Review - Cytokinin Response Factors: Responding to more than cytokinin

CRISPR-mediated mutation of cytokinin signaling genes (SlHP2 and SlHP3) in tomato: Morphological, physiological, and molecular characterization

Synergistic and antagonistic relationships between cytokinins and other plant growth regulators are important in response to changing environmental conditions. Our study aimed to determine the functions of SlHP2 and SlHP3, two members of cytokinin signaling in tomato, in drought stress response using CRISPR/Cas9-mediated mutagenesis. Ten distinct genome-edited lines were generated via Agrobacterium tumefaciens-mediated gene transfer and confirmed through Sanger sequencing. Stress experiments were conducted with two of these lines (slhp2,3-10 and slhp2,3-11), which harbored homozygous mutations in both genes. The responses of two lines carrying homozygous mutations in both genes under polyethylene glycol (PEG)-induced stress were examined using morphological, physiological, biochemical, and molecular methods. The genome-edited lines demonstrated enhanced water retention, reduced stomatal density, and less oxidative damage compared to the wild-type plants under PEG-induced stress. Moreover, the slhp2,3 double mutant plants exhibited improved root growth, showcasing their superior drought tolerance over wild-type plants by accessing deeper water sources and maintaining hydration in water-limited environments. To investigate the involvement of cytokinin signaling regulators and genes associated with stomatal formation and differentiation, the expression of genes (Speechless [SPCH], FAMA, MUTE, TMM, HB25, HB31, RR6, RR7, and Solyc02g080860) was assessed. The results revealed that all regulators were downregulated, with SPCH, TMM, RR7, and RR6 showing significant reductions under PEG-induced stress. These results emphasize the promise of utilizing CRISPR/Cas9 to target cytokinin signaling pathways, enhancing drought tolerance in tomatoes through improvements in water retention and root growth, along with a reduction in stomatal density and malondialdehyde content.

Genome-wide identification of CRF gene family members in four rice subspecies and expression analysis of OsCRF members in response to cold stress at seedling stage

Cytokinin Response Factors (CRFs) play a crucial role in plant growth and development, hormone signaling, and responses to biotic and abiotic stresses. However, there have been no reports on CRF genes in rice until now. We analyzed the CRF families in four rice subspecies: cultivated rice Oryza sativa Japonica Group, Oryza sativa Indica Group, and Oryza sativa (circum-Aus1 var. N22), as well as wild rice Oryza rufipogon. We identified 7, 6, 6, and 7 CRF in their genomes, respectively, distributed across different chromosomes. The protein motifs and gene structures of CRF in these four types of rice show high conservation. Cis-regulatory element analysis revealed that the promoter regions of the CRF contain numerous hormone and stress-related elements. The number of CRF in these four types of rice is not influenced by gene duplication. The expression pattern showed that OsCRF exhibit significant tissue-specific expression. The qRT-PCR results showed that OsCRF strongly responded to low-temperature stress and can be induced by melatonin and cytokinin to increase expression levels. In addition, the nuclear localisation of OsCRF4/5 was confirmed to be as predicted. The results above will provide a foundation for further and deeper investigation of CRFs.

Small chemical molecules regulating the phytohormone signalling alter the plant's physiological processes to improve stress adaptation, growth and productivity

Small chemical molecules are attractive agents for improving the plant processes associated with plant growth and stress tolerance. Recent advances in chemical biology and structure-assisted drug discovery approaches have opened up new avenues in plant biology to discover new drug-like molecules to improve plant processes for sustained food production. Several compounds targeting phytohormone biosynthesis or signalling cascades were designed to alter plant physiological mechanisms. Altering Abscisic acid synthesis and its signalling process can improve drought tolerance, and the processes targeted are reversible. Molecules targeting cytokinin, Auxin, and gibberellic acid regulate plant physiological processes and can potentially improve plant growth, biomass and productivity. The potential of molecules may be exploited as agrochemicals to enhance agricultural productivity. The discovery of small molecules provides new avenues to improve crop production in changing climatic conditions and the nutritional quality of foods. We present the rational combinations of small molecules with inhibitory and co-stimulatory effects and discuss future opportunities in this field.

