Localized induction of the ATP-binding cassette B19 auxin transporter enhances adventitious root formation in Arabidopsis

The additional phosphosites of PalPIN6b contribute to the modulation of growth and stress responses in poplars

The PIN-FORMED (PIN) family plays vital roles in plant growth and development by orchestrating the distribution of auxin across disparate tissues and organs. As an intermediate member, the functional characteristics of PIN6 proteins remain largely unexplored. Our findings indicate that PIN6s originated in the core angiosperms, and were subsequently lost in monocotyledons. Additionally, we identified a gene duplication event involving PIN6s in the Populus genome. Overexpression of PalPIN6a or PalPIN6b resulted in the inhibition of plant growth and the induction of root malformation, accompanied by local auxin accumulation at the apex and the bent regions of roots, as well as the leaf veins and the leaf margins, where the fluxes of IAA and proton (H+) were significantly suppressed. Furthermore, three additional phosphosites unique to Populus-specific PIN6s, were identified to determine the subcellular localization of PIN6 and to modulate its auxin transport function, thereby increased the plant sensitivity to salt stress. Our results offer new insights into auxin transport mechanisms and stress responses associated with PIN6s, and highlight the role of PalPIN6 phosphorylation.

Effect of exogenous IBA on root morphology and endogenous hormone Metabolic pathways in castor seedlings under Pb/Zn stress

Ricinus communis, a plant of significant industrial value for its oil, is renowned for its robust root system and vigorous growth, qualities that render it an exemplary candidate for the ecological remediation of soils contaminated with heavy metals. The impact of heavy metal stress on root development is characterized by inhibition, a phenomenon whose underlying mechanisms are not fully elucidated. To shed light on this, a study was conducted wherein varying concentrations of the exogenous auxin, IBA, were applied to the roots of Ricinus communis to scrutinize its influence on the endogenous indole-3-acetic acid (IAA) metabolism in seedlings and to delineate the molecular underpinnings of its effects on root morphology. It was observed that IBA significantly amplified the total root surface area by a factor of 1.29 and increased the number of root tips by 40.11% under lead (Pb) stress, and by 32.29% and 91.19%, respectively, under zinc (Zn) stress. These findings underscore the efficacy of IBA in promoting the proliferation of lateral roots in seedlings subjected to stress induced by either Pb or Zn. Further analysis of auxin signaling pathways revealed that the presence of Pb or Zn impedes root growth and lateral root formation by perturbing auxin transporters and signaling molecules. Notably, IBA was found to foster the development of lateral roots by modulating the expression of specific transporters. Post-application of IBA, the endogenous levels of IAA in roots exhibited a 2.80-fold elevation under Pb stress, IBA stimulated the activity of key biosynthetic enzymes, such as RcNIT and RcTAR, culminating in elevated IAA levels. Conversely, under Zn stress, IBA was observed to diminish the levels of RcTAR, which in turn led to reduced IAA levels. These outcomes contribute to a deeper comprehension of the modulatory role of IBA in the context of heavy metal stress.

Identification of the AHP family reveals their critical response to cytokinin regulation during adventitious root formation in apple rootstock

Adventitious root (AR) formation is a bottleneck for vegetative proliferation. In this study, 13 AHP genes (MdAHPs) were identified in the apple genome. Phylogenetic analysis grouped them into 3 clusters (I, II, III), with 4, 4, and 5 genes respectively. The 13 MdAHPs family members were named MdAHP1 to MdAHP13 by chromosome positions. The physicochemical properties, phylogenetic relationship, motifs, and elements of their proteins were also analyzed. The amino acid quantity varied from 60~189 aa, isoelectric point lay between 4.10 and 8.93, and there were 3~7 protein-conserving motifs. Excluding MdAHP6, other members' promoter sequences behaved 2-4 CTK response elements. Additionally, the expression characteristics of MdAHPs family members at key stages of AR formation and in different tissues were also examined with exogenous 6-BA and Lov treatments. The results showed that MdAHP3 might be a key member in AR formation. GUS staining indicated that the activity of the MdAHP3 promoter was also significantly enhanced by CTK treatment. The protein interactions of MdAHP3/MdAHP1 and MdAHP3/MdAHP6 were verified. Compared with WT, 35S::MdAHP3 transgenic poplars inhibited AR formation. The above experimental results suggested that MdAHP3, as a key family member, interacts with MdAHP1 and MdAHP6 proteins to jointly mediate AR formation in apple rootstocks.

Signal transducer of IAA related gene expression induces transporters of hyperaccumulator Arabis alpina for Pb accumulation

Lead (Pb) pollution in soil affects growth of plants. Plants' endogenous hormones play an important role in resistance to Pb of plant. In order to explore the hormone-based mechanisms of Pb accumulationin in hyperaccumulator Arabis alpina, a pot experiment was conducted to analyze the contents of endogenous hormones (auxin, gibberellin, abscisic acid, and cytokinin) and related genes expressions, and Pb contents of A. alpina, as well as the transporter (cation exchangers (CAX), heavy metal ATPases (HMA), and ATP-binding cassette (ABC)) concentrations under foliar spraying of indoleacetic acid (IAA). The results showed that the soluble components (vacuoles) Pb contents under 300 mg kg-1 Pb2+ treatment in shoots and roots increased by 238.8% and 896.3%, respectively, compared to 100 mg kg-1 Pb2+ treatment. The content of endogenous hormones in leaves and roots increased under increasing Pb-treatment concentrations. Compared with the control (0 mg kg-1 Pb2+ treatment), the content of auxin in roots and leaves under the 100 mg kg-1 Pb treatment increased by 176.2% and 585.3%, respectively. The auxin content in xylem saps under the 100 and 300 mg kg-1 Pb treatments increased by 283.1% and 100.3%, respectively. The gene expression related to auxin transport was up-regulated. The expression of three genes related to the auxin-repressed 12.5 kDa protein and the auxin-responsive GH3 (Gretchen Hagen 3) family were down-regulated. Under foliar spraying of IAA, the Pb content in leaves increased by 29.81%, and the Pb content in the symplast sap was higher than that without IAA spraying treatment. The concentrations of CAX and HMA in the roots of A. alpina increased by 9.6% and 8.8%, respectively, with foliar spraying treatment with IAA, while the ABC concentration decreased by 21.9%. In general, the transport and accumulation of Pb is related to the IAA content and the gene expression of AaGDCST, a signal transducer for inducing increased concentrations of the transporter CAX and HMA in the roots of A. alpina. Pb transport via the symplast pathway under IAA application. Regarding the Pb hyperaccumulation of A. alpina, gene AaGDCST has the potential to be utilized as a candidate gene.

