Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

Glutamate induction of whole potatoes alleviated the browning of fresh cuts: Jasmonate signalling may play a key role

Enzymatic browning is one of the most troublesome issues for fresh-cut fruits and vegetables, as it not only reduces product quality and shelf life but also causes great waste and economic loss. Although many antibrowning technologies have been explored, few noncontact methods have been reported. In particular, the effect of using glutamate (Glu) is unknown. This study revealed that Glu treatment of whole tubers significantly reduced browning in fresh-cut potatoes. This whole-tuber Glu induction under optimal conditions (1 % Glu for 12 h) produced a brighter colour and better sensory quality than soaking slices in solutions of Glu or ascorbic acid. Notably, Glu induction led to increased jasmonic acid (JA) and jasmonate-isoleucine (JA-Ile) accumulation. The activities of 12-oxophytodienoic acid reductase 3 (OPR3), jasmonate-resistant 1 (JAR1), and coronatine-insensitive 1 (COI1) in the jasmonate synthesis pathway and the expression of their corresponding genes also increased. Additionally, phenylpropane metabolism was upregulated, as evidenced by increased levels of phenylalanine ammonia-lyase (PAL), 4-coumaric acid coenzyme a ligase (4CL), phenolic compounds and flavonoids. Moreover, the reactive oxygen species (ROS)-redox balance improved, the contents of hydrogen peroxide and malondialdehyde (MDA) decreased, and the catalase (CAT) activity and 1,1-diphenyl-2-picryl-hydrazyl radical (DPPH) scavenging capacity increased. Finally, Glu induction increased microbiological safety, resulting in a lower total bacterial count. Thus, Glu induction may modulate jasmonic acid synthesis and signalling, regulate phenylpropane metabolism and the reactive oxygen species (ROS)-redox balance, and ultimately slow browning and improve storage quality in fresh-cut potatoes. This is the first report of a noncontact browning control technique involving Glu, which provides new ideas for the fresh-cut industry.

Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana

Developmental processes are known to be circadian-regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals that entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diel oscillations of the Arabidopsis transcriptome have typically been measured in seedlings. We collected RNA sequencing (RNA-seq) data from Arabidopsis leaves over developmental and diel timescales, concurrently: every 4 h d-1, on three separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diel timescale, including genes related to a key energy sensor: the sucrose nonfermenting-1-related protein kinase complex. Moreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diel patterns that varied in amplitude, but not phase, over development. Some previously identified reverse transcription quantitative polymerase chain reaction housekeeping genes display undesirable levels of variation over both timescales. We identify which common reverse transcription quantitative polymerase chain reaction housekeeping genes are most stable across developmental and diel timescales. In summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diel patterns of expression change over developmental timescales.

Arabidopsis GH3.10 conjugates jasmonates

Jasmonates regulate plant development and defence. In angiosperms, the canonical bioactive jasmonate is jasmonoyl-isoleucine (JA-Ile), which is formed in Arabidopsis thaliana by JAR1 and GH3.10. In contrast to other jasmonate biosynthesis or perception mutants, however, gh3.10 jar1 knockout lines are still fertile. Therefore we investigated whether further jasmonates and GH3 enzymes contribute to regulation of fertility. Jasmonate levels were analysed by liquid chromatography-mass spectrometry. The substrate range of recombinant GH3.10 and related GH3 enzymes was studied using non-targeted ex vivo metabolomics with flower and leaf extracts of A. thaliana and in vitro enzyme assays. Jasmonate application experiments were performed to study their potential bioactivity. In flowers and wounded leaves of gh3.10 jar1 knockout lines JA-Ile was below the detection limit. While 12-hydroxy-JA was identified as the preferred substrate of GH3.10, no other recombinant GH3 enzymes tested were capable of JA-Ile formation. Additional JA conjugates found in wounded leaves (JA-Gln) or formed in flowers upon MeJA treatment in the absence of JA-Ile (JA-Gln, JA-Asn, JA-Glu) were identified. The aos gh3.10 jar1 was introduced as a novel tool to test for the bioactivity of JA-Gln to regulate fertility. This study found JAR1 and GH3.10 are the only contributors to JA-Ile biosynthesis in Arabidopsis and identified a number of JA conjugates as potential bioactive jasmonates acting in the absence of JA-Ile. However, their contribution in regulating fertility is yet to be conclusively determined.