Genome-Wide Investigation of the CRF Gene Family in Maize and Functional Analysis of ZmCRF9 in Response to Multiple Abiotic Stresses

The cytokinin response factors (CRFs) are pivotal players in regulating plant growth, development, and responses to diverse stresses. Despite their significance, comprehensive information on CRF genes in the primary food crop, maize, remains scarce. In this study, a genome-wide analysis of CRF genes in maize was conducted, resulting in the identification of 12 members. Subsequently, we assessed the chromosomal locations, gene duplication events, evolutionary relationships, conserved motifs, and gene structures of all ZmCRF members. Analysis of ZmCRF promoter regions indicated the presence of cis-regulatory elements associated with plant growth regulation, hormone response, and various abiotic stress responses. The expression patterns of maize CRF genes, presented in heatmaps, exhibited distinctive patterns of tissue specificity and responsiveness to multiple abiotic stresses. qRT-PCR experiments were conducted on six selected genes and confirmed the involvement of ZmCRF genes in the plant's adaptive responses to diverse environmental challenges. In addition, ZmCRF9 was demonstrated to positively regulate cold and salt tolerance. Ultimately, we explored the putative interaction partners of ZmCRF proteins. In summary, this systematic overview and deep investigation of ZmCRF9 provides a solid foundation for further exploration into how these genes contribute to the complex interplay of plant growth, development, and responses to stress.

CRF transcription factors in the trade-off between abiotic stress response and plant developmental processes

Climate change-induced environmental stress significantly affects crop yield and quality. In response to environmental stressors, plants use defence mechanisms and growth suppression, creating a resource trade-off between the stress response and development. Although stress-responsive genes have been widely engineered to enhance crop stress tolerance, there is still limited understanding of the interplay between stress signalling and plant growth, a research topic that can provide promising targets for crop genetic improvement. This review focuses on Cytokinin Response Factors (CRFs) transcription factor's role in the balance between abiotic stress adaptation and sustained growth. CRFs, known for their involvement in cytokinin signalling and abiotic stress responses, emerge as potential targets for delaying senescence and mitigating yield penalties under abiotic stress conditions. Understanding the molecular mechanisms regulated by CRFs paves the way for decoupling stress responses from growth inhibition, thus allowing the development of crops that can adapt to abiotic stress without compromising development. This review highlights the importance of unravelling CRF-mediated pathways to address the growing need for resilient crops in the face of evolving climatic conditions.

TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response

Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.

A cytokinin response factor PtCRF1 is involved in the regulation of wood formation in poplar

Wood formation is a complex developmental process under the control of multiple levels of regulatory transcriptional network and hormone signals in trees. It is well known that cytokinin (CK) signaling plays an important role in maintaining the activity of the vascular cambium. The CK response factors (CRFs) encoding a subgroup of AP2 transcription factors have been identified to mediate the CK-dependent regulation in different plant developmental processes. However, the functions of CRFs in wood development remain unclear. Here, we characterized the function of PtCRF1, a CRF transcription factor isolated from poplar, in the process of wood formation. The PtCRF1 is preferentially expressed in secondary vasculature, especially in vascular cambium and secondary phloem, and encodes a transcriptional activator. Overexpression of PtCRF1 in transgenic poplar plants led to a significant reduction in the cell layer number of vascular cambium. The development of wood tissue was largely promoted in the PtCRF1-overexpressing lines, while it was significantly compromised in the CRISPR/Cas9-generated double mutant plants of PtCRF1 and its closest homolog PtCRF2. The RNA sequencing (RNA-seq) and quantitative reverse transcription PCR (RT-qPCR) analyses showed that PtCRF1 repressed the expression of the typical CK-responsive genes. Furthermore, bimolecular fluorescence complementation assays revealed that PtCRF1 competitively inhibits the direct interactions between histidine phosphotransfer proteins and type-B response regulator by binding to PtHP protein. Collectively, these results indicate that PtCRF1 negatively regulates CK signaling and is required for woody cell differentiation in poplar.

Overexpression of SlCRF6 in tomato inhibits leaf development and affects plant morphology

Cytokinin response factors (CRFs) are transcription factors (TFs) that are specific to plants and have diverse functions in plant growth and stress responses. However, the precise roles of CRFs in regulating tomato plant architecture and leaf development have not been comprehensively investigated. Here, we identified a novel CRF, SlCRF6, which is involved in the regulation of plant growth via the gibberellin (GA) signaling pathway. SlCRF6-overexpressing (SlCRF6-OE) plants displayed pleiotropic phenotypic changes, including reduced internode length and leaf size, which caused dwarfism in tomato plants. This dwarfism could be alleviated by application of exogenous GA3. Remarkably, quantitative real-time PCR (qRTPCR), a dual luciferase reporter assay and a yeast one-hybrid (Y1H) assay revealed that SlCRF6 promoted the expression of SlDELLA (a GA signal transduction inhibitor) in vivo. Furthermore, transgenic plants displayed variegated leaves and diminished chlorophyll content, resulting in decreased photosynthetic efficiency and less starch than in wild-type (WT) plants. The results of transient expression assays and Y1H assays indicated that SlCRF6 suppressed the expression of SlPHAN (leaf morphology-related gene). Collectively, these findings suggest that SlCRF6 plays a crucial role in regulating tomato plant morphology, leaf development, and the accumulation of photosynthetic products.

