Cytokinin regulates vegetative phase change in Arabidopsis thaliana through the miR172/TOE1-TOE2 module

Genome-wide analysis of the SPL family in Zanthoxylum armatum and ZaSPL21 promotes flowering and improves salt tolerance in transgenic Nicotiana benthamiana

Z. armatum is an economically valued crop known for its rich aroma and medicinal properties. This study identified 45 members of the SQUAMOSA-PROMOTER BINDING PROTEIN LIKE (SPL) gene family in the genome of Z. armatum. Phylogenetic and collinearity analyzes demonstrated a close relationship between ZaSPLs and ZbSPLs from B subgenomes of Zanthoxylum bungeanum. Our miRNA sequencing revealed a high degree of conservation of miR156a within Z. armatum, with the za-miR156a sequence identical to miR156-5p in Arabidopsis thaliana and Citrus sinensis. Of the 45 genes identified by ZaSPLs, 21 were targeted by za-miR156a, transient co-expression experiments in N. benthamiana demonstrated the targeting relationship between za-miR156 and ZaSPL21. Furthermore, RNA-seq and qRT-PCR analysis revealed that ZaSPL genes exhibited elevated expression levels in juvenile tissues of Z. armatum. The expression of nine representative ZaSPL genes were upregulated under polyethylene glycol (PEG) and abscisic acid (ABA). Overexpression of ZaSPL21 delayed the germination of transgenic tobacco and facilitated the flowering process in transgenic N. benthamiana. Significant up-regulation in the expression levels of flowering-related genes such as NbFT1, NbPIP2;1, NbTCP1, NbCOL1, NbGI2, NbGAI1, NbCKX2, and NbARR4 was observed in transgenic plants, suggesting that ZaSPL21 may stimulate plant flowering by regulation of these genes. Furthermore, ZaSPL21 also increased the germination speed of transgenic tobacco seeds during drought and salt stress conditions, and improved the salt tolerance of transgenic seedlings. In conclusion, our study contributes to understanding the functional analysis of the SPL gene family in Z. armatum and emphasizes the crucial role of ZaSPL21 in improving tolerance to salt and promoting flowering. The results offer potential strategies for the further utilization of these genes to improve the salt tolerance of Z. armatum.

RNA Metabolism and the Role of Small RNAs in Regulating Multiple Aspects of RNA Metabolism

RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell is shaped by the processes such as RNA biosynthesis, maturation (RNA processing, folding, and modification), intra- and inter-cellular transport, transcriptional and post-transcriptional regulation, modification, catabolic decay, and retrograde signaling, all of which are interconnected and are essential for cellular RNA homeostasis. In eukaryotes, sRNAs, typically 20-31 nucleotides in length, are a class of ncRNAs found to function as nodes in various gene regulatory networks. sRNAs are known to play significant roles in regulating RNA population at the transcriptional, post-transcriptional, and translational levels. Along with sRNAs, such as miRNAs, siRNAs, and piRNAs, new categories of ncRNAs, i.e., lncRNAs and circRNAs, also contribute to RNA metabolism regulation in eukaryotes. In plants, various genetic screens have demonstrated that sRNA biogenesis mutants, as well as RNA metabolism pathway mutants, exhibit similar growth and development defects, misregulated primary and secondary metabolism, as well as impaired stress response. In addition, sRNAs are both the "products" and the "regulators" in broad RNA metabolism networks; gene regulatory networks involving sRNAs form autoregulatory loops that affect the expression of both sRNA and the respective target. This review examines the interconnected aspects of RNA metabolism with sRNA regulatory pathways in plants. It also explores the potential conservation of these pathways across different kingdoms, particularly in plants and animals. Additionally, the review highlights how cellular RNA homeostasis directly impacts adaptive responses to environmental changes as well as different developmental aspects in plants.

Transcriptome Profiling Reveals Key Regulatory Networks for Age-Dependent Vernalization in Welsh Onion (Allium fistulosum L.)

Plants exhibit diverse pathways to regulate the timing of flowering. Some plant species require a vegetative phase before being able to perceive cold stimuli for the acceleration of flowering through vernalization. This research confirms the correlation between the vernalization process and seedling age in Welsh onions. Findings from two vernalization experiments conducted at different time intervals demonstrate that seedlings must reach a vegetative phase of at least 8 weeks to consistently respond to vernalization. Notably, 8-week-old seedlings subjected to 6 weeks of vernalization displayed the shortest time to bolting, with an average duration of 138.1 days. Transcriptome analysis led to the identification of genes homologous to those in Arabidopsis thaliana that regulate flowering. Specifically, AfisC7G05578 (CO), AfisC2G05881 (AP1), AfisC1G07745 (FT), AfisC1G06473 (RAP2.7), and AfisC2G01843 (VIM1) were identified and suggested to have potential significance in age-dependent vernalization in Welsh onions. This study not only presents a rapid vernalization method for Welsh onions but also provides a molecular foundation for understanding the interplay between seedling age and vernalization.