Combating plant diseases through transition metal allocation

Understanding how plants fend-off invading microbes is essential for food security and the economy of large parts of the world. Consequently, a sustained and dedicated effort has been directed at unveiling how plants protect themselves from invading microbes. Major defense hormone signaling pathways have been characterized, the identity of many immune response-triggering molecules as well as many of their receptors have been determined, and the mechanisms of pathogen-host arms race are being studied. In recent years, evidence for a new layer of plant innate immunity involving transition metals has been brought forward. This would link plant metal nutrition with plant immune responses and open up possible new strategies for pathogen control involving metal fertilizers instead of pesticides. In this review, we outline our current understanding of metal-mediated plant immune response and indicate the future avenues of exploration of this topic.

Warm temperature and mild drought remodel transcriptome and alter Arabidopsis responses to mite herbivory

In the context of climate change, increased temperature and decreased water availability are expected to have profound effects on plant-herbivore interactions. To gain further insight into this issue, this work focuses on the dissection of the response of the Arabidopsis thaliana plant to the mite pest Tetranychus urticae under environmental conditions that resemble climate change. Phenotypical and molecular changes were analyzed in plants grown under mild drought and/or warm temperatures. When the transcriptome results were compared in standard and altered climate conditions, a large number of genes were found to be differentially expressed. Mite infestations in these plants showed that basal alterations conditioned the subsequent response of the plant to a specific biotic stressor. Warm temperatures favored mite performance and decreased jasmonic acid accumulation. Reduced plant damage in mild drought conditions was correlated with a higher jasmonic acid accumulation and the up-regulation of many genes involved in the production of defensive compounds. In conclusion, the use of ambient conditions that resemble climate change highlighted the drastic alterations in gene expression that may occur in nature. Understanding how these changes affect specific plant-herbivore interactions is crucial to determining how global warming will affect crop production in the future.

Biocontrol mechanisms of antagonistic yeasts on postharvest fruits and vegetables and the approaches to enhance the biocontrol potential of antagonistic yeasts

During storage and transportation, fruits and vegetables are susceptible to various pathogens, leading to quality degradation and significant economic losses. Currently, chemical pesticides are primarily used for control; however, their overuse poses serious threats to human health and causes environmental pollution. Biocontrol, known for its environmentally friendly characteristics, has been extensively studied. Among biocontrol agents, yeasts are widely distributed and possesses strong antagonistic abilities, making them crucial agents against numerous pathogenic fungi. Despite their considerable promise, the full potential of antagonistic yeasts for broader application remains untapped. Therefore, this paper reviews the mechanisms of antagonistic yeasts as biocontrol agents for postharvest diseases, including space and nutrients competition, competition for scarce iron resources, parasitism, production of soluble and volatile antifungal compounds, and induction of host systemic resistance. The paper also introduces research on the combined application of antagonistic yeasts with physical, chemical, and other microbial methods. Ultimately, this review provides a potential pathway to enhance the biocontrol effectiveness of antagonistic yeasts and expand their application prospects.

SlASR3 mediates crosstalk between auxin and jasmonic acid signaling to regulate trichome formation in tomato

Trichomes play a pivotal role in plant resistance to biotic and abiotic stresses. Both auxin and jasmonic acid (JA) could induce tomato type II, V, and VI trichome formation. However, the existence of crosstalk between auxin and JA in trichome formation is not yet fully elucidated. In this study, we identified a Trihelix/MYB-like gene, SlASR3, is inhibited by both auxin and JA and is expressed in type II and VI trichomes in tomatoes. Knock-down or knockout of SlASR3 increased the densities of type II and VI trichomes, whereas overexpression of SlASR3 reduced the densities of type II and VI trichomes. SlASR3 was involved in the indole acetic acid (IAA)- and JA-induced formation of these trichome types. SlARF4 negatively regulated the transcription of SlASR3, and its effect on IAA-induced trichome formation depended on SlASR3. Likewise, SlMYC1 negatively regulated the transcription of SlASR3, and the regulation of SlMYC1 on JA-induced trichome formation was also SlASR3-dependent. Knock-down or knockout of SlASR3 increased the resistance to two-spotted spider mites in tomatoes. The research findings demonstrate that SlASR3 acts as a mediator in the crosstalk between JA and auxin signaling to regulate trichome formation and provide a new candidate gene for enhancing resistance to two-spotted spider mites.