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.

Factors governing cellular reprogramming competence in Arabidopsis adventitious root formation

Developmental reprogramming allows for flexibility in growth and adaptation to changing environmental conditions. In plants, wounding events can result in new stem cell niches and lateral organs. Adventitious roots develop from aerial parts of the plant and are regulated by multiple stimuli, including wounding. Here, we find that Arabidopsis thaliana seedlings wounded at the hypocotyl-root junction reprogram certain pericycle cells to produce adventitious roots proximal to the wound site. We have determined that competence for this reprogramming is controlled; basal cells close to the wound site can produce adventitious roots, whereas cells distal from the wound site mostly cannot. We found that altering cytokinin response or indole-3-butyric acid (IBA)-to-(indole-3-acetic acid) IAA conversion resulted in an expanded adventitious root competence zone and delineated the connection between these pathways. Our work highlights the importance of endogenous IBA-derived auxin and its interaction with cytokinin in adventitious root formation and the regenerative properties of plants.

Ocimum kilimandscharicum 4CL11 negatively regulates adventitious root development via accumulation of flavonoid glycosides

4-Coumarate-CoA Ligase (4CL) is an important enzyme in the phenylpropanoid biosynthesis pathway. Multiple 4CLs are identified in Ocimum species; however, their in planta functions remain enigmatic. In this study, we independently overexpressed three Ok4CL isoforms from Ocimum kilimandscharicum (Ok4CL7, -11, and -15) in Nicotiana benthamiana. Interestingly, Ok4CL11 overexpression (OE) caused a rootless or reduced root growth phenotype, whereas overexpression of Ok4CL15 produced normal adventitious root (AR) growth. Ok4CL11 overexpression in N. benthamiana resulted in upregulation of genes involved in flavonoid biosynthesis and associated glycosyltransferases accompanied by accumulation of specific flavonoid-glycosides (kaempferol-3-rhamnoside, kaempferol-3,7-O-bis-alpha-l-rhamnoside [K3,7R], and quercetin-3-O-rutinoside) that possibly reduced auxin levels in plants, and such effects were not seen for Ok4CL7 and -15. Docking analysis suggested that auxin transporters (PINs/LAXs) have higher binding affinity to these specific flavonoid-glycosides, and thus could disrupt auxin transport/signaling, which cumulatively resulted in a rootless phenotype. Reduced auxin levels, increased K3,7R in the middle and basal stem sections, and grafting experiments (intra and inter-species) indicated a disruption of auxin transport by K3,7R and its negative effect on AR development. Supplementation of flavonoids and the specific glycosides accumulated by Ok4CL11-OE to the wild-type N. benthamiana explants delayed the AR emergence and also inhibited AR growth. While overexpression of all three Ok4CLs increased lignin accumulation, flavonoids, and their specific glycosides were accumulated only in Ok4CL11-OE lines. In summary, our study reveals unique indirect function of Ok4CL11 to increase specific flavonoids and their glycosides, which are negative regulators of root growth, likely involved in inhibition of auxin transport and signaling.

Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials

Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.

Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation

Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.

Vanillin, a Newly Discovered Autotoxic Substance in Long-Term Potato Continuous Cropping Soil, Inhibits Plant Growth by Decreasing the Root Auxin Content and Reducing Adventitious Root Numbers

Phenolic acids are known to reduce root biomass and hinder plant development, but it is unclear how they affect potato root traits. Over a 10 year field experiment, we found a negative correlation between the potato yield and continuous cropping years. The substantial reduction in adventitious root (AR) numbers was found to be primarily inhibited by soil vanillin accumulation. The study also found that vanillin had a more pronounced inhibitory effect on the potato yield than commonly reported ferulic acid and p-hydroxybenzoic acid. The decrease in yield was attributed to the reduction of root indole-3-acetic acid (IAA) content, which impeded the formation of AR. Exogenous IAA was found to increase the root IAA content and stimulate AR formation under vanillin stress, ultimately leading to an increase in the potato yield. This study provides valuable insights into potential strategies for the degradation of autotoxic substances and breeding of potato cultivars with enhanced resistance to autotoxicity.

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

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

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

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

SlGH3.15, a member of the GH3 gene family, regulates lateral root development and gravitropism response by modulating auxin homeostasis in tomato

Multiple Gretchen Hagen 3 (GH3) genes have been implicated in a range of processes in plant growth and development through their roles in maintaining hormonal homeostasis. However, there has only been limited study on the functions of GH3 genes in tomato (Solanum lycopersicum). In this work, we investigated the important function of SlGH3.15, a member of the GH3 gene family in tomato. Overexpression of SlGH3.15 led to severe dwarfism in both the above- and below-ground sections of the plant, accompanied by a substantial decrease in free IAA content and reduction in the expression of SlGH3.9, a paralog of SlGH3.15. Exogenous supply of IAA negatively affected the elongation of the primary root and partially restored the gravitropism defects in SlGH3.15-overexpression lines. While no phenotypic change was observed in the SlGH3.15 RNAi lines, double knockout lines of SlGH3.15 and SlGH3.9 were less sensitive to treatments with the auxin polar transport inhibitor. Overall, these findings revealed important roles of SlGH3.15 in IAA homeostasis and as a negative regulator of free IAA accumulation and lateral root formation in tomato.