Overexpression of lily MicroRNA156-resistant SPL13A stimulates stem elongation and flowering in Lilium formosanum under non-inductive (non-chilling) conditions

Flowering plants undergo juvenile vegetative, adult vegetative, and reproductive phases. Lily plants (Lilium spp.) develop scaly leaves during their juvenile vegetative phase. Stem elongation occurs in the adult vegetative phase and is followed by floral transition. As the duration of the juvenile vegetative phase is long in lilies, the microRNA156 (miR156) and SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) modules are expected to play a major role in vegetative phase change and flower induction. In the present study, we aimed to explore the functions of lily SLP13A. We evaluated phenotypic changes and gene expression in L. formosanum plants overexpressing miR156-resistant SPL13A (rSPL13A) and examined the accumulation levels of gene transcripts and mature miRNAs in non-transformed L. longiflorum plants. Lily plants overexpressing rSPL13A exhibited stem elongation under non-inductive conditions, and FLOWERING LOCUS T (FT) genes were poorly involved in this stem elongation. Flowering was induced in the transformed plants with elongated stems, and the accumulation of MADS5 (APETALA1) transcripts and mature miR172 was elevated in these plants. In non-transformed lilies, SPL13A transcripts were highly accumulated in the shoot apices of both juvenile and adult plants. As mature miR156 was poorly accumulated in the shoot apices of the adult plants, SPL13A was active enough to stimulate stem elongation and flower induction. In contrast, mature miR156 was reliably detected in shoot apices of the juvenile plants. Because our transient assay using tobacco plants expressing a SPL13A-GFP fusion protein indicated that miR156 repressed SPL13A expression mainly at the translational level, SPL13A activity should be insufficient to stimulate stem elongation in the juvenile plants. In addition, the accumulation of MADS5 transcripts and mature miR172 in the shoot apices increased with plant growth and peaked before the transition to the reproductive phase. Therefore, we conclude that SPL13A regulates stem elongation in the adult vegetative phase, which differs from the mechanisms evaluated in Arabidopsis and rice, wherein stem elongation proceeds in a reproductive phase and FT genes are heavily involved in it, and that SPL13A induces flowering by the activation of genes related to the age pathway underlying floral transition, as APETALA1 and primary-MIR172 are mainly involved in this pathway.

Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition

Plants undergo rapid developmental transitions, which occur contemporaneously with gradual changes in physiology. Moreover, individual plants within a population undergo developmental transitions asynchronously. Single-plant-omics has the potential to distinguish between transcriptional events that are associated with these binary and continuous processes. Furthermore, we can use single-plant-omics to order individual plants by their intrinsic biological age, providing a high-resolution transcriptional time series. We performed RNA-seq on leaves from a large population of wild-type Arabidopsis (Arabidopsis thaliana) during the vegetative-to-reproductive transition. Though most transcripts were differentially expressed between bolted and unbolted plants, some regulators were more closely associated with leaf size and biomass. Using a pseudotime inference algorithm, we determined that some senescence-associated processes, such as the reduction in ribosome biogenesis, were evident in the transcriptome before a bolt was visible. Even in this near-isogenic population, some variants are associated with developmental traits. These results support the use of single-plant-omics to uncover rapid transcriptional dynamics by exploiting developmental asynchrony.

Harnessing miRNA156: A molecular Toolkit for reshaping plant development and achieving ideal architecture

Achieving ideal plant architecture is of utmost importance for plant improvement to meet the demands of ever-increasing population. The wish list of ideal plant architecture traits varies with respect to its utilization and environmental conditions. Late seed development in woody plants poses difficulties for their propagation, and an increase in regeneration capacity can overcome this problem. The transition of a plant through sequential developmental stages e.g., embryonic, juvenile, and maturity is a well-orchestrated molecular and physiological process. The manipulation in the timing of phase transition to achieve ideal plant traits and regulation of metabolic partitioning will unlock new plant potential. Previous studies demonstrate that micro RNA156 (miR156) impairs the expression of its downstream genes to resist the juvenile-adult-reproductive phase transition to prolonged juvenility. The phenomenon behind prolonged juvenility is the maintenance of stem cell integrity and regeneration is an outcome of re-establishment of the stem cell niche. The previously reported vital and diverse functions of miR156 make it a more important case of study to explore its functions and possible ways to use it in molecular breeding. In this review, we proposed how genetic manipulation of miR156 can be used to reshape plant development phase transition and achieve ideal plant architecture. We have summarized recent studies on miR156 to describe its functional pattern and networking with up and down-stream molecular factors at each stage of the plant developmental life cycle. In addition, we have highlighted unaddressed questions, provided insights and devised molecular pathways that will help researchers to design their future studies.