Transcriptome analysis reveals regulatory mechanism of methyl jasmonate-induced monoterpenoid biosynthesis in Mentha arvensis L

Mentha arvensis L. (M. arvensis) is an aromatic plant of the Mentha genus, renowned for its medicinal and economic importance. The primary components of its essential oils (EOs) are monoterpenoids, synthesized and stored in peltate glandular trichomes (PGTs). In general, the EO content in M. arvensis is relatively low. Methyl jasmonate (MJ) has been reported as an effective elicitor of terpenoid biosynthesis in medicinal plants, but the specific mechanisms underlying MJ's influence on M. arvensis remain unclear. In this study, exogenous application of MJ significantly increased the EO content, yield, and PGT density in a dose-dependent manner. At a 5 mM dose, the EO content and PGT density peaked, with increases of 71.20% and 53.69%, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis indicated that, in general, MJ treatment did not significantly alter the types or relative proportions of EO components of M. arvensis. However, L-menthol content decreased slightly by 7.90% under 5 mM MJ treatment. Transcriptome analysis identified 4,659 differentially expressed genes (DEGs) in MJ-treated leaves. KEGG enrichment analysis revealed that "Monoterpenoid biosynthesis" was among the most significantly enriched metabolic pathways. Key genes involved in jasmonic acid (JA) signaling (JAZs and MYCs) and monoterpenoid biosynthesis (GPPSs, LSs, L3Hs, and IPRs) were significantly up-regulated. Co-expression analysis, promoter binding element analysis and weighted gene co-expression network analysis (WGCNA) indicated that transcription factors (TFs) such as AP2/ERF, WRKY, MYB, and bHLH play crucial roles in regulating MJ-mediated monoterpenoid biosynthesis. Several key candidate TFs potentially involved in regulating monoterpenoid biosynthesis in M. arvensis were identified. These findings provide valuable insights into the molecular mechanisms regulating monoterpenoid accumulation in the Mentha genus.

Combined Transcriptomics and Metabolomics Uncover the Potential Mechanism of Plant Growth-Promoting Rhizobacteria on the Regrowth of Leymus chinensis After Mowing

Mowing significantly influences nutrient cycling and stimulates metabolic adjustments in plants to promote regrowth. Plant growth-promoting rhizobacteria (PGPR) are crucial for enhancing plant growth, nutrient absorption, and stress resilience; however, whether inoculation with PGPR after mowing can enhance plant regrowth capacity further, as well as its specific regulatory mechanisms, remains unexplored. In this study, PGPR Pantoea eucalyptus (B13) was inoculated into mowed Leymus chinensis to evaluate its effects on phenotypic traits, root nutrient contents, and hormone levels during the regrowth process and to further explore its role in the regrowth of L. chinensis after mowing. The results showed that after mowing, root nutrient and sugar contents decreased significantly, while the signal pathways related to stress hormones were activated. This indicates that after mowing, root resources tend to sacrifice a part of growth and prioritize defense. After mowing, B13 inoculation regulated the plant's internal hormone balance by reducing the levels and signal of JA, SA, and ABA and upregulated the signal transduction of growth hormones in the root, thus optimizing growth and defense in a mowing environment. Transcriptomic and metabolomic analyses indicated that B13 promoted nutrient uptake and transport in L. chinensis root, maintained hormone homeostasis, enhanced metabolic pathways related to carbohydrates, energy, and amino acid metabolism to cope with mowing stress, and promoted root growth and regeneration of shoot. This study reveals the regenerative strategy regulated by B13 in perennial forage grasses, helping optimize resource utilization, increase yield, and enhance grassland stability and resilience.