Metabolic and Molecular Rearrangements of Sauvignon Blanc (Vitis vinifera L.) Berries in Response to Foliar Applications of Specific Dry Yeast

Dry yeast extracts (DYE) are applied to vineyards to improve aromatic and secondary metabolic compound content and wine quality; however, systematic information on the underpinning molecular mechanisms is lacking. This work aimed to unravel, through a systematic approach, the metabolic and molecular responses of Sauvignon Blanc berries to DYE treatments. To accomplish this, DYE spraying was performed in a commercial vineyard for two consecutive years. Berries were sampled at several time points after the treatment, and grapes were analyzed for sugars, acidity, free and bound aroma precursors, amino acids, and targeted and untargeted RNA-Seq transcriptional profiles. The results obtained indicated that the DYE treatment did not interfere with the technological ripening parameters of sugars and acidity. Some aroma precursors, including cys-3MH and GSH-3MH, responsible for the typical aromatic nuances of Sauvignon Blanc, were stimulated by the treatment during both vintages. The levels of amino acids and the global RNA-seq transcriptional profiles indicated that DYE spraying upregulated ROS homeostatic and thermotolerance genes, as well as ethylene and jasmonic acid biosynthetic genes, and activated abiotic and biotic stress responses. Overall, the data suggested that the DYE reduced berry oxidative stress through the regulation of specific subsets of metabolic and hormonal pathways.

PagERF81 regulates lignin biosynthesis and xylem cell differentiation in poplar

Lignin is a major component of plant cell walls and is essential for plant growth and development. Lignin biosynthesis is controlled by a hierarchical regulatory network involving multiple transcription factors. In this study, we showed that the gene encoding an APETALA 2/ethylene-responsive element binding factor (AP2/ERF) transcription factor, PagERF81, from poplar 84 K (Populus alba × P. glandulosa) is highly expressed in expanding secondary xylem cells. Two independent homozygous Pagerf81 mutant lines created by gene editing, produced significantly more but smaller vessel cells and longer fiber cells with more lignin in cell walls, while PagERF81 overexpression lines had less lignin, compared to non-transgenic controls. Transcriptome and reverse transcription quantitative PCR data revealed that multiple lignin biosynthesis genes including Cinnamoyl CoA reductase 1 (PagCCR1), Cinnamyl alcohol dehydrogenase 6 (PagCAD6), and 4-Coumarate-CoA ligase-like 9 (Pag4CLL9) were up-regulated in Pagerf81 mutants, but down-regulated in PagERF81 overexpression lines. In addition, a transient transactivation assay revealed that PagERF81 repressed the transcription of these three genes. Furthermore, yeast one hybrid and electrophoretic mobility shift assays showed that PagERF81 directly bound to a GCC sequence in the PagCCR1 promoter. No known vessel or fiber cell differentiation related genes were differentially expressed, so the smaller vessel cells and longer fiber cells observed in the Pagerf81 lines might be caused by abnormal lignin deposition in the secondary cell walls. This study provides insight into the regulation of lignin biosynthesis, and a molecular tool to engineer wood with high lignin content, which would contribute to the lignin-related chemical industry and carbon sequestration.

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.

Molecular Regulation and Evolution of Cytokinin Signaling in Plant Abiotic Stresses

The sustainable production of crops faces increasing challenges from global climate change and human activities, which leads to increasing instances of many abiotic stressors to plants. Among the abiotic stressors, drought, salinity and excessive levels of toxic metals cause reductions in global agricultural productivity and serious health risks for humans. Cytokinins (CKs) are key phytohormones functioning in both normal development and stress responses in plants. Here, we summarize the molecular mechanisms on the biosynthesis, metabolism, transport and signaling transduction pathways of CKs. CKs act as negative regulators of both root system architecture plasticity and root sodium exclusion in response to salt stress. The functions of CKs in mineral-toxicity tolerance and their detoxification in plants are reviewed. Comparative genomic analyses were performed to trace the origin, evolution and diversification of the critical regulatory networks linking CK signaling and abiotic stress. We found that the production of CKs and their derivatives, pathways of signal transduction and drought-response root growth regulation are evolutionarily conserved in land plants. In addition, the mechanisms of CK-mediated sodium exclusion under salt stress are suggested for further investigations. In summary, we propose that the manipulation of CK levels and their signaling pathways is important for plant abiotic stress and is, therefore, a potential strategy for meeting the increasing demand for global food production under changing climatic conditions.

Bromodomain-containing factor GTE4 regulates Arabidopsis immune response

Background

Plants are continuously challenged with biotic stress from environmental pathogens, and precise regulation of defense responses is critical for plant survival. Defense systems require considerable amounts of energy and resources, impairing plant growth, and plant hormones controlling transcriptional regulation play essential roles in establishing the appropriate balance between defense response to pathogens and growth. Chromatin regulators modulating gene transcription are broadly involved in regulating stress-responsive genes. However, which chromatin factors are involved in coordinating hormone signaling and immune responses in plants, and their functional mechanisms, remains unclear. Here, we identified a role of bromodomain-containing protein GTE4 in negatively regulating defense responses in Arabidopsis thaliana.