Epigenetics and plant hormone dynamics: a functional and methodological perspective

Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.

Age-dependent changes in leaf size in apple are governed by a cytokinin-integrated module

Plants undergo various age-dependent changes in leaf morphology during juvenile to adult vegetative stage. However, the precise molecular mechanisms governing these changes in apple (Malus domestica) remain unknown. Here, we showed that CYTOKININ OXIDASE/DEHYDROGENASE5 (MdCKX5), an age-dependent gene, encodes a functional CKX enzyme and serves as the common downstream target of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor MdSPL14 and WRKY transcription factor MdWRKY24 to control the degradation of cytokinin (CK). As the target of mdm-microRNA156a, MdSPL14 interacts with MdWRKY24 to coordinately repress the transcription of MdCKX5 by forming the age-mediated mdm-miR156a-MdSPL14-MdWRKY24 module, which regulates age-dependent changes in CK during the juvenile-to-adult phase transition. We further demonstrated that MdARR6, a type-A ARABIDOPSIS RESPONSE REGULATOR (ARR), is a negative feedback regulator in the CK signaling pathway. Silencing of MdARR6 in apple resulted in large leaves with smaller epidermal cells and a greater number of epidermal cells. Biochemical analysis showed that the mdm-miR156a-MdSPL14-MdWRKY24 module acts as a transcriptional repressor to directly regulate MdARR6 expression, thus controlling the age-dependent changes in leaf size by reducing CK responses. These findings established a link between the age pathway and CK signaling and revealed the molecular mechanism underlying age-dependent changes during the juvenile-to-adult phase transition; our results also provide targets for the genetic improvement of the vegetative phase transition in apple.

miR156-PvSPL2 controls culm development by transcriptional repression of switchgrass CYTOKININ OXIDASE/DEHYDROGENASE4

Culm development in grasses can be controlled by both miR156 and cytokinin. However, the crosstalk between the miR156-SPL module and the cytokinin metabolic pathway remains largely unknown. Here, we found CYTOKININ OXIDASE/DEHYDROGENASE4 (PvCKX4) plays a negative regulatory role in culm development of the bioenergy grass Panicum virgatum (switchgrass). Overexpression of PvCKX4 in switchgrass reduced the internode diameter and length without affecting tiller number. Interestingly, we also found that PvCKX4 was always upregulated in miR156 overexpressing (miR156OE) transgenic switchgrass lines. Additionally, upregulation of either miR156 or PvCKX4 in switchgrass reduced the content of isopentenyl adenine (iP) without affecting trans-zeatin (tZ) accumulation. It is consistent with the evidence that the recombinant PvCKX4 protein exhibited much higher catalytic activity against iP than tZ in vitro. Furthermore, our results showed that miR156-targeted SPL2 bound directly to the promoter of PvCKX4 to repress its expression. Thus, alleviating the SPL2-mediated transcriptional repression of PvCKX4 through miR156 overexpression resulted in a significant increase in cytokinin degradation and impaired culm development in switchgrass. On the contrary, suppressing PvCKX4 in miR156OE transgenic plants restored iP content, internode diameter, and length to wild-type levels. Most strikingly, the double transgenic lines retained the same increased tiller numbers as the miR156OE transgenic line, which yielded more biomass than the wild type. These findings indicate that the miR156-SPL module can control culm development through transcriptional repression of PvCKX4 in switchgrass, which provides a promising target for precise design of shoot architecture to yield more biomass from grasses.

