscape and controls cell identity transition during plant regeneration

BACKGROUND

Plants possess a high potential for somatic cell reprogramming, enabling the transition from differentiated tissue to pluripotent callus, followed by the formation of de novo shoots during plant regeneration. Despite extensive studies on the molecular network and key genetic factors involved in this process, the underlying epigenetic landscape remains incompletely understood.

RESULTS

Here, we explored the dynamics of the methylome and transcriptome during the two-step plant regeneration process. During the leaf-to-callus transition in Arabidopsis Ler, CG methylation shifted across genic regions, exhibiting a similar number of differentially methylated regions (DMRs) for both hypo- and hypermethylation. Pericentromeric regions underwent substantial CG and extensive CHH hypomethylation, alongside some CHG hypermethylation. Upon shoot regeneration from callus, genic regions displayed extensive reconfiguration of CG methylation, while pericentromeric methylation levels highly increased across all cytosine contexts, coinciding with the activation of the RNA-directed DNA methylation (RdDM) pathway. However, mutation in DEMETER (DME) DNA demethylase gene resulted in significant genic CG redistribution and global non-CG hypomethylation in pericentromeric regions, particularly during shoot regeneration. This non-CG hypomethylation observed in dme-2 mutants was, at least partly, due to RdDM downregulation. The dme-2 mutants affected gene expression involved in pluripotency and shoot meristem development, resulting in enhanced shoot regeneration through a reprogrammed state established by pericentromeric hypomethylation compared to wild type.

CONCLUSION

Our study demonstrates epigenetic changes, accompanied by transcriptome alterations, during pluripotency acquisition (leaf-to-callus) and regeneration (callus-to-de novo shoot). Additionally, it highlights the functions of the DME demethylase, particularly its close association with the RdDM pathway, which underlies pericentromeric non-CG methylation maintenance. These results provide important insights into the epigenetic reconfiguration associated with cell identity transition during somatic cell reprogramming.

Physiological and transcriptomic analysis reveal the regulation of adventitious root formation in Cinnamomum parthenoxylon cuttings

Cinnamomum parthenoxylon is a significant essential oil plant in southern China, however, the challenge of rooting cuttings poses a hindrance to its development and widespread cultivation. Adventitious root (AR) formation is a vital mechanism for plants to acclimate to environmental changes, yet the precise regulatory mechanisms governing this process remain largely unknown. This study investigated the morphological, physiological, and transcriptomic alterations during AR formation in C. parthenoxylon. Our findings revealed that the AR in C. parthenoxylon originated from callus tissue. Nutrients, enzymes, and plant hormones exerted crucial functions in cutting propagation, with some gradually shifting roles in the rooting process until the pivotal stage of root primordium initiation. Analysis of differentially expressed genes (DEGs) highlighted the significance of auxin, ethylene, and plant wound signaling pathways in regulating AR. Furthermore, 14 hub genes were identified through protein-protein interaction (PPI) networks, shedding light on key molecular players. Understanding the dynamics involved in AR formation enhances our comprehension of the regulatory mechanisms, offering insights for optimizing cutting treatment methods.

Depletion of Gibberellin Signaling Up-Regulates LBD16 Transcription and Promotes Adventitious Root Formation in Arabidopsis Leaf Explants

Adventitious root (AR) formation in plants originates from non-root organs such as leaves and hypocotyls. Auxin signaling is essential for AR formation, but the roles of other phytohormones are less clear. In Arabidopsis, at least two distinct mechanisms can produce ARs, either from hypocotyls as part of the general root architecture or from wounded organs during de novo root regeneration (DNRR). In previous reports, gibberellin acid (GA) appeared to play reverse roles in both types of ARs, since GA treatment blocks etiolation-induced AR formation from hypocotyls, whereas GA synthesis and signaling mutants apparently displayed reduced DNRR from detached leaves. In order to clarify this contradiction, we employed the GA biosynthesis inhibitor paclobutrazol (PBZ) and found that PBZ had positive effects on both types of AR formation in Arabidopsis. Consistently, GA treatment had negative effects on both AR formation mechanisms, while loss of GA synthesis and signaling promoted DNRR under our conditions. Our results show that PBZ treatment can rescue declined AR formation in difficult-to-root leaf explants such as erecta receptor mutants. Furthermore, transcriptional profiling revealed that PBZ treatment altered GA, brassinosteroids, and auxin responses, which included the up-regulation of LBD16 that is well known for its pivotal role in AR initiation.