Results

GTE4 mainly functions as activator of gene expression upon infection with Pseudomonas syringe. Genome-wide profiling of GTE4 occupancy shows that GTE4 tends to bind to active genes, including ribosome biogenesis related genes and maintains their high expression levels during pathogen infection. However, GTE4 is also able to repress gene expression. GTE4 binds to and represses jasmonate biosynthesis gene OPR3. Disruption of GTE4 results in overaccumulation of jasmonic acid (JA) and enhanced JA-responsive gene expression. Unexpectedly, over-accumulated JA content in gte4 mutant is coupled with downregulation of JA-mediated immune defense genes and upregulation of salicylic acid (SA)-mediated immune defense genes, and enhanced resistance to Pseudomonas, likely through a noncanonical pathway.

Conclusions

Overall, we identified a new role of the chromatin factor GTE4 as negative regulator of plant immune response through inhibition of JA biosynthesis, which in turn noncanonically activates the defense system against Pseudomonas. These findings provide new knowledge of chromatic regulation of plant hormone signaling during defense responses.

Expression of Genes Involved in ABA and Auxin Metabolism and LEA Gene during Embryogenesis in Hemp

The level of phytohormones such as abscisic acid (ABA) and auxins (Aux) changes dynamically during embryogenesis. Knowledge of the transcriptional activity of the genes of their metabolic pathways is essential for a deeper understanding of embryogenesis itself; however, it could also help breeding programs of important plants, such as Cannabis sativa, attractive for the pharmaceutical, textile, cosmetic, and food industries. This work aimed to find out how genes of metabolic pathways of Aux (IAA-1, IAA-2, X15-1, X15-2) and ABA (PP2C-1) alongside one member of the LEA gene family (CanLea34) are expressed in embryos depending on the developmental stage and the embryo cultivation in vitro. Walking stick (WS) and mature (M) cultivated and uncultivated embryos of C. sativa cultivars 'KC Dora' and 'USO 31' were analyzed. The RT-qPCR results indicated that for the development of immature (VH) embryos, the genes (IAA-1, IAA-2) are likely to be fundamental. Only an increased expression of the CanLea34 gene was characteristic of the fully maturated (M) embryos. In addition, this feature was significantly increased by cultivation. In conclusion, the cultivation led to the upsurge of expression of all studied genes.

The SlTPL3-SlWUS module regulates multi-locule formation in tomato by modulating auxin and gibberellin levels in the shoot apical meristem

Malformed fruits depreciate a plant's market value. In tomato (Solanum lycopersicum), fruit malformation is associated with the multi-locule trait, which involves genes regulating shoot apical meristem (SAM) development. The expression pattern of TOPLESS3 (SlTPL3) throughout SAM development prompted us to investigate its functional significance via RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9 (Cas9)-mediated gene editing. Lower SlTPL3 transcript levels resulted in larger fruits with more locules and larger SAMs at the 5 d after germination (DAG5) stage. Differentially expressed genes in the SAM of wild-type (WT) and SlTPL3-RNAi plants, identified by transcriptome deep sequencing (RNA-seq), were enriched in the gibberellin (GA) biosynthesis and plant hormone signaling pathways. Moreover, exogenous auxin and paclobutrazol treatments rescued the multi-locule phenotype, indicating that SlTPL3 affects SAM size by mediating auxin and GA levels in the SAM. Furthermore, SlTPL3 interacted with WUSCHEL (SlWUS), which plays an important role in SAM size maintenance. We conducted RNA-seq and DNA affinity purification followed by sequencing (DAP-seq) analyses to identify the genes regulated by SlTPL3 and SlWUS in the SAM and to determine how they regulate SAM size. We detected 24 overlapping genes regulated by SlTPL3 and SlWUS and harboring an SlWUS-binding motif in their promoters. Furthermore, functional annotation revealed a notable enrichment for functions in auxin transport, auxin signal transduction, and GA biosynthesis. Dual-luciferase assays also revealed that SlTPL3 enhances SlWUS-mediated regulation (repression and activation) of SlPIN3 and SlGA2ox4 transcription, indicating that the SlTPL3-SlWUS module regulates SAM size by mediating auxin distribution and GA levels, and perturbations of this module result in enlarged SAM. These results provide novel insights into the molecular mechanism of SAM maintenance and locule formation in tomato and highlight the SlTPL3-SlWUS module as a key regulator.