Natural variation in CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 reveals a novel role of calcium signaling in vegetative phase change in Arabidopsis

The timing of vegetative phase change (VPC) in plants is regulated by a temporal decline in the expression of miR156. Both exogenous cues and endogenous factors, such as temperature, light, sugar, nutrients, and epigenetic regulators, have been shown to affect VPC by altering miR156 expression. However, the genetic basis of natural variation in VPC remains largely unexplored. Here, we conducted a genome-wide association study on the variation of the timing of VPC in Arabidopsis. We identified CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 (CNGC4) as a significant locus associated with the diversity of VPC. Mutations in CNGC4 delayed VPC, accompanied by an increased expression level of miR156 and a corresponding decrease in SQUAMOSA PROMOTER BINDING-LIKE (SPL) gene expression. Furthermore, mutations in CNGC2 and CATION EXCHANGER 1/3 (CAX1/3) also led to a delay in VPC. Polymorphisms in the CNGC4 promoter contribute to the natural variation in CNGC4 expression and the diversity of VPC. Specifically, the early CNGC4 variant promotes VPC and enhances plant adaptation to local environments. In summary, our findings offer genetic insights into the natural variation in VPC in Arabidopsis, and reveal a previously unidentified role of calcium signaling in the regulation of VPC.

Epigenetic regulation and epigenetic memory resetting during plant rejuvenation

Reversal of plant developmental status from the mature to the juvenile phase, thus leading to the restoration of the developmental potential, is referred to as plant rejuvenation. It involves multilayer regulation, including resetting gene expression patterns, chromatin remodeling, and histone modifications, eventually resulting in the restoration of juvenile characteristics. Although plants can be successfully rejuvenated using some forestry practices to restore juvenile morphology, physiology, and reproductive capabilities, studies on the epigenetic mechanisms underlying this process are in the nascent stage. This review provides an overview of the plant rejuvenation process and discusses the key epigenetic mechanisms involved in DNA methylation, histone modification, and chromatin remodeling in the process of rejuvenation, as well as the roles of small RNAs in this process. Additionally, we present new inquiries regarding the epigenetic regulation of plant rejuvenation, aiming to advance our understanding of rejuvenation in sexually and asexually propagated plants. Overall, we highlight the importance of epigenetic mechanisms in the regulation of plant rejuvenation, providing valuable insights into the complexity of this process.

Temporal regulation of vegetative phase change in plants

During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.

The cytokinin receptor OHK4/OsHK4 regulates inflorescence architecture in rice via an IDEAL PLANT ARCHITECTURE1/WEALTHY FARMER'S PANICLE-mediated positive feedback circuit

Inflorescence architecture is important for rice (Oryza sativa) grain yield. The phytohormone cytokinin (CK) has been shown to regulate rice inflorescence development; however, the underlying mechanism mediated by CK perception is still unclear. Employing a forward genetic approach, we isolated an inactive variant of the CK receptor OHK4/OsHK4 gene named panicle length1, which shows decreased panicle size due to reduced inflorescence meristem (IM) activity. A 2-amino acid deletion in the long α-helix stalk of the sensory module of OHK4 impairs the homodimerization and ligand-binding capacity of the receptor, even though the residues do not touch the ligand-binding domain or the dimerization interface. This deletion impairs CK signaling that occurs through the type-B response regulator OsRR21, which acts downstream of OHK4 in controlling inflorescence size. Meanwhile, we found that IDEAL PLANT ARCHITECTURE1(IPA1)/WEALTHY FARMER'S PANICLE (WFP), encoding a positive regulator of IM development, acts downstream of CK signaling and is directly activated by OsRR21. Additionally, we revealed that IPA1/WFP directly binds to the OHK4 promoter and upregulates its expression through interactions with 2 TCP transcription factors, forming a positive feedback circuit. Altogether, we identified the OHK4-OsRR21-IPA1 regulatory module, providing important insights into the role of CK signaling in regulating rice inflorescence architecture.

N4-acetylation of cytidine in mRNA plays essential roles in plants

The biological function of RNA can be modulated by base modifications. Here, we unveiled the occurrence of N4-acetylation of cytidine in plant RNA, including mRNA, by employing LC-MS/MS and acRIP-seq. We identified 325 acetylated transcripts from the leaves of 4-week-old Arabidopsis (Arabidopsis thaliana) plants and determined that 2 partially redundant N-ACETYLTRANSFERASEs FOR CYTIDINE IN RNA (ACYR1 and ACYR2), which are homologous to mammalian NAT10, are required for acetylating RNA in vivo. A double-null mutant was embryo lethal, while eliminating 3 of the 4 ACYR alleles led to defects in leaf development. These phenotypes could be traced back to the reduced acetylation and concomitant destabilization of the transcript of TOUGH, which is required for miRNA processing. These findings indicate that N4-acetylation of cytidine is a modulator of RNA function with a critical role in plant development and likely many other processes.