Functional Analysis of CLE26 in Controlling De Novo Root Regeneration from Detached Arabidopsis Leaves

De novo root regeneration is the process by which adventitious roots form around the wound site from wounded or detached plant organs. The de novo root regeneration process has been widely exploited in cutting technology used for vegetative propagation. Here, we employed detached leaf explants from Arabidopsis thaliana to form adventitious roots for studying the process of de novo root regeneration. GUS staining showed that the expression of CLAVATA3/EMBRYO SURROUNDING REGION-RELATED26(CLE26) was gradually increased surrounding the wound site of leaf explants during adventitious root formation. Semi-thin sections further showed that the expression pattern of CLE26 was closely linked to the formation of adventitious roots. Next, genetic analyses confirmed that the CLE26 gene was involved in de novo root regeneration. Furthermore, RNA sequencing (RNA-seq) of the leaf explants revealed that stress-related genes might be involved in CLE26-mediated adventitious root formation. Specifically, genes associated with the hydrogen peroxide catabolic process and oxidative stress response were predominantly upregulated in the cle26 mutant. In contrast, genes involved in the response to salicylic acid were largely downregulated in the cle26 mutant. Overall, our study indicates that the mutation in CLE26 might upregulate the expression of genes involved in reactive oxygen species metabolism or suppress the expression of genes associated with salicylic acid synthesis, thus promoting the formation of adventitious roots. These findings suggest that CLE26 is a potential candidate for the genetic improvement of adventitious rooting in cuttings.

The Identification and Characterization of WOX Family Genes in Coffea arabica Reveals Their Potential Roles in Somatic Embryogenesis and the Cold-Stress Response

WUSCHEL-related homeobox (WOX) genes play significant roles in plant development and stress responses. Difficulties in somatic embryogenesis are a significant constraint on the uniform seedling production and genetic modification of Coffea arabica, hindering efforts to improve coffee production in Yunnan, China. This study comprehensively analyzed WOX genes in three Coffea species. A total of 23 CaWOXs, 12 CcWOXs, and 10 CeWOXs were identified. Transcriptomic profile analysis indicated that about half of the CaWOX genes were actively expressed during somatic embryogenesis. The most represented CaWOXs were CaWOX2a, CaWOX2b, CaWOX8a, and CaWOX8b, which are suggested to promote the induction and development of the embryogenic callus, whereas CaWOX13a and CaWOX13b are suggested to negatively impact these processes. Co-expression analysis revealed that somatic embryogenesis-related CaWOXs were co-expressed with genes involved in embryo development, post-embryonic development, DNA repair, DNA metabolism, phenylpropanoid metabolism, secondary metabolite biosynthesis, and several epigenetic pathways. In addition, qRT-PCR showed that four WOX genes responded to cold stress. Overall, this study offers valuable insights into the functions of CaWOX genes during somatic embryogenesis and under cold stress. The results suggest that certain WOX genes play distinct regulatory roles during somatic embryogenesis, meriting further functional investigation. Moreover, the cold-responsive genes identified here are promising candidates for further molecular analysis to assess their potential to enhance cold tolerance.

The emerging roles of WOX genes in development and stress responses in woody plants

Woody plants represent the world largest biomass which are actually developed from small amounts of stem cells. The programing and re-programing of these stem cells significantly affect the plastic development and environmental adaptation of woody plants. The WUSCHEL-related homeobox (WOX) genes constitute a family of plant-specific homeodomain transcription factors that perform key functions in plant development, including embryonic patterning, stem-cell maintenance, and organ formation. There also is emerging evidence supporting their participation in stress responses, although whether these functions are stem-cell-mediated is unknown. Past research has mainly focused on the WOX protein family in non-woody plants, such as Arabidopsis thaliana and Oryza sativa. The roles of WOX genes in woody plant stem cell regulation are less understood, partially due to their long life cycles, large physical sizes and challenges in obtaining transgenic trees. Recent advancements in transformation protocols in various tree species have begun to reveal the functions of WOXs in woody plants. Here, we summarize current understanding of WOXs in embryogenesis, organogenesis, and stress responses, highlighting an emerging molecular network centered on WOXs in woody plants.

Plant Growth Regulators: An Overview of WOX Gene Family

The adaptation of plants to land requires sophisticated biological processes and signaling. Transcription factors (TFs) regulate several cellular and metabolic activities, as well as signaling pathways in plants during stress and growth and development. The WUSCHEL-RELATED HOMEOBOX (WOX) genes are TFs that are part of the homeodomain (HD) family, which is important for the maintenance of apical meristem, stem cell niche, and other cellular processes. The WOX gene family is divided into three clades: ancient, intermediate, and modern (WUS) based on historical evolution linkage. The number of WOX genes in the plant body increases as plants grow more complex and varies in different species. Numerous research studies have discovered that the WOX gene family play a role in the whole plant's growth and development, such as in the stem, embryo, root, flower, and leaf. This review comprehensively analyzes roles of the WOX gene family across various plant species, highlighting the evolutionary significance and potential biotechnological applications in stress resistance and crop improvement.