An APETALA2/ethylene responsive factor transcription factor GmCRF4a regulates plant height and auxin biosynthesis in soybean

Plant height is one of the key agronomic traits affecting soybean yield. The cytokinin response factors (CRFs), as a branch of the APETALA2/ethylene responsive factor (AP2/ERF) super gene family, have been reported to play important roles in regulating plant growth and development. However, their functions in soybean remain unknown. This study characterized a soybean CRF gene named GmCRF4a by comparing the performance of the homozygous Gmcrf4a-1 mutant, GmCRF4a overexpression (OX) and co-silencing (CS) lines. Phenotypic analysis showed that overexpression of GmCRF4a resulted in taller hypocotyls and epicotyls, more main stem nodes, and higher plant height. While down-regulation of GmCRF4a conferred shorter hypocotyls and epicotyls, as well as a reduction in plant height. The histological analysis results demonstrated that GmCRF4a promotes epicotyl elongation primarily by increasing cell length. Furthermore, GmCRF4a is required for the expression of GmYUCs genes to elevate endogenous auxin levels, which may subsequently enhance stem elongation. Taken together, these observations describe a novel regulatory mechanism in soybean, and provide the basis for elucidating the function of GmCRF4a in auxin biosynthesis pathway and plant heigh regulation in plants.

Cytokinin and abiotic stress tolerance -What has been accomplished and the way forward?

More than a half-century has passed since it was discovered that phytohormone cytokinin (CK) is essential to drive cytokinesis and proliferation in plant tissue culture. Thereafter, cytokinin has emerged as the primary regulator of the plant cell cycle and numerous developmental processes. Lately, a growing body of evidence suggests that cytokinin has a role in mitigating both abiotic and biotic stress. Cytokinin is essential to defend plants against excessive light exposure and a unique kind of abiotic stress generated by an altered photoperiod. Secondly, cytokinin also exhibits multi-stress resilience under changing environments. Furthermore, cytokinin homeostasis is also affected by several forms of stress. Therefore, the diverse roles of cytokinin in reaction to stress, as well as its interactions with other hormones, are discussed in detail. When it comes to agriculture, understanding the functioning processes of cytokinins under changing environmental conditions can assist in utilizing the phytohormone, to increase productivity. Through this review, we briefly describe the biological role of cytokinin in enhancing the performance of plants growth under abiotic challenges as well as the probable mechanisms underpinning cytokinin-induced stress tolerance. In addition, the article lays forth a strategy for using biotechnological tools to modify genes in the cytokinin pathway to engineer abiotic stress tolerance in plants. The information presented here will assist in better understanding the function of cytokinin in plants and their effective investigation in the cropping system.

A lineage-specific arginine in POS1 is required for fruit size control in Physaleae (Solanaceae) via gene co-option

Solanaceae have important economic value mainly due to their edible fruits. Physalis organ size 1/cytokinin response factor 3 (POS1/CRF3), a unique gene in Solanaceae, is involved in fruit size variation in Physalis but not in Solanum. However, the underlying mechanisms remain elusive. Here, we found that POS1/CRF3 was likely created via the fusion of CRF7 and CRF8 duplicates. Multiple genetic manipulations revealed that only POS1 and Capsicum POS1 (CaPOS1) functioned in fruit size control via the positive regulation of cell expansion. Comparative studies in a phylogenetic framework showed the directional enhancement of POS1-like expression in the flowers and fruits of Physaleae and the specific gain of certain interacting proteins associated with cell expansion by POS1 and CaPOS1. A lineage-specific single nucleotide polymorphism (SNP) caused the 68th amino acid histidine in the POS1 orthologs of non-Physaleae (Nicotiana and Solanum) to change to arginine in Physaleae (Physalis and Capsicum). Substituting the arginine in Physaleae POS1-like by histidine completely abolished their function in the fruits and the protein-protein interaction (PPI) with calreticulin-3. Transcriptomic comparison revealed the potential downstream pathways of POS1, including the brassinosteroid biosynthesis pathway. However, POS1-like may have functioned ancestrally in abiotic stress within Solanaceae. Our work demonstrated that heterometric expression and a SNP caused a single amino acid change to establish new PPIs, which contributed to the co-option of POS1 in multiple regulatory pathways to regulate cell expansion and thus fruit size in Physaleae. These results provide new insights into fruit morphological evolution and fruit yield control.