Mapping of the Classical Mutation rosette Highlights a Role for Calcium in Wound-Induced Rooting

Removal of the root system induces the formation of new roots from the remaining shoot. This process is primarily controlled by the phytohormone auxin, which interacts with other signals in a yet unresolved manner. Here, we study the classical tomato mutation rosette (ro), which lacks shoot-borne roots. ro mutants were severely inhibited in formation of wound-induced roots (WiRs) and had reduced auxin transport rates. We mapped ro to the tomato ortholog of the Arabidopsis thaliana BIG and the mammalians UBR4/p600. RO/BIG is a large protein of unknown biochemical function. In A. thaliana, BIG was implicated in regulating auxin transport and calcium homeostasis. We show that exogenous calcium inhibits WiR formation in tomato and A. thaliana ro/big mutants. Exogenous calcium antagonized the root-promoting effects of the auxin indole-3-acetic-acid but not of 2,4-dichlorophenoxyacetic acid, an auxin analog that is not recognized by the polar transport machinery, and accumulation of the auxin transporter PIN-FORMED1 (PIN1) was sensitive to calcium levels in the ro/big mutants. Consistent with a role for calcium in mediating auxin transport, both ro/big mutants and calcium-treated wild-type plants were hypersensitive to treatment with polar auxin transport inhibitors. Subcellular localization of BIG suggests that, like its mammalian ortholog, it is associated with the endoplasmic reticulum. Analysis of subcellular morphology revealed that ro/big mutants exhibited disruption in cytoplasmic streaming. We suggest that RO/BIG maintains auxin flow by stabilizing PIN membrane localization, possibly by attenuating the inhibitory effect of Ca2+ on cytoplasmic streaming.

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.

The clonal growth in Aconitum carmichaelii Debx

Aconitum carmichaelii Debx. is used as traditional herbal medicine in China, Japan, and other Asian countries. A. carmichaelii has two modes for reproduction: sexual reproduction with seed and vegetative reproduction with vegetative propagules. The vegetative propagules are belowground and invisible. To date, only a handful of studies for the clonal growth are available. In this study, we investigated the clonal growth by anatomical and morphological changes. Results revealed that the axillary bud appeared on the rhizome. Furthermore, the axillary meristem in the axillary bud differentiated a bud upwards and an adventitious root (AR) downwards. The AR expanded to a tuberous root in order to provide the bud nutrients for the new plant. The AR branched LRs. In addition, some lateral roots (LRs) on the AR also swelled. Both the AR and LR were found to follow a similar pattern of development. However, high lignification in the stele region of LRs inhibited further expansion. AR development was attributed to activities of the cambium and meristem cell, starch accumulation, stele lignification, and a polyarch stele. Our study not only provides a better understanding of clonal growth but also provides clues to explore the regulatory mechanisms underlying AR development in A. carmichaelii.

PagWOX11/12a positively regulates the PagSAUR36 gene that enhances adventitious root development in poplar

Adventitious root (AR) development is an extremely complex biological process that is affected by many intrinsic factors and extrinsic stimuli. Some WUSCHEL-related homeobox (WOX) transcription factors have been reported to play important roles in AR development, but their functional relationships with auxin signaling are poorly understood, especially the developmental plasticity of roots in response to adversity stress. Here, we identified that the WOX11/12a-SMALL AUXIN UP RNA36 (SAUR36) module mediates AR development through the auxin pathway in poplar, as well as under salt stress. PagWOX11/12a displayed inducible expression during AR development, and overexpression of PagWOX11/12a significantly promoted AR development and increased salt tolerance in poplar, whereas dominant repression of PagWOX11/12a produced the opposite phenotype. PagWOX11/12a proteins directly bind to the SAUR36 promoter to regulate SAUR36 transcription, and this binding was enhanced during salt stress. Genetic modification of PagWOX11/12a-PagSAUR36 expression revealed that the PagWOX11/12a-PagSAUR36 module is crucial for controlling AR development via the auxin pathway. Overall, our results indicate that a novel WOX11-SAUR-auxin signaling regulatory module is required for AR development in poplar. These findings provide key insights and a better understanding of the involvement of WOX11 in root developmental plasticity in saline environments.

Chemical genetic screening identifies nalacin as an inhibitor of GH3 amido synthetase for auxin conjugation

Auxin inactivation is critical for plant growth and development. To develop plant growth regulators functioning in auxin inactivation pathway, we performed a phenotype-based chemical screen in Arabidopsis and identified a chemical, nalacin, that partially mimicked the effects of auxin. Genetic, pharmacological, and biochemical approaches demonstrated that nalacin exerts its auxin-like activities by inhibiting indole-3-acetic acid (IAA) conjugation that is mediated by Gretchen Hagen 3 (GH3) acyl acid amido synthetases. The crystal structure of Arabidopsis GH3.6 in complex with D4 (a derivative of nalacin) together with docking simulation analysis revealed the molecular basis of the inhibition of group II GH3 by nalacin. Sequence alignment analysis indicated broad bioactivities of nalacin and D4 as inhibitors of GH3s in vascular plants, which were confirmed, at least, in tomato and rice. In summary, our work identifies nalacin as a potent inhibitor of IAA conjugation mediated by group II GH3 that plays versatile roles in hormone-regulated plant development and has potential applications in both basic research and agriculture.

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.

Transcriptome and hormone Analyses reveal that melatonin promotes adventitious rooting in shaded cucumber hypocotyls

Melatonin, a multi-regulatory molecule, stimulates root generation and regulates many aspects of plant growth and developmental processes. To gain insight into the effects of melatonin on adventitious root (AR) formation, we use cucumber seedings subjected to one of three treatments: EW (hypocotyl exposed and irrigated with water), SW (hypocotyl shaded and irrigated with water) and SM (hypocotyl shaded and irrigated with 100 µM melatonin). Under shaded conditions, melatonin induced significant AR formation in the hypocotyl. To explore the mechanism of this melatonin-induced AR formation, we used transcriptome analysis to identify 1296 significant differentially expressed genes (DEGs). Comparing SM with SW, a total of 774 genes were upregulated and 522 genes were downregulated. The DEGs were classified among different metabolic pathways, especially those connected with the synthesis of secondary metabolites, with hormone signal transduction and with plant-pathogen interactions. Analyses indicate exogenous melatonin increased contents of endogenous auxin, jasmonic acid, salicylic acid, cytokinin and abscisic acid levels during AR formation. This study indicates melatonin promotes AR formation in cucumber seedings by regulating the expressions of genes related to hormone synthesis, signaling and cell wall formation, as well as by increasing the contents of auxin, cytokinin, jasmonic acid, salicylic acid and abscisic acid. This research elucidates the molecular mechanisms of melatonin's role in promoting AR formation in the hypocotyl of cucumber seedings under shaded conditions.