Bioenergy sorghum nodal root bud development: morphometric, transcriptomic and gene regulatory network analysis

Bioenergy sorghum's large and deep nodal root system and associated microbiome enables uptake of water and nutrients from and deposition of soil organic carbon into soil profiles, key contributors to the crop's resilience and sustainability. The goal of this study was to increase our understanding of bioenergy sorghum nodal root bud development. Sorghum nodal root bud initiation was first observed on the stem node of the 7th phytomer below the shoot apex. Buds were initiated near the upper end of the stem node pulvinus on the side of the stem opposite the tiller bud, then additional buds were added over the next 6-8 days forming a ring of 10-15 nascent nodal root buds around the stem. Later in plant development, a second ring of nodal root buds began forming on the 17th stem node immediately above the first ring of buds. Overall, nodal root bud development can take ~40 days from initiation to onset of nodal root outgrowth. Nodal root buds were initiated in close association with vascular bundles in the rind of the pulvinus. Stem tissue forming nascent nodal root buds expressed sorghum homologs of genes associated with root initiation (WOX4), auxin transport (LAX2, PIN4), meristem activation (NGAL2), and genes involved in cell proliferation. Expression of WOX11 and WOX5, genes involved in root stem niche formation, increased early in nodal root bud development followed by genes encoding PLTs, LBDs (LBD29), LRP1, SMB, RGF1 and root cap LEAs later in development. A nodal root bud gene regulatory network module expressed during nodal root bud initiation predicted connections linking PFA5, SPL9 and WOX4 to genes involved in hormone signaling, meristem activation, and cell proliferation. A network module expressed later in development predicted connections among SOMBRERO, a gene involved in root cap formation, and GATA19, BBM, LBD29 and RITF1/RGF1 signaling. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for understanding the regulation of sorghum nodal root bud formation and development.

Novel mechanism of MicroRNA408 in callus formation from rice mature embryo

Mature embryos are the main explants of tissue culture used in rice transgenic technology. However, the mechanism of mature embryo callus formation remains unclear. In this study, a microRNA-mediated gene regulatory network of rice calli was established using degradome sequencing. We identified a microRNA, OsmiR408, that regulates the formation of the callus derived from the mature rice embryo. OsUCLACYANIN 30 (OsUCL 30), a target gene of OsmiR408, was the most abundant cleavage mRNA in rice callus. OsUCL17 was verified as a target gene of OsmiR408 using RNA ligase-mediated 5'-RACE. In analysis of the OsmiR408 promoter reporter line and pri-miR408 transcript level, the promoter activity and transcript level of MIR408 were increased dramatically during callus formation. In phenotypic observations, OsmiR408 knockout caused severe defects in mature embryo callus formation, whereas OsmiR408 overexpression promoted callus formation. Transcriptome analysis demonstrated that OsUCLs and certain genes related to the plant hormone signal transduction and phenylpropanoid-flavonoid biosynthesis pathway had different differential expression patterns between OsmiR408 knockout and overexpression calli. Thus, OsmiR408 may regulate callus formation mainly by affecting plant hormone signal transduction and phenylpropanoid-flavonoid biosynthesis pathway. Our findings provide insight into OsmiR408/UCLs module function in callus formation.

WOX11-mediated cell size control in Arabidopsis attenuates growth and fecundity of endoparasitic cyst nematodes

Cyst nematodes establish permanent feeding structures called syncytia inside the host root vasculature, disrupting the flow of water and minerals. In response, plants form WOX11-mediated adventitious lateral roots at nematode infection sites. WOX11 adventitious lateral rooting modulates tolerance to nematode infections; however, whether this also benefits nematode parasitism remains unknown. Here, we report on bioassays using a 35S::WOX11-SRDX transcriptional repressor mutant to investigate whether WOX11 adventitious lateral rooting promotes syncytium development and thereby female growth and fecundity. Moreover, we chemically inhibited cellulose biosynthesis to verify if WOX11 directly modulates cell wall plasticity in syncytia. Finally, we performed histochemical analyses to test if WOX11 mediates syncytial cell wall plasticity via reactive oxygen species (ROS). Repression of WOX11-mediated transcription specifically enhanced the radial expansion of syncytial elements, increasing both syncytium size and female offspring. The enhanced syncytial hypertrophy observed in the 35S::WOX11-SRDX mutant could be phenocopied by chemical inhibition of cellulose biosynthesis and was associated with elevated levels of ROS at nematode infection sites. We, therefore, conclude that WOX11 restricts radial expansion of nematode-feeding structures and female growth and fecundity, likely by modulating ROS-mediated cell wall plasticity mechanisms. Remarkably, this novel role of WOX11 in plant cell size control is distinct from WOX11 adventitious lateral rooting underlying disease tolerance.