CYTOKININ RESPONSE FACTOR 2 is involved in modulating the salt stress response

Cytokinin has strong connections to development and a growing role in the abiotic stress response. Here we show that CYTOKININ RESPONSE FACTOR 2 (CRF2) is additionally involved in the salt (NaCl) stress response. CRF2 promoter-GUS expression indicates CRF2 involvement in the response to salt stress as well as the previously known cytokinin response. Interestingly, CRF2 mutant seedlings are quite similar to the wild type (WT) under non-stressed conditions yet have many distinct changes in response to salt stress. Cytokinin levels measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS) that increased in the WT after salt stress are decreased in crf2, potentially from CRF2 regulation of cytokinin biosynthesis genes. Ion content measured by inductively coupled plasma optical emission spectrometry (ICP-OES) was increased in the WT for Na, K, Mn, Ca and Mg after salt stress, whereas the corresponding Ca and Mg increases are lacking in crf2. Many genes examined by RNA-seq analysis were altered transcriptionally by salt stress in both the WT and crf2, yet interestingly approximately one-third of salt-modified crf2 transcripts (2655) showed unique regulation. Different transcript profiles for salt stress in crf2 compared with the WT background was further supported through an examination of co-expressed genes by weighted gene correlation network analysis (WGCMA) and principal component analysis (PCA). Additionally, Gene Ontology (GO) enrichment terms found from salt-treated transcripts revealed most photosynthesis-related terms as only being affected in crf2, leading to an examination of chlorophyll levels and the efficiency of photosystem II (via the ratio of variable fluorescence to maximum fluorescence, F_v /F_m ) as well as physiology after salt treatment. Salt stress-treated crf2 plants had both reduced chlorophyll levels and lower F_v /F_m values compared with the WT, suggesting that CRF2 plays a role in the modulation of salt stress responses linked to photosynthesis.

ARF6s Identification and Function Analysis Provide Insights Into Flower Development of Punica granatum L

Based on the genome and small-RNA sequencing of pomegranate, miRNA167 and three target genes PgARF6 were identified in "Taishanhong" genome. Three PgARF6 genes and their corresponding protein sequences, expression patterns in pomegranate flower development and under exogenous hormones treatments were systematically analyzed in this paper. We found that PgARF6s are nuclear proteins with conserved structures. However, PgARF6s had different protein structures and expression profiles in pomegranate flower development. At the critical stages of pomegranate ovule sterility (8.1-14.0 mm), the expression levels of PgARF6s in bisexual flowers were lower than those in functional male flowers. Interestingly, PgARF6c expression level was significantly higher than PgARF6a and PgARF6b. Under the treatment of exogenous IBA and 6-BA, PgARF6s were down-regulated, and the expression of PgARF6c was significantly inhibited. PgmiR167a and PgmiR167d had the binding site on PgARF6 genes sequences, and PgARF6a has the directly targeted regulatory relationship with PgmiR167a in pomegranate. At the critical stage of ovule development (8.1-12.0 mm), exogenous IBA and 6-BA promoted the content of GA and ZR accumulation, inhibited BR accumulation. There was a strong correlation between the expression of PgARF6a and PgARF6b. Under exogenous hormone treatment, the content of ZR, BR, GA, and ABA were negatively correlated with the expressions of PgARF6 genes. However, JA was positively correlated with PgARF6a and PgARF6c under IBA treatment. Thus, our results provide new evidence for PgARF6 genes involving in ovule sterility in pomegranate flowers.

Isopentenyltransferases as master regulators of crop performance: their function, manipulation, and genetic potential for stress adaptation and yield improvement

Isopentenyltransferase (IPT) in plants regulates a rate-limiting step of cytokinin (CTK) biosynthesis. IPTs are recognized as key regulators of CTK homeostasis and phytohormone crosstalk in both biotic and abiotic stress responses. Recent research has revealed the regulatory function of IPTs in gene expression and metabolite profiles including source-sink modifications, energy metabolism, nutrient allocation and storage, stress defence and signalling pathways, protein synthesis and transport, and membrane transport. This suggests that IPTs play a crucial role in plant growth and adaptation. In planta studies of IPT-driven modifications indicate that, at a physiological level, IPTs improve stay-green characteristics, delay senescence, reduce stress-induced oxidative damage and protect photosynthetic machinery. Subsequently, these improvements often manifest as enhanced or stabilized crop yields and this is especially apparent under environmental stress. These mechanisms merit consideration of the IPTs as 'master regulators' of core cellular metabolic pathways, thus adjusting plant homeostasis/adaptive responses to altered environmental stresses, to maximize yield potential. If their expression can be adequately controlled, both spatially and temporally, IPTs can be a key driver for seed yield. In this review, we give a comprehensive overview of recent findings on how IPTs influence plant stress physiology and yield, and we highlight areas for future research.