Expression analysis of defense signaling marker genes in Capsicum annuum in response to phytohormones elicitation

BACKGROUND

To tolerate biotic stress, plants employ phytohormones such as jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) to regulate the immune response against different pathogens. Phytohormone-responsive genes, known as "Defense signaling marker genes," are used to evaluate plant disease resistance during pathogen infection. Most information on these marker genes derives from studies on the model plant Arabidopsis thaliana. The present study was aimed analyze the effect of hormonal elicitation at different concentrations at 24 h pos-treatment in the transcript level of 8 traditional genes selected for molecular studies plant-pathogen interactions in Capsicum.

METHODS AND RESULTS

Chemical treatment was achieved by spraying leaves of in vitro seedlings C. annuum L. with 0.1 mM, 1 mM or 2.5 mM ET; 1 mM, 2.5 mM, or 5 mM SA; 2.5 mM BABA; or 0.150 mM MeJA. Twenty-four hours after treatments were applied molecular analyses were carried out using qPCR to investigate the expression. Results revealed that 1 mM of ET or 0.15 mM of MeJA activated the expression CaPR1 (18--11.64-fold change), CaLOX2 (13.80-fold), CaAP2/ERF06 (22- 5.3- fold change), and CaPDF1.2 (2.3-1.5- fold). While, 5 mM of SA present effect of negative regulation on the expression in most of these genes.

CONCLUSIONS

Our results show that the expression profile induced by phytohormones in CaPR1 are particular in C. annuum, because were significantly induced for ET/MeJA, and dow-regulation with SA Contrary to Arabidopsis. Although, on both plants it is observed the cross talk between JA/ET and SA mediated signal pathways for the regulation of this gene.

Heterografting enhances chrysanthemum resistance to Alternaria alternata via jasmonate-mediated increases in trichomes and terpenoids

Trichomes are specialized hair-like structures in the epidermal cells of the above-ground parts of plants and help to protect them from pests and pathogens, and produce valuable metabolites. Chrysanthemum morifolium, which is used in tea products, has both ornamental and medicinal value; however, it is susceptible to infection by the fungus Alternaria alternata, which can result in substantial economic losses. Increasing the density of glandular trichomes enhances disease resistance and improves the production of medicinal metabolites in chrysanthemums, and jasmonate (JA) is known to promote the formation of trichomes in various plants. However, it remains unclear whether glandular trichomes in chrysanthemums are regulated by JA. In addition, grafting, a technique that can improve plant resistance to biotic stresses, has been poorly examined for its impact on glandular trichomes, terpenoids, and disease resistance. In this study, we demonstrate that grafting with Artemisia vulgaris rootstocks improves the resistance of chrysanthemum scions to A. alternata. Heterografted chrysanthemums exhibited higher trichome density and terpenoid content compared to self-grafted counterparts. Transcriptome analysis highlighted the significant role of CmJAZ1-like in disease resistance in heterografted chrysanthemums. Lines overexpressing CmJAZ1-like exhibited sensitivity to A. alternata, and this was characterized by reduced glandular trichome density and limited terpenoid content. Conversely, CmJAZ1-like silenced lines exhibited resistance to A. alternata and showed increased glandular trichome density and terpenoid content. Higher JA content was found in the heterografted chrysanthemum scions compared to self-grafted ones. Furthermore, we established that JA promoted the development of glandular trichomes and the synthesis of terpenoids while also inducing the degradation of CmJAZ1-like proteins in chrysanthemums. Our findings suggest that higher JA increases trichome density and terpenoid content, thereby enhancing resistance to A. alternata by regulating CmJAZ1-like in heterografted chrysanthemums.