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

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

Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus

The AlkB homologs (ALKBH) gene family regulates N⁶-methyladenosine (m⁶A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7-10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana, 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype (P. alba  ×  P. tremula var. glandulosa), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m⁶A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m⁶A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m⁶A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H₂O₂ and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.

Phytochrome-interacting factors orchestrate hypocotyl adventitious root initiation in Arabidopsis

Adventitious roots (ARs) are an important type of plant root and display high phenotypic plasticity in response to different environmental stimuli. It is known that photoreceptors inhibit darkness-induced hypocotyl adventitious root (HAR) formation by directly stabilizing Aux/IAA proteins. In this study, we further report that phytochrome-interacting factors (PIFs) plays a central role in HAR initiation by simultaneously inducing the expression of genes involved in auxin biosynthesis, auxin transport and the transcriptional control of root primordium initiation. We found that, on the basis of their activity downstream of phytochrome, PIFs are required for darkness-induced HAR formation. Specifically, PIFs directly bind to the promoters of some genes involved in root formation, including auxin biosynthesis genes YUCCA2 (YUC2) and YUC6, the auxin influx carrier genes AUX1 and LAX3, and the transcription factors WOX5/7 and LBD16/29, to activate their expression. These findings reveal a previously uncharacterized transcriptional regulatory network underlying HAR formation.

Loss of Multiple ABCB Auxin Transporters Recapitulates the Major twisted dwarf 1 Phenotypes in Arabidopsis thaliana

FK506-BINDING PROTEIN 42/TWISTED DWARF 1 (FKBP42/TWD1) directly regulates cellular trafficking and activation of multiple ATP-BINDING CASSETTE (ABC) transporters from the ABCB and ABCC subfamilies. abcb1 abcb19 double mutants exhibit remarkable phenotypic overlap with twd1 including severe dwarfism, stamen elongation defects, and compact circinate leaves; however, twd1 mutants exhibit greater loss of polar auxin transport and additional helical twisting of roots, inflorescences, and siliques. As abcc1 abcc2 mutants do not exhibit any visible phenotypes and TWD1 does not interact with PIN or AUX1/LAX auxin transporters, loss of function of other ABCB auxin transporters is hypothesized to underly the remaining morphological phenotypes. Here, gene expression, mutant analyses, pharmacological inhibitor studies, auxin transport assays, and direct auxin quantitations were used to determine the relative contributions of loss of other reported ABCB auxin transporters (4, 6, 11, 14, 20, and 21) to twd1 phenotypes. From these analyses, the additional reduction in plant height and the twisted inflorescence, root, and silique phenotypes observed in twd1 compared to abcb1 abcb19 result from loss of ABCB6 and ABCB20 function. Additionally, abcb6 abcb20 root twisting exhibited the same sensitivity to the auxin transport inhibitor 1-napthalthalamic acid as twd1 suggesting they are the primary contributors to these auxin-dependent organ twisting phenotypes. The lack of obvious phenotypes in higher order abcb4 and abcb21 mutants suggests that the functional loss of these transporters does not contribute to twd1 root or shoot twisting. Analyses of ABCB11 and ABCB14 function revealed capacity for auxin transport; however, their activities are readily outcompeted by other substrates, suggesting alternate functions in planta, consistent with a spectrum of relative substrate affinities among ABCB transporters. Overall, the results presented here suggest that the ABCB1/19 and ABCB6/20 pairs represent the primary long-distance ABCB auxin transporters in Arabidopsis and account for all reported twd1 morphological phenotypes. Other ABCB transporters appear to participate in highly localized auxin streams or mobilize alternate transport substrates.

A conserved superlocus regulates above- and belowground root initiation

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

Bradyrhizobium japonicum IRAT FA3 Alters Arabidopsis thaliana Root Architecture via Regulation of Auxin Efflux Transporters PIN2, PIN3, PIN7, and ABCB19

Beneficial rhizobacteria can stimulate changes in plant root development. Although root system growth is mediated by multiple factors, the regulated distribution of the phytohormone auxin within root tissues plays a principal role. Auxin transport facilitators help to generate the auxin gradients and maxima that determine root structure. Here, we show that the plant-growth-promoting rhizobacterial strain Bradyrhizobium japonicum IRAT FA3 influences specific auxin efflux transporters to alter Arabidopsis thaliana root morphology. Gene expression profiling of host transcripts in control and B. japonicum-inoculated roots of the wild-type A. thaliana accession Col-0 confirmed upregulation of PIN2, PIN3, PIN7, and ABCB19 with B. japonicum and identified genes potentially contributing to a diverse array of auxin-related responses. Cocultivation of the bacterium with loss-of-function auxin efflux transport mutants revealed that B. japonicum requires PIN3, PIN7, and ABCB19 to increase lateral root development and utilizes PIN2 to reduce primary root length. Accelerated lateral root primordia production due to B. japonicum was not observed in single pin3, pin7, or abcb19 mutants, suggesting independent roles for PIN3, PIN7, and ABCB19 during the plant-microbe interaction. Our work demonstrates B. japonicum's influence over host transcriptional reprogramming during plant interaction with this beneficial microbe and the subsequent alterations to root system architecture.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Mobile Messenger RNAs in Grafts of Salix matsudana Are Associated with Plant Rooting

Messenger RNAs exchanged between scions and rootstocks of grafted plants seriously affect their traits performance. The study goals were to identify the long-distance mRNA transmission events in grafted willows using a transcriptome analysis and to reveal the possible effects on rooting traits. The results showed that the Salix matsudana variety 9901 has better rooting ability than YJ, which reasonably improved the rooting performance of the heterologous grafts 9901 (scion)/YJ (rootstock). A transcriptome analysis showed that 2948 differentially expressed genes (DEGs) were present in the rootstock of 9901/YJ grafted plants in comparison with YJ/YJ. Among them, 692 were identified as mRNAs moved from 9901 scion based on SNP analysis of two parents. They were mostly 1001–1500 bp, had 40–45% GC contents, or had expression abundance values less than 10. However, mRNAs over 4001 bp, having 50–55% GC contents, or having expression abundance values of 10–20 were preferentially transferred. Eight mRNAs subjected to long-distance trafficking were involved in the plant hormone pathways and may significantly promote the root growth of grafted plants. In summary, heterologous grafts of Salix matsudana could efficiently influence plant rooting of the mRNAs transport from scion to rootstock.