Osmotic stress-induced somatic embryo maturation of coffee Coffea arabica L., shoot and root apical meristems development and robustness

Somatic embryogenesis (SE) is the most important plant biotechnology process for plant regeneration, propagation, genetic transformation and genome editing of coffee, Coffea arabica L. Somatic embryo (SEs) conversion to plantlets is the principal bottleneck for basic and applied use of this process. In this study we focus on the maturation of SEs of C. arabica var. Typica. SEs conversion to plantlet up to 95.9% was achieved under osmotic stress, using 9 g/L gelrite, as compared with only 39.34% in non-osmotic stress. Mature SEs induced in osmotic stress developed shoot and root apical meristems, while untreated SEs were unable to do it. C. arabica regenerated plants from osmotic stress were robust, with higher leaf and root area and internode length. To understand a possible regulatory mechanism, gene expression of key genes of C. arabica, homologous to sequences in the Arabidopsis thaliana genome, were analyzed. A set of two component system and cytokinin signaling-related coding genes (AHK1, AHK3, AHP4 and ARR1) which interact with WUSCHEL and WOX5 homedomains and morphogenic genes, BABY-BOOM, LEC1, FUS3 and AGL15, underwent significant changes during maturation of SEs of C. arabica var. Typica. This protocol is currently being applied in genetic transformation with high rate of success.

Three Strains of Tobacco etch virus Distinctly Alter the Transcriptome of Apical Stem Tissue in Capsicum annuum during Infection

Tobacco etch virus (TEV; genus Potyvirus) is flexuous rod shaped with a single molecule of single-stranded RNA and causes serious yield losses in species in the Solanaceae. Three TEV strains (HAT, Mex21, and N) are genetically distinct and cause different disease symptoms in plants. Here, a transcriptomic RNA sequencing approach was taken for each TEV strain to evaluate gene expression of the apical stem segment of pepper plants during two stages of disease development. Distinct profiles of Differentially Expressed Genes (DEGs) were identified for each TEV strain. DEG numbers increased with degree of symptom severity: 24 from HAT, 1190 from Mex21, and 4010 from N. At 7 days post-inoculation (dpi), when systemic symptoms were similar, there were few DEGs for HAT- and Mex21-infected plants, whereas N-infected plants had 2516 DEGs. DEG patterns from 7 to 14 dpi corresponded to severity of disease symptoms: milder disease with smaller DEG changes for HAT and Mex21 and severe disease with larger DEG changes for N. Strikingly, in each of these comparisons, there are very few overlapping DEGs among the TEV strains, including no overlapping DEGs between all three strains at 7 or 14 dpi.

Clade III cytokinin response factors share common roles in response to oxidative stress responses linked to cytokinin synthesis

Cytokinin response factors (CRFs) are transcription factors that are involved in cytokinin (CK) response, as well as being linked to abiotic stress tolerance. In particular, oxidative stress responses are activated by Clade III CRF members, such as AtCRF6. Here we explored the relationships between Clade III CRFs and oxidative stress. Transcriptomic responses to oxidative stress were determined in two Clade III transcription factors, Arabidopsis AtCRF5 and tomato SlCRF5. AtCRF5 was required for regulated expression of >240 genes that are involved in oxidative stress response. Similarly, SlCRF5 was involved in the regulated expression of nearly 420 oxidative stress response genes. Similarities in gene regulation by these Clade III members in response to oxidative stress were observed between Arabidopsis and tomato, as indicated by Gene Ontology term enrichment. CK levels were also changed in response to oxidative stress in both species. These changes were regulated by Clade III CRFs. Taken together, these findings suggest that Clade III CRFs play a role in oxidative stress response as well as having roles in CK signaling.

Convergence and Divergence of Sugar and Cytokinin Signaling in Plant Development

Plants adjust their growth and development through a sophisticated regulatory system integrating endogenous and exogenous cues. Many of them rely on intricate crosstalk between nutrients and hormones, an effective way of coupling nutritional and developmental information and ensuring plant survival. Sugars in their different forms such as sucrose, glucose, fructose and trehalose-6-P and the hormone family of cytokinins (CKs) are major regulators of the shoot and root functioning throughout the plant life cycle. While their individual roles have been extensively investigated, their combined effects have unexpectedly received little attention, resulting in many gaps in current knowledge. The present review provides an overview of the relationship between sugars and CKs signaling in the main developmental transition during the plant lifecycle, including seed development, germination, seedling establishment, root and shoot branching, leaf senescence, and flowering. These new insights highlight the diversity and the complexity of the crosstalk between sugars and CKs and raise several questions that will open onto further investigations of these regulation networks orchestrating plant growth and development.