The LOB domain protein, a novel transcription factor with multiple functions: A review

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein, named for its LATERAL ORGAN BOUNDARIES (LOB) domain, is a member of a class of specific transcription factors commonly found in plants and is absent from all other groups of organisms. LBD TFs have been systematically identified in about 35 plant species and are involved in regulating various aspects of plant growth and development. However, research on the signaling network and regulatory functions of LBD TFs is insufficient, and only a few members have been studied. Moreover, a comprehensive review of these existing studies is lacking. In this review, the structure, regulatory mechanism and function of LBD TFs in recent years were reviewed in order to better understand the role of LBD TFs in plant growth and development, and to provide a new perspective for the follow-up study of LBD TFs.

A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis

The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement. This developmental process incorporates a series of cell fate transitions and reprogramming. However, our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited. Here, we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0, 1, and 4 days, and the construction of a detailed single-cell transcriptional atlas of the callus induction process. We identify the cell types responsible for initiating the early callus: lateral root primordium-initiating (LRPI)-like cells and quiescent center (QC)-like cells. LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia. We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells. QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration. We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions. Overall, our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation, significantly improving our understanding of callus formation.

A point mutation in the IAA14 promoter enhances callus formation and regeneration

Callus formation induced by auxin accumulation is considered the first step of in vitro plant regeneration. In Arabidopsis, degradation of the Aux/IAA protein, IAA14, in response to auxin signaling, which activates the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 along with a series of downstream transcription factors, also plays a critical role in this process. However, the specific mechanism by which auxin regulates callus formation remains unclear. By screening mutant library in the solitary root 1 (iaa14/slr) Arabidopsis background we obtained the callus formation related 2 (cfr2) mutant. The cfr2 mutant exhibited a stronger capacity for callus formation, as well as lateral root and adventitious root regeneration from leaf explants than wild type (WT) seedlings, but did not recover gravitropism capability. The auxin signal in cfr2 was significantly enhanced, and the expression of some downstream transcription factors was increased. Map-based cloning, whole genome resequencing, and phenotypic complementation experiments showed that the phenotypes observed in the cfr2 mutant were caused by a point mutation in the IAA14 promoter region. This mutation, which is predicted to disrupt the binding of LBD16, LBD19, and LBD30 to the IAA14 promoter, changed the expression pattern of IAA14 in cfr2. Taken together, our results identified a new mutation in the IAA14 promoter region, which affects the expression pattern of IAA14 and in turn its ability to control plant regeneration.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01493-y.

Genome mining of WOX-ARF gene linkage in Machilus pauhoi underpinned cambial activity associated with IAA induction

As an upright tree with multifunctional economic application, Machilus pauhoi is an excellent choice in modern forestry from Lauraceae. The growth characteristics is of great significance for its molecular breeding and improvement. However, there still lack the information of WUSCHEL-related homeobox (WOX) and Auxin response factor (ARF) gene family, which were reported as specific transcription factors in plant growth as well as auxin signaling. Here, a total of sixteen MpWOX and twenty-one MpARF genes were identified from the genome of M. pauhoi. Though member of WOX conserved in the Lauraceae, MpWOX and MpARF genes were unevenly distributed on 12 chromosomes as a result of region duplication. These genes presented 45 and 142 miRNA editing sites, respectively, reflecting a potential post-transcriptional restrain. Overall, MpWOX4, MpWOX13a, MpWOX13b, MpARF6b, MpARF6c, and MpARF19a were highly co-expressed in the vascular cambium, forming a working mode as WOX-ARF complex. MpWOXs contains typical AuxRR-core and TGA-element cis-acting regulatory elements in this auxin signaling linkage. In addition, under IAA and NPA treatments, MpARF2a and MpWOX1a was highly sensitive to IAA response, showing significant changes after 6 hours of treatment. And MpWOX1a was significantly inhibited by NPA treatment. Through all these solid analysis, our findings provide a genetic foundation to growth mechanism analysis and further molecular designing breeding in Machilus pauhoi.

MpANT regulates meristem development in Marchantia polymorpha

Meristems are crucial for organ formation, but our knowledge of their molecular evolution is limited. Here, we show that AINTEGUMENTA (MpANT) in the euANT branch of the APETALA2-like transcription factor family is essential for meristem development in the nonvascular plant Marchantia polymorpha. MpANT is expressed in the thallus meristem. Mpant mutants show defects to maintain meristem identity and undergo meristem duplication, while MpANT overexpressers show ectopic thallus growth. MpANT directly upregulates MpGRAS9 in the SHORT-ROOT (SHR) branch of the GRAS family. In the vascular plant Arabidopsis thaliana, the euANT-branch genes PLETHORAs (AtPLTs) and AtANT are involved in the formation and maintenance of root/shoot apical meristems and lateral organ primordia, and AtPLTs directly target SHR-branch genes. In addition, euANTs bind through a similar DNA-binding motif to many conserved homologous genes in M. polymorpha and A. thaliana. Overall, the euANT pathway has an evolutionarily conserved role in meristem development.