The central role of stem cells in determining plant longevity variation

Vascular plants display a huge variety of longevity patterns, from a few weeks for several annual species up to thousands of years for some perennial species. Understanding how longevity variation is structured has long been considered a fundamental aspect of the life sciences in view of evolution, species distribution, and adaptation to diverse environments. Unlike animals, whose organs are typically formed during embryogenesis, vascular plants manage to extend their life by continuously producing new tissues and organs in apical and lateral directions via proliferation of stem cells located within specialized tissues called meristems. Stem cells are the main source of plant longevity. Variation in plant longevity is highly dependent on the activity and fate identity of stem cells. Multiple developmental factors determine how stem cells contribute to variation in plant longevity. In this review, we provide an overview of the genetic mechanisms, hormonal signaling, and environmental factors involved in controlling plant longevity through long-term maintenance of stem cell fate identity.

miR172: a messenger between nodulation and flowering

Legumes coordinate nodulation and plant development to maximize reproductive success, but the underlying molecular mechanisms are not well understood. A recent study by Yun et al. has revealed that nodulation drives root-to-shoot movement of microRNA172 (miR172) to accelerate flowering time, thus building a new bridge between nodulation and plant growth regulation.

Differentially Expressed Conserved Plant Vegetative Phase-Change-Related microRNAs in Mature and Rejuvenated Silver Birch In Vitro Propagated Tissues

In plants, phase change from the juvenile stage to maturity involves physiological and anatomical changes, which are initiated and controlled by evolutionary highly conserved microRNAs. This process is of particular significance for the in vitro propagation of woody plant species, as individuals or tissues that have undergone the transition to vegetative maturity are recalcitrant to propagation. Conserved miRNAs differentially expressed between juvenile (including rejuvenated) and mature silver birch tissues were identified using high-throughput sequencing of small RNA libraries. Expression of some miR156 isoforms was high in juvenile tissues and has been previously reported to regulate phase transitions in a range of species. Additional miRNAs, such as miR394 and miR396, that were previously reported to be highly expressed in juvenile woody plant tissues were also differentially expressed in this study. However, expression of miR172, previously reported to be highly expressed in mature tissues, was low in all sample types in this study. The obtained results will provide insight for further investigation of the molecular mechanisms regulating vegetative phase change in silver birch and other perennial woody plant species, by analysing a wider range of genotypes, tissue types and maturation stages. This knowledge can potentially assist in identification of rejuvenated material at an earlier stage than currently possible, increasing the efficiency of silver birch in vitro propagation.

Coordinated regulation of vegetative phase change by brassinosteroids and the age pathway in Arabidopsis

Vegetative phase change in plants is regulated by a gradual decline in the level of miR156 and a corresponding increase in the expression of its targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes. Gibberellin (GA), jasmonic acid (JA), and cytokinin (CK) regulate vegetative phase change by affecting genes in the miR156-SPL pathway. However, whether other phytohormones play a role in vegetative phase change remains unknown. Here, we show that a loss-of-function mutation in the brassinosteroid (BR) biosynthetic gene, DWARF5 (DWF5), delays vegetative phase change, and the defective phenotype is primarily attributable to reduced levels of SPL9 and miR172, and a corresponding increase in TARGET OF EAT1 (TOE1). We further show that GLYCOGEN SYNTHASE KINASE3 (GSK3)-like kinase BRASSINOSTEROID INSENSITIVE2 (BIN2) directly interacts with and phosphorylates SPL9 and TOE1 to cause subsequent proteolytic degradation. Therefore, BRs function to stabilize SPL9 and TOE1 simultaneously to regulate vegetative phase change in plants.

Halostachys caspica pathogenesis-related protein 10 acts as a cytokinin reservoir to regulate plant growth and development