Global View on the Cytokinin Regulatory System in Potato

Cytokinins (CKs) were earlier shown to promote potato tuberization. Our study aimed to identify and characterize CK-related genes which constitute CK regulatory system in the core potato (Solanum tuberosum) genome. For that, CK-related genes were retrieved from the sequenced genome of the S. tuberosum doubled monoploid (DM) Phureja group, classified and compared with Arabidopsis orthologs. Analysis of selected gene expression was performed with a transcriptome database for the S. tuberosum heterozygous diploid line RH89-039-16. Genes responsible for CK signaling, biosynthesis, transport, and metabolism were categorized in an organ-specific fashion. According to this database, CK receptors StHK2/3 predominate in leaves and flowers, StHK4 in roots. Among phosphotransmitters, StHP1a expression largely predominates. Surprisingly, two pseudo-phosphotransmitters intended to suppress CK effects are hardly expressed in studied organs. Among B-type RR genes, StRR1b, StRR11, and StRR18a are actively expressed, with StRR1b expressing most uniformly in all organs and StRR11 exhibiting the highest expression in roots. By cluster analysis four types of prevailing CK-signaling chains were identified in (1) leaves and flowers, StHK2/3→S t H P1a→StRR1b/+; (2) shoot apical meristems, stolons, and mature tubers, StHK2/4→S t H P1a→StRR1b/+; (3) stems and young tubers, StHK2/4→S t H P1a→StRR1b/11/18a; and (4) roots and tuber sprouts, StHK4→S t H P1a→StRR11/18a. CK synthesis genes StIPT3/5 and StCYP735A are expressed mainly in roots followed by tuber sprouts, but rather weakly in stolons and tubers. By contrast, CK-activation genes StLOGs are active in stolons, and StLOG3b expression is even stolon-confined. Apparently, the main CK effects on tuber initiation are realized via activity of StLOG1/3a/3b/7c/8a genes in stolons. Current advances and future directions in potato research are discussed.

Cytokinin-regulated targets of Cytokinin Response Factor 6 are involved in potassium transport

Cytokinin (CK) is a plant hormone crucial to plant development and growth. Cytokinin Response Factor 6 (CRF6) is a CK-induced transcription factor that is part of the CK signaling cascade. While the role of CRF6 has been examined in oxidative stress response, there has been surprisingly little investigation of CRF6 in the context of CK signaling, including identifying CK-regulated targets of CRF6. Here, we conduct a transcriptomic study of Arabidopsis examining the CRF6 mutant (crf6) in the presence and absence of CK, revealing 163 downstream CRF6-dependent CK-regulated differentially expressed genes (DEGs). 15.3% of these DEGS were found as overlapping with larger number of standardly identified CK-regulated DEGs, suggesting that CRF6 is involved in regulating a subset of downstream CK responses through these gene targets. The general transcriptional regulation of CRF6-dependent CK-regulated DEGs indicates that CRF6 may function as a negative regulator of CK response. We investigated one subset of CRF6 CK-dependent targets (SKOR, HAK5, and NRT1. 5) involved in an underexamined functional role of CK response: the uptake and transportation of potassium. To determine how CK and CRF6 are involved in potassium acquisition and distribution, ionomic and physiological experiments were conducted on plants grown in media with sufficient and deficient potassium concentrations and in the presence and absence of CK. In order to investigate how CK alone affects potassium transport, similar experiments were performed on skor, hak5, and nrt1.5 mutant lines of these CRF6-dependent CK-regulated targets. These findings indicate novel connections between CK and potassium transport, which appear to be regulated in a CRF6-dependent manner.

Research Progress on the Roles of Cytokinin in Plant Response to Stress

Cytokinins promote plant growth and development under normal plant growth conditions and also play an important role in plant resistance to stress. Understanding the working mechanisms of cytokinins under adverse conditions will help to make full use of cytokinins in agriculture to increase production and efficiency of land use. In this article, we review the progress that has been made in cytokinin research in plant response to stress and propose its future application prospects.

Comparative transcriptome analysis between a resistant and a susceptible Chinese cabbage in response to Hyaloperonospora brassicae

Downy mildew caused by Hyaloperonosporabrassicae (H. brassicae) leads to up to 90% of the crop yield loss in Chinese cabbage in China. A transcriptome analysis was carried out between a resistant line (13-13, R) and a susceptible line (15-14, S) of Chinese cabbage in response to H. brassicae. The NOISeq method was used to find differentially expressed genes (DEGs) between these two groups and GO and KEGG were carried out to find R genes related to downy mildew response of Chinese cabbage. qRT-PCR was carried out to verify the reliability of RNA-seq expression data. A total of 3,055 DEGs were screened out from 41,020 genes and clustered into 6 groups with distinct expression patterns. A total of 87 candidate DEGs were identified by functional annotation based on GO and KEGG analysis. These candidate genes are involved in plant-pathogen interaction pathway, among which 54 and 33 DEGs were categorized into plant-pathogen interaction proteins and transcription factors, respectively. Proteins encoded by these genes have been reported to play an important role in the pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) processes of disease responses in some model plants, such as Arabidopsis, rice, tobacco, and tomato. However, little is known about the mechanisms of these genes in resistance to downy mildew in Chinese cabbage. Our findings are useful for further characterization of these candidate genes and helpful in breeding resistant strains.