Guard-Cell-Specific Expression of Phototropin2 C-Terminal Fragment Enhances Leaf Transpiration

Phototropins (phot1 and phot2) are plant-specific blue light receptors that mediate chloroplast movement, stomatal opening, and phototropism. Phototropin is composed of the N-terminus LOV1 and LOV2 domains and the C-terminus Ser/Thr kinase domain. In previous studies, 35-P2CG transgenic plants expressing the phot2 C-terminal fragment–GFP fusion protein (P2CG) under the control of 35S promoter showed constitutive phot2 responses, including chloroplast avoidance response, stomatal opening, and reduced hypocotyl phototropism regardless of blue light, and some detrimental growth phenotypes. In this study, to exclude the detrimental growth phenotypes caused by the ectopic expression of P2C and to improve leaf transpiration, we used the PHOT2 promoter for the endogenous expression of GFP-fused P2C (GP2C) (P2-GP2C) and the BLUS1 promoter for the guard-cell-specific expression of GP2C (B1-GP2C), respectively. In P2-GP2C plants, GP2C expression induced constitutive phototropin responses and a relatively dwarf phenotype as in 35-P2CG plants. In contrast, B1-GP2C plants showed the guard-cell-specific P2C expression that induced constitutive stomatal opening with normal phototropism, chloroplast movement, and growth phenotype. Interestingly, leaf transpiration was significantly improved in B1-GP2C plants compared to that in P2-GP2C plants and WT. Taken together, this transgenic approach could be applied to improve leaf transpiration in indoor plants.

Genome-wide identification and expression profiles of ABCB gene family in Chinese hickory (Carya cathayensis Sarg.) during grafting

Chinese hickory (Carya cathayensis Sarg.) is an important nut tree species native to China. Excessive plant height and long juvenile phase has restricted development of its industry. Recently, grafting has been used increasingly in production practice of this species to solve the problems above. Previous studies have proved the importance of auxin during Chinese hickory grafting. However, the function of ATP-binding cassette subfamily B (ABCB) genes during Chinese hickory grafting is less studied. In this study, 23 ABCB genes were identified and characterized in Chinese hickory (CcABCBs). The expression profiles of auxin-related ABCBs among tissues, under auxin-related phytohormone treatments and during grafting were determined. CcABCB proteins were divided into half-size and full-size transporters. Many phytohormone-related cis-acting regulatory elements were detected on the promoters of CcABCB genes. Four CcABCB genes homologous to auxin-related AtABCB1, 6, 19 and 20 in Arabidopsis were selected for expression analysis. The four genes displayed varying expression patterns in different tissues of Chinese hickory. Expressions of the four CcABCB genes were regulated by auxin-related phytohormones to varying degrees. Expression levels of the four genes were significantly changed at different stages of grafting, especially 7 days after grafting, indicating their involvement of auxin homeostasis regulation during grafting. In addition, the expressions of CcABCB1 were regulated by IAA and NPA treatments during grafting in comparison with CK treatment, while expressions of the other 3 CcABCB genes were slightly affected. This study will lay the foundation for understanding the potential regulatory roles of CcABCB genes during Chinese hickory grafting.

PIN3-mediated auxin transport contributes to blue light-induced adventitious root formation in Arabidopsis

Adventitious rooting is a heritable quantitative trait that is influenced by multiple endogenous and exogenous factors in plants, and one important environmental factor required for efficient adventitious root formation is light signaling. However, the physiological significance and molecular mechanism of light underlying adventitious root formation are still largely unexplored. Here, we report that blue light-induced adventitious root formation is regulated by PIN-FORMED3 (PIN3)-mediated auxin transport in Arabidopsis. Adventitious root formation is significantly impaired in the loss-of-function mutants of the blue light receptors, PHOTOROPIN1 (PHOT1) and PHOTOROPIN2 (PHOT2), as well as the phototropic transducer, NON-PHOTOTROPIC HYPOCOTYL3 (NPH3). In addition, blue light enhanced the auxin content in the adventitious root, and the pin3 loss-of-function mutant had a reduced adventitious rooting response under blue light compared to the wild type. The PIN3 protein level was higher in plants treated with blue light than in those in darkness, especially in the hypocotyl pericycle, while PIN3-GFP failed to accumulate in nph3 PIN3::PIN3-GFP. Furthermore, the results showed that PIN3 physically interacted with NPH3, a key transducer in phototropic signaling. Taken together, our study demonstrates that blue light induces adventitious root formation through the phototropic signal transducer, NPH3, which regulates adventitious root formation by affecting PIN3-mediated auxin transport.

Dynamic Hormone Gradients Regulate Wound-Induced de novo Organ Formation in Tomato Hypocotyl Explants

Plants have a remarkable regenerative capacity, which allows them to survive tissue damage after biotic and abiotic stresses. In this study, we use Solanum lycopersicum 'Micro-Tom' explants as a model to investigate wound-induced de novo organ formation, as these explants can regenerate the missing structures without the exogenous application of plant hormones. Here, we performed simultaneous targeted profiling of 22 phytohormone-related metabolites during de novo organ formation and found that endogenous hormone levels dynamically changed after root and shoot excision, according to region-specific patterns. Our results indicate that a defined temporal window of high auxin-to-cytokinin accumulation in the basal region of the explants was required for adventitious root formation and that was dependent on a concerted regulation of polar auxin transport through the hypocotyl, of local induction of auxin biosynthesis, and of local inhibition of auxin degradation. In the apical region, though, a minimum of auxin-to-cytokinin ratio is established shortly after wounding both by decreasing active auxin levels and by draining auxin via its basipetal transport and internalization. Cross-validation with transcriptomic data highlighted the main hormonal gradients involved in wound-induced de novo organ formation in tomato hypocotyl explants.