Pathogenesis-related class 10 (PR-10) proteins play a role in plant growth and development, but the underlying molecular mechanisms are unclear. Here, we isolated a salt-induced PR-10 gene from the halophyte Halostachys caspica and named it HcPR10. HcPR10 was constitutively expressed during development and HcPR10 localized to the nucleus and cytoplasm. HcPR10-mediated phenotypes including bolting, earlier flowering, increased branch number and siliques per plant are highly correlated with increased cytokinin levels in transgenic Arabidopsis. Meanwhile, increased levels of cytokinin in plants is temporally correlated with HcPR10 expression patterns. Although the expression of cytokinin biosynthesis genes validated was not upregulated, cytokinin-related genes including chloroplast-related genes, cytokinin metabolism and cytokinin responses genes and flowering-related genes were significantly upregulated in the transgenic Arabidopsis compared to the wild type by transcriptome deep sequencing. Analysis of the crystal structure of HcPR10 revealed a trans-zeatin riboside (a type of cytokinin) located deep in its cavity, with a conserved conformation and protein-ligand interactions, supporting HcRP10 acts as a cytokinin reservoir. Moreover, HcPR10 in Halostachys caspica predominantly accumulated in vascular tissue, the site of long-distance translocation of plant hormones. Collectively, we draw that HcPR10 as a cytokinin reservoir induces cytokinin-related signal transduction in plants, thereby promoting plant growth and development. These findings could provide intriguing insights into the role of HcPR10 proteins in phytohormone regulation in plants and advance our understanding of cytokinin-mediated plant development and could facilitate the breeding of transgenic crops with earlier mature, higher yielding agronomic traits.

Comparative transcriptome analysis reveals hormone, transcriptional and epigenetic regulation involved in prickle formation in Zanthoxylum armatum

Zanthoxylum armatum is an evergreen plant with high economical and medicinal values. The presence of prickles on stems and leaves is undesirable for them make picking difficult. To date, little is known of prickle formation in Z. armatum. Herein, the morphological and molecular features of prickle initiation in prickless (WC) and three types of prickly Z. armatum were characterized. Compared to WC, the levels of cytokinin and auxin were increased, while GA and JA declined in prickly Z. armatum. Transcriptome analysis identified 6258 differentially expressed genes (DEGs)between prickless and prickly Z. armatum. Among them, several DEGs related to hormone metabolism and signaling, including LOG7, CKX3, AHK1, three DELLAs, six JAZs and TIR1, were candidate genes involved in prickle formation. Transcription factors associated with prickle formation was screened, including MYB6-1/MYB6-2, WER, GL3-2, SPL4/5, SOC1, and SCL32. Of them, MYB6-1 and WER might negatively regulate prickles initiation via interacting with GL3-2. Additionally, the histone acetylation and DNA methylation levels, the transcripts of histone acetyltransferase/deacetylase and DNA methyltransferases showed significant differences between prickless and prickly plants, indicating their involvements in prickle initiation. These findings illustrate the regulation of prickle formation might be mediated by phytohormones (especially cytokinin), transcription factors and epigenetic modifications in Z. armatum.

Cytokinin Response Factor 9 Represses Cytokinin Responses in Flower Development

A multi-step phosphorelay system is the main conduit of cytokinin signal transduction. However, several groups of additional factors that also play a role in this signaling pathway have been found-among them the Cytokinin Response Factors (CRFs). In a genetic screen, CRF9 was identified as a regulator of the transcriptional cytokinin response. It is mainly expressed in flowers. Mutational analysis indicates that CRF9 plays a role in the transition from vegetative to reproductive growth and silique development. The CRF9 protein is localized in the nucleus and functions as a transcriptional repressor of Arabidopsis Response Regulator 6 (ARR6)-a primary response gene for cytokinin signaling. The experimental data suggest that CRF9 functions as a repressor of cytokinin during reproductive development.

Reproductive competence is regulated independently of vegetative phase change in Arabidopsis thaliana

A long-standing question in plant biology is how the acquisition of reproductive competence is related to the juvenile-to-adult vegetative transition. We addressed this question by examining the expression pattern and mutant phenotypes of two families of miRNAs-miR156/miR157 and miR172-that operate in the same pathway and play important roles in these processes. The phenotype of mutants deficient for miR156/miR157, miR172, and all three miRNAs demonstrated that miR156/miR157 regulate the timing of vegetative phase change but have only a minor effect on reproductive competence, whereas miR172 has a minor role in vegetative phase change but has a major effect on reproductive competence. MIR172B is directly downstream of the miR156/SPL module, but temporal variation in the level of miR156 in the shoot apex and leaf-to-leaf variation in miR156 expression in young primordia was not associated with a change in the level of miR172 in these tissues. Additionally, although miR172 levels increase from leaf to leaf later in leaf development, this variation is largely insensitive to changes in the abundance of miR156. Our results indicate that the acquisition of reproductive competence in Arabidopsis is regulated by miR172 through a mechanism that is independent of the vegetative phase change pathway.