Genome-Wide Analysis of the WOX Family and Its Expression Pattern in Root Development of Paeonia ostii

Tree peony (Paeonia suffruticosa Andr.) is a woody plant with high ornamental, medicinal, and oil values. However, its low rooting rate and poor rooting quality are bottleneck issues in the micropropagation of P. ostii. The WUSCHEL-related homeobox (WOX) family plays a crucial role in root development. In this study, based on the screening of the genome and root transcriptome database, we identified ten WOX members in P. ostii. Phylogenetic analysis revealed that the ten PoWOX proteins clustered into three major clades, the WUS, intermediate, and ancient clade, respectively. The conserved motifs and tertiary structures of PoWOX proteins located in the same clade exhibited higher similarity. The analysis of cis-regulatory elements in the promoter indicated that PoWOX genes are involved in plant growth and development, phytohormones, and stress responses. The expression analysis revealed that PoWOX genes are expressed in distinct tissues. PoWOX4, PoWOX5, PoWOX11, and PoWOX13b are preferentially expressed in roots at the early stage of root primordium formation, suggesting their role in the initiation and development of roots. These results will provide a comprehensive reference for the evolution and potential function of the WOX family and offer guidance for further study on the root development of tree peony.

ESR2-HDA6 complex negatively regulates auxin biosynthesis to delay callus initiation in Arabidopsis leaf explants during tissue culture

Plants exhibit an astonishing ability to regulate organ regeneration upon wounding. Excision of leaf explants promotes the biosynthesis of indole-3-acetic acid (IAA), which is polar-transported to excised regions, where cell fate transition leads to root founder cell specification to induce de novo root regeneration. The regeneration capacity of plants has been utilized to develop in vitro tissue culture technologies. Here, we report that IAA accumulation near the wounded site of leaf explants is essential for callus formation on 2,4-dichlorophenoxyacetic acid (2,4-D)-rich callus-inducing medium (CIM). Notably, a high concentration of 2,4-D does not compensate for the action of IAA because of its limited efflux; rather, it lowers IAA biosynthesis via a negative feedback mechanism at an early stage of in vitro tissue culture, delaying callus initiation. The auxin negative feedback loop in CIM-cultured leaf explants is mediated by an auxin-inducible APETALA2 transcription factor, ENHANCER OF SHOOT REGENERATION 2 (ESR2), along with its interacting partner HISTONE DEACETYLASE 6 (HDA6). The ESR2-HDA6 complex binds directly to, and removes the H3ac mark from, the YUCCA1 (YUC1), YUC7, and YUC9 loci, consequently repressing auxin biosynthesis and inhibiting cell fate transition on 2,4-D-rich CIM. These findings indicate that negative feedback regulation of auxin biosynthesis by ESR2 and HDA6 interferes with proper cell fate transition and callus initiation.

A method of genetic transformation and gene editing of succulents without tissue culture

Succulents, valued for their drought tolerance and ornamental appeal, are important in the floriculture market. However, only a handful of succulent species can be genetically transformed, making it difficult to improve these plants through genetic engineering. In this study, we adapted the recently developed cut-dip-budding (CDB) gene delivery system to transform three previously recalcitrant succulent varieties - the dicotyledonous Kalanchoe blossfeldiana and Crassula arborescens and the monocotyledonous Sansevieria trifasciata. Capitalizing on the robust ability of cut leaves to regenerate shoots, these plants were successfully transformed by directly infecting cut leaf segments with the Agrobacterium rhizogenes strain K599. The transformation efficiencies were approximately 74%, 5% and 3.9%-7.8%, respectively, for K. blossfeldiana and C. arborescens and S. trifasciata. Using this modified CDB method to deliver the CRISPR/Cas9 construct, gene editing efficiency in K. blossfeldiana at the PDS locus was approximately 70%. Our findings suggest that succulents with shoot regeneration ability from cut leaves can be genetically transformed using the CDB method, thus opening up an avenue for genetic engineering of these plants.

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.

Thermodynamic Analysis of n-Nonadecane (C19H40)/1-Octadecanol (C18H37OH) Blends

The article delves into the intricate phase transitions of 1-Octadecanol and n-Nonadecane within a binary system, unveiling dynamic structural changes under varying conditions. Through Fourier transform infrared (FTIR) analysis, specific molecular vibrations were identified, shedding light on the molecular composition and interactions. The study highlights the challenges in detecting subtle phase transitions and emphasises the individuality of molecular behaviours in closely related compounds. The findings underscore the complexity of phase transitions in binary systems and advocate for a nuanced approach to studying molecular structures and behaviours.

Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower

Cauliflower (Brassica oleracea L. var. botrytis) is a distinctive vegetable that supplies a nutrient-rich edible inflorescence meristem for the human diet. However, the genomic bases of its selective breeding have not been studied extensively. Herein, we present a high-quality reference genome assembly C-8 (V2) and a comprehensive genomic variation map consisting of 971 diverse accessions of cauliflower and its relatives. Genomic selection analysis and deep-mined divergences were used to explore a stepwise domestication process for cauliflower that initially evolved from broccoli (Curd-emergence and Curd-improvement), revealing that three MADS-box genes, CAULIFLOWER1 (CAL1), CAL2 and FRUITFULL (FUL2), could have essential roles during curd formation. Genome-wide association studies identified nine loci significantly associated with morphological and biological characters and demonstrated that a zinc-finger protein (BOB06G135460) positively regulates stem height in cauliflower. This study offers valuable genomic resources for better understanding the genetic bases of curd biogenesis and florescent development in crops.

PagWOX11/12a from hybrid poplar enhances drought tolerance by modulating reactive oxygen species

WOX11/12 is a homeobox gene of WOX11 and WOX12 in Arabidopsis that plays important roles in crown root development and growth. It has been reported that WOX11/12 participates in adventitious root (AR) formation and different abiotic stress responses, but the downstream regulatory network of WOX11/12 in poplar remains to be further investigated. In this study, we found that PagWOX11/12a is strongly induced by PEG-simulated drought stress. PagWOX11/12a-overexpressing poplar plantlets showed lower oxidative damage levels, greater antioxidant enzyme activities and reactive oxygen species (ROS) scavenging capacity than non-transgenic poplar plants, whereas PagWOX11/12a dominant repression weakened root biomass accumulation and drought tolerance in poplar. RNA-seq analysis revealed that several differentially expressed genes (DEGs) regulated by PagWOX11/12a are involved in redox metabolism and drought stress response. We used RT-qPCR and yeast one-hybrid (Y1H) assays to validate the downstream target genes of PagWOX11/12a. These results provide new insights into the biological function and molecular regulatory mechanism of WOX11/12 in the abiotic resistance processes of poplar.

ENHANCER OF SHOOT REGENERATION1 promotes de novo root organogenesis after wounding in Arabidopsis leaf explants

Plants have an astonishing ability to regenerate new organs after wounding. Here, we report that the wound-inducible transcription factor ENHANCER OF SHOOT REGENERATION1 (ESR1) has a dual mode of action in activating ANTHRANILATE SYNTHASE ALPHA SUBUNIT1 (ASA1) expression to ensure auxin-dependent de novo root organogenesis locally at wound sites of Arabidopsis (Arabidopsis thaliana) leaf explants. In the first mode, ESR1 interacts with HISTONE DEACETYLASE6 (HDA6), and the ESR1-HDA6 complex directly binds to the JASMONATE-ZIM DOMAIN5 (JAZ5) locus, inhibiting JAZ5 expression through histone H3 deacetylation. As JAZ5 interferes with the action of ETHYLENE RESPONSE FACTOR109 (ERF109), the transcriptional repression of JAZ5 at the wound site allows ERF109 to activate ASA1 expression. In the second mode, the ESR1 transcriptional activator directly binds to the ASA1 promoter to enhance its expression. Overall, our findings indicate that the dual biochemical function of ESR1, which specifically occurs near wound sites of leaf explants, maximizes local auxin biosynthesis and de novo root organogenesis in Arabidopsis.

The Evolution of the WUSCHEL-Related Homeobox Gene Family in Dendrobium Species and Its Role in Sex Organ Development in D. chrysotoxum

The WUSCHEL-related homeobox (WOX) transcription factor plays a vital role in stem cell maintenance and organ morphogenesis, which are essential processes for plant growth and development. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are valued for their ornamental and medicinal properties. However, the specific functions of the WOX gene family in Dendrobium species are not well understood. In our study, a total of 30 WOX genes were present in the genomes of the three Dendrobium species (nine DchWOXs, 11 DhuWOXs, and ten DnoWOXs). These 30 WOXs were clustered into ancient clades, intermediate clades, and WUS/modern clades. All 30 WOXs contained a conserved homeodomain, and the conserved motifs and gene structures were similar among WOXs belonging to the same branch. D. chrysotoxum and D. huoshanense had one pair of fragment duplication genes and one pair of tandem duplication genes, respectively; D. nobile had two pairs of fragment duplication genes. The cis-acting regulatory elements (CREs) in the WOX promoter region were mainly enriched in the light response, stress response, and plant growth and development regulation. The expression pattern and RT-qPCR analysis revealed that the WOXs were involved in regulating the floral organ development of D. chrysotoxum. Among them, the high expression of DchWOX3 suggests that it might be involved in controlling lip development, whereas DchWOX5 might be involved in controlling ovary development. In conclusion, this work lays the groundwork for an in-depth investigation into the functions of WOX genes and their regulatory role in Dendrobium species' floral organ development.