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

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

Mdm-MIR393b-mediated adventitious root formation by targeted regulation of MdTIR1A expression and weakened sensitivity to auxin in apple rootstock

Adventitious root (AR) formation is of great significance for apple rootstock breeding. It is widely accepted that miR393 influences AR formation in many plant species; however, the molecular mechanism by which factors regulate AR formation remains insufficient. In this study, the evolutionary relationship of mdm-miR393 and candidate target genes MdTIR1/AFB was systematically identified, and the expression patterns were analysed. Multisequence alignment analysis of miR393 family members suggests that miR393 conservatively evolved between different species. The evolutionary relationship of the TIR1/AFBs can be divided into G1, G2 and G3 subgroups. During AR formation, the expression level of mdm-miR393a/b/c was significantly upregulated at 1 d and 7 d by exogenous auxin treatment. Furthermore, the expression levels of MdTIR1A, MdTIR1D, MdAFB1, MdAFB2, MdAFB3, MdAFB4 and MdAFB8 also appeared to be significantly changed by exogenous auxin induction. Subsequently, tissue-specific expression analysis showed that the expression levels of mdm-miR393 and MdTIR1/AFBs in different tissues exhibited significant differences. The promoter of mdm-miR393 contains multiple elements that respond to ABA, adversity and light signals; auxin treatment can activate the mdm-MIR393b promoter but is obviously inhibited by NPA treatment. The targeting relationship between mdm-MIR393b and MdTIR1A was verified by expression patterns, degradation group data, transient tobacco conversion results, and genes functions experiments. Heterologous overexpression of mdm-MIR393b (35S::mdm-MIR393b) decreased the number of ARs in the phenotype and reduced the expression level of the target gene NtTIR1 in tobacco. Compared to the wild type, the 35S::mdm-MIR393b transgenic plants demonstrated insensitivity to auxin. Furthermore, tir1 mutant exhibited reduced root system structure relative to the control. The above results illustrated that mdm-MIR393b is involved in mediating AR formation by targeted regulation of MdTIR1A expression in apple rootstock.

The microRNA476a-RFL module regulates adventitious root formation through a mitochondria-dependent pathway in Populus

For woody plants, clonal propagation efficiency is largely determined by adventitious root (AR) formation at the bases of stem cuttings. However, our understanding of the molecular mechanisms contributing to AR morphogenesis in trees remains limited, despite the importance of vegetative propagation, currently the most common practice for tree breeding and commercialization. Here, we identified Populus-specific miR476a as a regulator of wound-induced adventitious rooting that acts by orchestrating mitochondrial homeostasis. MiR476a exhibited inducible expression during AR formation and directly targeted several Restorer of Fertility like (RFL) genes encoding mitochondrion-localized pentatricopeptide repeat proteins. Genetic modification of miR476a-RFL expression revealed that miR476a/RFL-mediated dynamic regulation of mitochondrial homeostasis influences AR formation in poplar. Mitochondrial perturbation via exogenous application of a chemical inhibitor indicated that miR476a/RFL-directed AR formation depends on mitochondrial regulation that acts via auxin signaling. Our results thus establish a microRNA-directed mitochondrion-auxin signaling cascade required for AR development, providing insights into the role of mitochondrial regulation in the developmental plasticity of plants.

Understanding the Intricate Web of Phytohormone Signalling in Modulating Root System Architecture

Root system architecture (RSA) is an important developmental and agronomic trait that is regulated by various physical factors such as nutrients, water, microbes, gravity, and soil compaction as well as hormone-mediated pathways. Phytohormones act as internal mediators between soil and RSA to influence various events of root development, starting from organogenesis to the formation of higher order lateral roots (LRs) through diverse mechanisms. Apart from interaction with the external cues, root development also relies on the complex web of interaction among phytohormones to exhibit synergistic or antagonistic effects to improve crop performance. However, there are considerable gaps in understanding the interaction of these hormonal networks during various aspects of root development. In this review, we elucidate the role of different hormones to modulate a common phenotypic output, such as RSA in Arabidopsis and crop plants, and discuss future perspectives to channel vast information on root development to modulate RSA components.

Adventitious root formation in crops-Potato as an example

The root system of potato is made up of adventitious roots (AR) that form at the base of a sprout once it emerges from the mother tuber. By definition, AR originate from dormant preformed meristems, or from cells neighboring vascular tissues in stems or leaves. This may occur as part of the developmental program of the plant (e.g., potato), or when replacing the embryonic primary roots in response to stress conditions, such as flooding, nutrient deprivation, or wounding. AR formation is studied mainly in cereals and model plants, and less is known about its developmental program in root and tuber crops. In this review, we summarize the recent data on AR development in potato and relate this knowledge to what is known from model plants. For example, AR formation following stem cutting in potato follows a pattern of initiation, expression, and emergence phases that are known for other plants and involves auxin, the master regulator of AR induction and development. Molecular regulation of AR formation and the effect of environmental stresses are discussed. Understanding the origin and nature of AR systems in important crops will contribute to increased production and improve global food security.

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

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

Use of Transcriptomic Analyses to Elucidate the Mechanism Governing Nodal Root Development in Eremochloa ophiuroides (Munro) Hack

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] is a perennial warm-season grass that originated in China, and its speed of nodal rooting is important for lawn establishment. In our study, centipedegrass nodal rooting ability was limited by node aging. Transcriptome sequencing of nodal roots after 0, 2, 4, and 8 days of water culture was performed to investigate the molecular mechanisms of root development. GO enrichment and KEGG pathway analyses of DEGs indicated that plant hormone signal transduction and transcription factors might play important roles in centipedegrass nodal root growth. Among them, E3 ubiquitin-protein ligases participated in multiple hormone signal transduction pathways and interacted with transcription factors. Furthermore, an E3 ubiquitin protein ligase EoSINAT5 overexpressed in rice resulted in longer roots and more numerous root tips, while knockout of LOC_Os07g46560 (the homologous gene of EoSINAT5 in rice) resulted in shorter roots and fewer root tips. These results indicated that EoSINAT5 and its homologous gene are able to promote nodal root development. This research presents the transcriptomic analyses of centipedegrass nodal roots, and may contribute to elucidating the mechanism governing the development of nodal roots and facilitates the use of molecular breeding in improving rooting ability.