Is auxin enough? Cytokinins and margin patterning in simple leaves

The interplay between auxin and cytokinins affects facets of plant development as different as ovule formation and lateral root initiation. Moreover, cytokinins favor complexity in the development of Solanum lycopersicum and Cardamine hirsuta compound leaves. Nevertheless, no role has been proposed for cytokinins in patterning the margins of the simple leaves of Arabidopsis thaliana, a process that is assumed to be sufficiently explained by auxin localization. Here, we discuss evidence supporting the hypothesis that cytokinins play a role in simple leaf margin morphogenesis via crosstalk with auxin, as occurs in other plant developmental events. Indeed, mutant or transgenic arabidopsis plants defective in cytokinin biosynthesis or signaling, or with increased cytokinin degradation have leaf margins less serrated than the wild type.

Effects of the vegetative propagation method on juvenility in Robinia pseudoacacia L

Vegetative propagation is an important method of reproduction and rejuvenation in forestry. The growth and development of asexually propagated trees are influenced by the age and position of the propagule on the plant, effects referred to as cyclophysis and topophysis, respectively. Due to the long lifespans and large body sizes of woody trees, the selection of propagules is critically important. Here, we used three vegetative propagation methods (shoot cutting, root sprouting, and root cutting) to study the effect of different regeneration methods on juvenility of the resulting black locust plants, with seed-derived seedlings used as a control. Most characteristics of plantlets generated by root-sprouting were similar to those of seed-derived seedlings, including leaf traits and leaf anatomical structure. However, there were significant differences between the plantlets derived from shoot-cuttings and seedlings from seeds. Furthermore, the data showed that some of these age-related small RNAs and genes differed in expression among propagation methods and between plantlets/seedlings and mature trees. These age-related small RNAs, genes, and transcription factors may be used as molecular markers of juvenility and phase transitions in black locust. Our results provide useful information for the optimal propagation of woody trees and for further research into the mechanisms of root regeneration.

Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

To survive in adverse environmental conditions, plants have evolved sophisticated genetic and epigenetic regulatory mechanisms to balance their growth and abiotic stress tolerance. An increasing number of non-coding RNAs (ncRNAs), including small RNAs (sRNAs) and long non-coding RNAs (lncRNAs) have been identified as essential regulators which enable plants to coordinate multiple aspects of growth and responses to environmental stresses through modulating the expression of target genes at both the transcriptional and posttranscriptional levels. In this review, we summarize recent advances in understanding ncRNAs-mediated prioritization towards plant growth or tolerance to abiotic stresses, especially to cold, heat, drought and salt stresses. We highlight the diverse roles of evolutionally conserved microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the underlying phytohormone-based signaling crosstalk in regulating the balance between plant growth and abiotic stress tolerance. We also review current discoveries regarding the potential roles of ncRNAs in stress memory in plants, which offer their descendants the potential for better fitness. Future ncRNAs-based breeding strategies are proposed to optimize the balance between growth and stress tolerance to maximize crop yield under the changing climate.

Mapping of a novel clubroot disease resistance locus in Brassica napus and related functional identification

Clubroot disease, caused by Plasmodiophora brassicae, is a devastating disease that results in substantial yield loss in Brassicaceae crops worldwide. In this study, we identified a clubroot disease resistance (CR) Brassica napus, "Kc84R," which was obtained by mutation breeding. Genetic analysis revealed that the CR trait of "Kc84R" was controlled by a single dominant locus. We used the bulked segregant analysis sequencing (BSA-seq) approach, combined with genetic mapping based on single nucleotide polymorphism (SNP) markers to identify CR loci from the F₂ population derived from crossing CR "Kc84R" and clubroot susceptible "855S." The CR locus was mapped to a region between markers BnSNP14198336 and BnSNP14462201 on the A03 chromosome, and this fragment of 267 kb contained 68 annotated candidate genes. Furthermore, we performed the CR relation screening of candidate genes with the model species Arabidopsis. An ERF family transcriptional activator, BnERF034, was identified to be associated with the CR, and the corresponding Arabidopsis homozygous knockout mutants exhibited more pronounced resistance compared with the wild-type Col-0 and the transgenic lines of BnERF034 in response to P. brassicae infection. Additionally, the expression analysis between resistant and susceptible materials indicated that BnERF034 was identified to be the most likely CR candidate for the resistance in Kc84R. To conclude, this study reveals a novel gene responsible for CR. Further analysis of BnERF034 may reveal the molecular mechanisms underlying the CR of plants and provide a theoretical basis for Brassicaceae resistance breeding.