An RdDM-independent function of Pol V transcripts in gene regulation and plant defence

RNA polymerase V (Pol V) and Pol IV are known to be specialized for RNA-directed DNA methylation (RdDM). Here we report that Pol V, but not Pol IV, regulates hundreds of genes including jasmonic acid-responsive genes and confers plant defence to Botrytis cinerea and Spodoptera exigua. About half of the Pol V-regulated genes are associated with Pol V transcripts (PVTs). We thus hypothesized that some PVTs could regulate gene expression in an RdDM-independent manner. To test this hypothesis, we studied three PVTs, PVT-ERF5a/b and PVT-ERF6, as models. PVT-ERF5a/b and PVT-ERF6 are transcribed from the upstream regions of ERF5 and ERF6 and positively regulate their transcription, thereby regulating plant defence. Such regulation involves PVT-dependent H3K4me3 deposition and requires the DRD1-DMS3-RDM1 complex that mediates Pol V recruitment to the target loci. These findings highlight an unprecedented role for PVTs in regulating gene transcription, apart from serving as scaffold RNAs to direct DNA methylation.

Multiomic analyses reveal key sectors of jasmonate-mediated defense responses in rice

The phytohormone jasmonate (JA) plays a central role in plant defenses against biotic stressors. However, our knowledge of the JA signaling pathway in rice (Oryza sativa) remains incomplete. Here, we integrated multiomic data from three tissues to characterize the functional modules involved in organizing JA-responsive genes. In the core regulatory sector, MYC2 transcription factor transcriptional cascades are conserved in different species but with distinct regulators (e.g. bHLH6 in rice), in which genes are early expressed across all tissues. In the feedback sector, MYC2 also regulates the expression of JA repressor and catabolic genes, providing negative feedback that truncates the duration of JA responses. For example, the MYC2-regulated NAC (NAM, ATAF1/2, and CUC2) transcription factor genes NAC1, NAC3, and NAC4 encode proteins that repress JA signaling and herbivore resistance. In the tissue-specific sector, many late-expressed genes are associated with the biosynthesis of specialized metabolites that mediate particular defensive functions. For example, the terpene synthase gene TPS35 is specifically induced in the leaf sheath and TPS35 functions in defense against oviposition by brown planthoppers and the attraction of this herbivore's natural enemies. Thus, by characterizing core, tissue-specific, and feedback sectors of JA-elicited defense responses, this work provides a valuable resource for future discoveries of key JA components in this important crop.

Architecture and dynamics of the abscisic acid gene regulatory network

The plant hormone abscisic acid (ABA) regulates essential processes in plant development and responsiveness to abiotic and biotic stresses. ABA perception triggers a post-translational signaling cascade that elicits the ABA gene regulatory network (GRN), encompassing hundreds of transcription factors (TFs) and thousands of transcribed genes. To further our knowledge of this GRN, we performed an RNA-seq time series experiment consisting of 14 time points in the 16 h following a one-time ABA treatment of 5-week-old Arabidopsis rosettes. During this time course, ABA rapidly changed transcription levels of 7151 genes, which were partitioned into 44 coexpressed modules that carry out diverse biological functions. We integrated our time-series data with publicly available TF-binding site data, motif data, and RNA-seq data of plants inhibited in translation, and predicted (i) which TFs regulate the different coexpression clusters, (ii) which TFs contribute the most to target gene amplitude, (iii) timing of engagement of different TFs in the ABA GRN, and (iv) hierarchical position of TFs and their targets in the multi-tiered ABA GRN. The ABA GRN was found to be highly interconnected and regulated at different amplitudes and timing by a wide variety of TFs, of which the bZIP family was most prominent, and upregulation of genes encompassed more TFs than downregulation. We validated our network models in silico with additional public TF-binding site data and transcription data of selected TF mutants. Finally, using a drought assay we found that the Trihelix TF GT3a is likely an ABA-induced positive regulator of drought tolerance.

Hydrogen sulfide enhances kiwifruit resistance to soft rot by regulating jasmonic acid signaling pathway