Application of Developmental Regulators for Enhancing Plant Regeneration and Genetic Transformation

Establishing plant regeneration systems and efficient genetic transformation techniques plays a crucial role in plant functional genomics research and the development of new crop varieties. The inefficient methods of transformation and regeneration of recalcitrant species and the genetic dependence of the transformation process remain major obstacles. With the advancement of plant meristematic tissues and somatic embryogenesis research, several key regulatory genes, collectively known as developmental regulators, have been identified. In the field of plant genetic transformation, the application of developmental regulators has recently garnered significant interest. These regulators play important roles in plant growth and development, and when applied in plant genetic transformation, they can effectively enhance the induction and regeneration capabilities of plant meristematic tissues, thus providing important opportunities for improving genetic transformation efficiency. This review focuses on the introduction of several commonly used developmental regulators. By gaining an in-depth understanding of and applying these developmental regulators, it is possible to further enhance the efficiency and success rate of plant genetic transformation, providing strong support for plant breeding and genetic engineering research.

Genome-wide prediction and functional analysis of WOX genes in blueberry

BACKGROUND

WOX genes are a class of plant-specific transcription factors. The WUSCHEL-related homeobox (WOX) family is a member of the homeobox transcription factor superfamily. Previous studies have shown that WOX members play important roles in plant growth and development. However, studies of the WOX gene family in blueberry plants have not been reported.

RESULTS

In order to understand the biological function of the WOX gene family in blueberries, bioinformatics were used methods to identify WOX gene family members in the blueberry genome, and analyzed the basic physical and chemical properties, gene structure, gene motifs, promoter cis-acting elements, chromosome location, evolutionary relationships, expression pattern of these family members and predicted their functions. Finally, 12 genes containing the WOX domain were identified and found to be distributed on eight chromosomes. Phylogenetic tree analysis showed that the blueberry WOX gene family had three major branches: ancient branch, middle branch, and WUS branch. Blueberry WOX gene family protein sequences differ in amino acid number, molecular weight, isoelectric point and hydrophobicity. Predictive analysis of promoter cis-acting elements showed that the promoters of the VdWOX genes contained abundant light response, hormone, and stress response elements. The VdWOX genes were induced to express in both stems and leaves in response to salt and drought stress.

CONCLUSIONS

Our results provided comprehensive characteristics of the WOX gene family and important clues for further exploration of its role in the growth, development and resistance to various stress in blueberry plants.

Histone modification-dependent production of peptide hormones facilitates acquisition of pluripotency during leaf-to-callus transition in Arabidopsis

Chromatin configuration is critical for establishing tissue identity and changes substantially during tissue identity transitions. The crucial scientific and agricultural technology of in vitro tissue culture exploits callus formation from diverse tissue explants and tissue regeneration via de novo organogenesis. We investigated the dynamic changes in H3ac and H3K4me3 histone modifications during leaf-to-callus transition in Arabidopsis thaliana. We analyzed changes in the global distribution of H3ac and H3K4me3 during the leaf-to-callus transition, focusing on transcriptionally active regions in calli relative to leaf explants, defined by increased accumulation of both H3ac and H3K4me3. Peptide signaling was particularly activated during callus formation; the peptide hormones RGF3, RGF8, PIP1 and PIPL3 were upregulated, promoting callus proliferation and conferring competence for de novo shoot organogenesis. The corresponding peptide receptors were also implicated in peptide-regulated callus proliferation and regeneration capacity. The effect of peptide hormones in plant regeneration is likely at least partly conserved in crop plants. Our results indicate that chromatin-dependent regulation of peptide hormone production not only stimulates callus proliferation but also establishes pluripotency, improving the overall efficiency of two-step regeneration in plant systems.

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks in a cell-type specific manner. Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings. This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets, addressing batch effects and conserving biological variance. This integration spans a broad spectrum of tissues, including both below- and above-ground parts. Utilizing a rigorous approach for cell type annotation, we identified 47 distinct cell types or states, largely expanding our current view of plant cell compositions. We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression. Taken together, our study not only offers extensive plant cell atlas exploration that serves as a valuable resource, but also provides molecular insights into gene-regulatory programs that varies from different cell types.