Genome-Wide Analysis of Long Non-coding RNAs Involved in Nodule Senescence in Medicago truncatula

Plant long non-coding RNAs (lncRNAs) are widely accepted to play crucial roles during diverse biological processes. In recent years, thousands of lncRNAs related to the establishment of symbiosis, root nodule organogenesis and nodule development have been identified in legumes. However, lncRNAs involved in nodule senescence have not been reported. In this study, senescence-related lncRNAs were investigated in Medicago truncatula nodules by high-throughput strand-specific RNA-seq. A total of 4576 lncRNAs and 126 differentially expressed lncRNAs (DElncRNAs) were identified. We found that more than 60% lncRNAs were associated with transposable elements, especially TIR/Mutator and Helitron DNA transposons families. In addition, 49 DElncRNAs were predicted to be the targets of micro RNAs. Functional analysis showed that the largest sub-set of differently expressed target genes of DElncRNAs were associated with the membrane component. Of these, nearly half genes were related to material transport, suggesting that an important function of DElncRNAs during nodule senescence is the regulation of substance transport across membranes. Our findings will be helpful for understanding the functions of lncRNAs in nodule senescence and provide candidate lncRNAs for further research.

The RpTOE1-RpFT Module Is Involved in Rejuvenation during Root-Based Vegetative Propagation in Robinia pseudoacacia

Vegetative propagation is an important method of reproduction and rejuvenation in horticulture and forestry plants with a long lifespan. Although substantial juvenile clones have been obtained through the vegetative propagation of ornamental plants, the molecular factors that regulate rejuvenation during vegetative propagation are largely unknown. Here, root sprouting and root cutting of Robinia pseudoacacia were used as two vegetative propagation methods. From two consecutive years of transcriptome data from rejuvenated seedlings and mature trees, one gene module and one miRNA module were found to be specifically associated with rejuvenation during vegetative propagation through weighted gene co-expression network analysis (WGCNA). In the gene module, a transcription factor-encoding gene showed high expression during vegetative propagation, and it was subsequently named RpTOE1 through homology analysis. Heterologous overexpression of RpTOE1 in wild-type Arabidopsis and toe1 toe2 double mutants prolonged the juvenile phase. The qRT-PCR results predicted RpFT to be a downstream gene that was regulated by RpTOE1. Further investigation of the protein-DNA interactions using yeast one-hybrid, electrophoretic mobility shift, and dual luciferase reporter assays confirmed that RpTOE1 negatively regulated RpFT by binding directly to the TOE binding site (TBS)-like motif on its promoter. On the basis of these results, we showed that the high expression of RpTOE1 during vegetative propagation and its inhibition of RpFT played a key role in the phase reversal of R. pseudoacacia.

Cytokinins: Wide-Spread Signaling Hormones from Plants to Humans with High Medical Potential

Nature is a rich source of biologically active novel compounds. Sixty years ago, the plant hormones cytokinins were first discovered. These play a major role in cell division and cell differentiation. They affect organogenesis in plant tissue cultures and contribute to many other physiological and developmental processes in plants. Consequently, the effect of cytokinins on mammalian cells has caught the attention of researchers. Many reports on the contribution and potential of cytokinins in the therapy of different human diseases and pathophysiological conditions have been published and are reviewed here. We compare cytokinin effects and pathways in plants and mammalian systems and highlight the most important biological activities. We present the strong profile of the biological actions of cytokinins and their possible therapeutic applications.

microRNAs and Their Roles in Plant Development

Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.

Cytokinin Perception in Ancient Plants beyond Angiospermae

Cytokinins (CKs) control many plant developmental processes and responses to environmental cues. Although the CK signaling is well understood, we are only beginning to decipher its evolution. Here, we investigated the CK perception apparatus in early-divergent plant species such as bryophyte Physcomitrium patens, lycophyte Selaginella moellendorffii, and gymnosperm Picea abies. Of the eight CHASE-domain containing histidine kinases (CHKs) examined, two CHKs, PpCHK3 and PpCHK4, did not bind CKs. All other CHK receptors showed high-affinity CK binding (K_D of nM range), with a strong preference for isopentenyladenine over other CK nucleobases in the moss and for trans-zeatin over cis-zeatin in the gymnosperm. The pH dependences of CK binding for these six CHKs showed a wide range, which may indicate different subcellular localization of these receptors at either the plasma- or endoplasmic reticulum membrane. Thus, the properties of the whole CK perception apparatuses in early-divergent lineages were demonstrated. Data show that during land plant evolution there was a diversification of the ligand specificity of various CHKs, in particular, the rise in preference for trans-zeatin over cis-zeatin, which indicates a steadily increasing specialization of receptors to various CKs. Finally, this distinct preference of individual receptors to different CK versions culminated in vascular plants, especially angiosperms.