Regulation of growth in peach roots by exogenous hydrogen sulfide based on RNA-Seq

Hydrogen sulfide (H₂S) has been shown to regulate many physiological processes of plants. In this study, we observed that 0.2 mM sodium hydrosulfide (NaHS), a donor of H₂S, can regulate the root architecture of peach seedlings, increasing the number of lateral roots by 40.63%. To investigate the specific mechanisms by which H₂S regulates root growth in peach, we used RNA sequencing and heterologous expression technology. Our results showed that exogenous H₂S led to a 44.50% increase in the concentration of endogenous auxin. Analyses of differentially expressed genes (DEGs) revealed that 963 and 1113 genes responded to H₂S on days one and five of treatment, respectively. Among the DEGs, 26 genes were involved in auxin biosynthesis, transport, and signal transduction. Using weighted correlation network analysis, we found that the auxin-related genes in the H₂S-specific gene module were disproportionately involved in polar transport, which may play an important role in H₂S-induced root growth. In addition, we observed that the expression of LATERAL ORGAN BOUNDARIES DOMAIN 16 (PpLBD16) was significantly up-regulated by exogenous application of H₂S in peach. Overexpression of PpLBD16 in an Arabidopsis system yielded a 66.83% increase in the number of lateral roots. Under exposure to exogenous H₂S, there was also increased expression of genes related to cell proliferation, indicating that H₂S regulates the growth of peach roots. Our work represents the first comprehensive transcriptomic analysis of the effects of exogenous application of H₂S on the roots of peach, and provides new insights into the mechanisms underlying H₂S-induced root growth.

Pars Pro Toto: Every Single Cell Matters

Compared to other species, plants stand out by their unparalleled self-repair capacities. Being the loss of a single cell or an entire tissue, most plant species are able to efficiently repair the inflicted damage. Although this self-repair process is commonly referred to as "regeneration," depending on the type of damage and organ being affected, subtle to dramatic differences in the modus operandi can be observed. Recent publications have focused on these different types of tissue damage and their associated response in initiating the regeneration process. Here, we review the regeneration response following loss of a single cell to a complete organ, emphasizing key molecular players and hormonal cues involved in the model species Arabidopsis thaliana. In addition, we highlight the agricultural applications and techniques that make use of these regenerative responses in different crop and tree species.

Molecular Bases for the Regulation of Adventitious Root Generation in Plants

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

ETHYLENE RESPONSE FACTOR 115 integrates jasmonate and cytokinin signaling machineries to repress adventitious rooting in Arabidopsis

Adventitious root initiation (ARI) is a de novo organogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate that ERF115 is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI.

A twist in the ABC: regulation of ABC transporter trafficking and transport by FK506-binding proteins

Post-transcriptional regulation of ATP-binding cassette (ABC) proteins has been so far shown to encompass protein phosphorylation, maturation, and ubiquitination. Yet, recent accumulating evidence implicates FK506-binding proteins (FKBPs), a type of peptidylprolyl cis-trans isomerase (PPIase) proteins, in ABC transporter regulation. In this perspective article, we summarize current knowledge on ABC transporter regulation by FKBPs, which seems to be conserved over kingdoms and ABC subfamilies. We uncover striking functional similarities but also differences between regulatory FKBP-ABC modules in plants and mammals. We dissect a PPIase- and HSP90-dependent and independent impact of FKBPs on ABC biogenesis and transport activity. We propose and discuss a putative new mode of transient ABC transporter regulation by cis-trans isomerization of X-prolyl bonds.

Auxin and Its Interaction With Ethylene Control Adventitious Root Formation and Development in Apple Rootstock

Adventitious root (AR) formation is indispensable for vegetative asexual propagation. Indole-3-butyric acid (IBA) functioned indirectly as precursor of IAA in regulating AR formation. Ethylene affects auxin synthesis, transport, and/or signaling processes. However, the interactions between auxin and ethylene that control AR formation in apple have not been elucidated. In this study, we investigated the effects of IBA and its interaction with ethylene on AR development in apple. The results revealed that IBA stimulated the formation of root primordia, increased the number of ARs, and upregulated expression of genes (MdWOX11, MdLBD16, and MdLBD29) involved in AR formation. Comparison of different periods of IBA application indicated that IBA was necessary for root primordium formation, while long time IBA treatment obviously inhibited root elongation. RNA-seq analysis revealed that many plant hormone metabolism and signal transduction related genes were differentially expressed. IBA stimulated the production of ethylene during AR formation. Auxin inhibiting ARs elongation depended on ethylene. Together, our results suggest that the inhibitory role of auxin on AR elongation in apples is partially mediated by stimulated ethylene production.

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

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

SAUR15 Promotes Lateral and Adventitious Root Development via Activating H+-ATPases and Auxin Biosynthesis

SMALL AUXIN-UP RNAs (SAURs) comprise the largest family of early auxin response genes. Some SAURs have been reported to play important roles in plant growth and development, but their functional relationships with auxin signaling remain unestablished. Here, we report Arabidopsis (Arabidopsis thaliana) SAUR15 acts downstream of the auxin response factors ARF6,8 and ARF7,19 to regulate auxin signaling-mediated lateral root (LR) and adventitious root (AR) formation. The loss-of-function mutant saur15-1 exhibits fewer LRs and ARs. By contrast, plants overexpressing SAUR15 exhibit more LRs and ARs. We find that the SAUR15 promoter contains four tandem auxin-responsive elements, which are directly bound by ARF6 and ARF7 and are essential for SAUR15 expression. LR and AR impairment in arf6 and arf7 mutants is partially reduced by ectopic expression of SAUR15 Additionally, we demonstrate that the ARF6,7-upregulated SAUR15 promotes LR and AR development using two mechanisms. On the one hand, SAUR15 interacts with PP2C-D subfamily type 2C protein phosphatases to inhibit their activities, thereby stimulating plasma membrane H+-ATPases, which drives cell expansion and facilitates LR and AR formation. On the other hand, SAUR15 promotes auxin accumulation, potentially by inducing the expression of auxin biosynthesis genes. A resulting increase in free auxin concentration likely triggers LR and AR formation, forming a feedback loop. Our study provides insights and a better understanding of how SAURs function at the molecular level in regulating auxin-mediated LR and AR development.