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

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

Transcription factor WOX11 modulates tolerance to cyst nematodes via adventitious lateral root formation

The transcription factor WUSCHEL-RELATED HOMEOBOX 11 (WOX11) in Arabidopsis (Arabidopsis thaliana) initiates the formation of adventitious lateral roots upon mechanical injury in primary roots. Root-invading nematodes also induce de novo root organogenesis leading to excessive root branching, but it is not known if this symptom of disease involves mediation by WOX11 and if it benefits the plant. Here, we show with targeted transcriptional repression and reporter gene analyses in Arabidopsis that the beet cyst nematode Heterodera schachtii activates WOX11-mediated adventitious lateral rooting from primary roots close to infection sites. The activation of WOX11 in nematode-infected roots occurs downstream of jasmonic acid-dependent damage signaling via ETHYLENE RESPONSE FACTOR109, linking adventitious lateral root formation to nematode damage to host tissues. By measuring different root system components, we found that WOX11-mediated formation of adventitious lateral roots compensates for nematode-induced inhibition of primary root growth. Our observations further demonstrate that WOX11-mediated rooting reduces the impact of nematode infections on aboveground plant development and growth. Altogether, we conclude that the transcriptional regulation by WOX11 modulates root system plasticity under biotic stress, which is one of the key mechanisms underlying the tolerance of Arabidopsis to cyst nematode infections.

A high-resolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis

Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive competence of angiosperms. In Arabidopsis (Arabidopsis thaliana), the gynoecium is composed of two fused carpels with different tissues that need to develop and differentiate to form a mature gynoecium and thus the reproductive competence of Arabidopsis. For these reasons, they have become the object of study for floral and fruit development. However, due to the complexity of the gynoecium, specific spatio-temporal tissue expression patterns are still scarce. In this study, we used precise laser-assisted microdissection and high-throughput RNA sequencing to describe the transcriptional profiles of the medial and lateral domain tissues of the Arabidopsis gynoecium. We provide evidence that the method used is reliable and that, in addition to corroborating gene expression patterns of previously reported regulators of these tissues, we found genes whose expression dynamics point to being involved in cytokinin and auxin homeostasis and in cell cycle progression. Furthermore, based on differential gene expression analyses, we functionally characterized several genes and found that they are involved in gynoecium development. This resource is available via the Arabidopsis eFP browser and will serve the community in future studies on developmental and reproductive biology.

Insights into plant regeneration: cellular pathways and DNA methylation dynamics

Plants, known for their immobility, employ various mechanisms against stress and damage. A prominent feature is the formation of callus tissue-a cellular growth phenomenon that remains insufficiently explored, despite its distinctive cellular plasticity compared to vertebrates. Callus formation involves dedifferentiated cells, with a subset attaining pluripotency. Calluses exhibit an extraordinary capacity to reinitiate cellular division and undergo structural transformations, generating de novo shoots and roots, thereby developing into regenerated plants-a testament to the heightened developmental plasticity inherent in plants. In this way, plant regeneration through clonal propagation is a widely employed technique for vegetative reproduction. Thus, exploration of the biological components involved in regaining pluripotency contributes to the foundation upon which methods of somatic plant propagation can be advanced. This review provides an overview of the cellular pathway involved in callus and subsequent de novo shoot formation from already differentiated plant tissue, highlighting key genes critical to this process. In addition, it explores the intricate realm of epigenetic regulatory processes, emphasizing the nuanced dynamics of DNA methylation that contribute to plant regeneration. Finally, we briefly discuss somaclonal variation, examining its relation to DNA methylation, and investigating the heritability of epigenomic changes in crops.

Rare earth elements perturb root architecture and ion homeostasis in Arabidopsis thaliana

Rare earth elements (REEs) are crucial elements for current high-technology and renewable energy advances. In addition to their increasing usage and their low recyclability leading to their release into the environment, REEs are also used as crop fertilizers. However, little is known regarding the cellular and molecular effects of REEs in plants, which is crucial for better risk assessment, crop safety and phytoremediation. Here, we analysed the ionome and transcriptomic response of Arabidopsis thaliana exposed to a light (lanthanum, La) and a heavy (ytterbium, Yb) REE. At the transcriptome level, we observed the contribution of ROS and auxin redistribution to the modified root architecture following REE exposure. We found indications for the perturbation of Fe homeostasis by REEs in both roots and leaves of Arabidopsis suggesting competition between REEs and Fe. Furthermore, we propose putative ways of entry of REEs inside cells through transporters of microelements. Finally, similar to REE accumulating species, organic acid homeostasis (e.g. malate and citrate) appears critical as a tolerance mechanism in response to REEs. By combining ionomics and transcriptomics, we elucidated essential patterns of REE uptake and toxicity response of Arabidopsis and provide new hypotheses for a better evaluation of the impact of REEs on plant homeostasis.