A Kinase-Phosphatase-Transcription Factor Module Regulates Adventitious Root Emergence in Arabidopsis Root-Hypocotyl Junctions

Adventitious roots form from non-root tissues as part of normal development or in response to stress or wounding. The root primordia form in the source tissue, and during emergence the adventitious roots penetrate the inner cell layers and the epidermis; however, the mechanisms underlying this emergence remain largely unexplored. Here, we report that a regulatory module composed of the AP2/ERF transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), the MAP kinases MPK3 and MPK6, and the phosphatase PP2C12 plays an important role in the emergence of junction adventitious roots (J-ARs) from the root-hypocotyl junctions in Arabidopsis thaliana. ABI4 negatively regulates J-AR emergence, preventing the accumulation of reactive oxygen species and death of epidermal cells, which would otherwise facilitate J-AR emergence. Phosphorylation by MPK3/MPK6 activates ABI4 and dephosphorylation by PP2C12 inactivates ABI4. MPK3/MPK6 also directly phosphorylate and inactivate PP2C12 during J-AR emergence. We propose that this "double-check" mechanism increases the robustness of MAP kinase signaling and finely regulates the local programmed cell death required for J-AR emergence.

Reactive oxygen species regulate auxin levels to mediate adventitious root induction in Arabidopsis hypocotyl cuttings

Adventitious root (AR) formation from leafy stem cuttings is critical for breeding of many forest and horticultural species. In addition to the plant hormone auxin, wound-induced signaling caused by the cutting excision is also essential for AR initiation. Here we found that reactive oxygen species (ROS) are rapidly generated at the excision site as a wound-induced signal and propagated throughout the hypocotyl cutting after excision of the Arabidopsis (Arabidopsis thaliana) primary root. ROS propagation was not observed in the presence of an NADPH oxidase inhibitor (diphenylene iodonium chloride) or in a knockout mutant of the NADPH oxidase gene respiratory burst oxidase homolog protein D (RBOHD). Respiratory burst oxidase homolog protein D was specifically upregulated in hypocotyl cuttings at 0.5 h post excision (hpe). Together, these data suggest that RBOHD mediates ROS propagation in hypocotyl cuttings. We also found that auxin levels increased significantly in the shoot apex at 5 hpe and at the base of the cutting at 6 hpe; these effects were blocked by treatment with ROS scavengers. Consistent with this, transcript levels of auxin biosynthesis and polar-transport genes generally increased between 1 to 6 hpe. Collectively, our results suggest that wound-induced ROS participate in AR induction through regulation of auxin biosynthesis and transport.

Sugar enhances waterlogging-induced adventitious root formation in cucumber by promoting auxin transport and signalling

Waterlogging is a severe environmental stress that causes severe crop productivity losses. Cucumber (Cucumis sativus L.) survives waterlogging by producing adventitious roots (ARs) that enhance gas exchange. Little is known about the role of light and sugars in the waterlogging-induced production of ARs. The role of these factors in AR production was therefore studied in cucumber seedlings grown in the absence or presence of waterlogging and different light conditions. The effect of photosynthesis was studied by removing the shoots of the seedlings and replacing them with exogenous applications of sucrose or stachyose. Shoot removal inhibited AR emergence and elongation. However, the exogenous application of sugars fully restored AR emergence and partially restored root elongation. The exogenous application of a synthetic auxin restored AR emergence but not AR elongation. Transcriptome profiling analysis was used to determine the effects of light on gene expression in the hypocotyls under these conditions. The levels of transcripts encoding proteins involved in auxin transport and signalling were higher in the light and following the exogenous application of sucrose and stachyose. These results show that the waterlogging-induced emergence of ARs is regulated by the interaction between sugars and auxin, whereas AR elongation depends only on sugars alone.

Auxin efflux carriers, MiPINs, are involved in adventitious root formation of mango cotyledon segments

Adventitious roots form only at the proximal cut surface (PCS) but not at the distal cut surface (DCS) of mango cotyledon segments. In this study, mango embryos treated with indole-3-butyric acid (IBA) showed significantly increased adventitious root formation, while those treated with 2, 3, 5-triiodobenzoic acid (TIBA) demonstrated complete inhibition of adventitious rooting. Mango embryos treated with auxin influx inhibitors demonstrated lower inhibition of adventitious roots than those treated with TIBA. The endogenous indol-3-acetic acid (IAA) content on the PCS and DCS was similar at 0 h, then increased on both surfaces after 6 h, and IAA content on the PCS were always higher than those on the DCS. We cloned three genes encoding auxin efflux carriers (i.e., MiPIN2-4) and examined their temporal and spatial expression patterns under different treatments. Relative expression of all MiPINs studied was very low at 0 h but significantly increased on both PCS and DCS from 1 d to 10 d, to varying degrees. We overexpressed MiPIN1-4 in Arabidopsis plants and found a significant increase in adventitious root quantity in MiPIN1 and MiPIN3 transgenic lines. Immunofluorescence results showed that MiPIN1 and MiPIN3 are primarily localized in the vascular tissues and the cells adjacent to abaxial surface. In conclusion, we propose that in mango cotyledon segments, wounding stimulates IAA biosynthesis, the transcription levels of PIN genes were significantly increased in different magnitudes on the PCS and DCS, resulting in polar IAA transport from the DCS to PCS via the vascular tissues, thereby triggering adventitious root formation.