As the third active gas signal molecule in plants, hydrogen sulfide (H2S) plays important roles in physiological metabolisms and biological process of fruits and vegetables during postharvest storage. In the present study, the effects of H2S on enhancing resistance against soft rot caused by Botryosphaeria dothidea and the involvement of jasmonic acid (JA) signaling pathway in kiwifruit during the storage were investigated. The results showed that 20 μL L-1 H2S fumigation restrained the disease incidence of B. dothidea-inoculated kiwifruit during storage, and delayed the decrease of firmness and the increase of soluble solids (SSC) content. H2S treatment increased the transcription levels of genes related to JA biosynthesis (AcLOX3, AcAOS, AcAOC2, and AcOPR) and signaling pathway (AcCOI1, AcJAZ5, AcMYC2, and AcERF1), as well as the JA accumulation. Meanwhile, H2S promoted the expression of defense-related genes (AcPPO, AcSOD, AcGLU, AcCHI, AcAPX, and AcCAT). Correlation analysis revealed that JA content was positively correlated with the expression levels of JA biosynthesis and defense-related genes. Overall, the results indicated that H2S could promote the increase of endogenous JA content and expression of defense-related genes by regulating the transcription levels of JA pathway-related genes, which contributed to the inhibition on the soft rot occurrence of kiwifruit.

Allele-Specific Hormone Dynamics in Highly Transgressive F2 Biomass Segregants in Sugarcane (Saccharum spp.)

Sugarcane holds global promise as a biofuel feedstock, necessitating a deep understanding of factors that influence biomass yield. This study unravels the intricate dynamics of plant hormones that govern growth and development in sugarcane. Transcriptome analysis of F2 introgression hybrids, derived from the cross of Saccharum officinarum "LA Purple" and wild Saccharum robustum "MOL5829", was conducted, utilizing the recently sequenced allele-specific genome of "LA Purple" as a reference. A total of 8059 differentially expressed genes were categorized into gene models (21.5%), alleles (68%), paralogs (10%), and tandemly duplicated genes (0.14%). KEGG analysis highlighted enrichment in auxin (IAA), jasmonic acid (JA), and abscisic acid (ABA) pathways, revealing regulatory roles of hormone repressor gene families (Aux/IAA, PP2C, and JAZ). Signaling pathways indicated that downregulation of AUX/IAA and PP2C and upregulation of JAZ repressor genes in high biomass segregants act as key players in influencing downstream growth regulatory genes. Endogenous hormone levels revealed higher concentrations of IAA and ABA in high biomass, which contrasted with lower levels of JA. Weighted co-expression network analysis demonstrated strong connectivity between hormone-related key genes and cell wall structural genes in high biomass genotypes. Expression analysis confirmed the upregulation of genes involved in the synthesis of structural carbohydrates and the downregulation of inflorescence and senescence-related genes in high biomass, which suggested an extended vegetative growth phase. The study underscores the importance of cumulative gene expression, including gene models, dominant alleles, paralogs, and tandemly duplicated genes and activators and repressors of disparate hormone (IAA, JA, and ABA) signaling pathways are the points of hormone crosstalk in contrasting biomass F2 segregants and could be applied for engineering high biomass acquiring varieties.

AraLeTA: An Arabidopsis leaf expression atlas across diurnal and developmental scales

Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll, and vascular cells. Notably, the proportion of these cells and the relative transcript concentrations within different cell types may change over time. While gene expression data at a single-cell level can provide cell-type-specific expression values, it is often too expensive to obtain these data for high-resolution time series. Although bulk RNA-seq can be performed in a high-resolution time series, RNA-seq using whole leaves measures average gene expression values across all cell types in each sample. In this study, we combined single-cell RNA-seq data with time-series data from whole leaves to assemble an atlas of cell-type-specific changes in gene expression over time for Arabidopsis (Arabidopsis thaliana). We inferred how the relative transcript concentrations of different cell types vary across diurnal and developmental timescales. Importantly, this analysis revealed 3 subgroups of mesophyll cells with distinct temporal profiles of expression. Finally, we developed tissue-specific gene networks that form a community resource: an Arabidopsis Leaf Time-dependent Atlas (AraLeTa). This allows users to extract gene networks that are confirmed by transcription factor-binding data and specific to certain cell types at certain times of day and at certain developmental stages. AraLeTa is available at https://regulatorynet.shinyapps.io/araleta/.

Recent advances in exploring transcriptional regulatory landscape of crops

Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.

Arabidopsis Transcriptomics Reveals the Role of Lipoxygenase2 (AtLOX2) in Wound-Induced Responses

In wounded Arabidopsis thaliana leaves, four 13S-lipoxygenases (AtLOX2, AtLOX3, AtLOX4, AtLOX6) act in a hierarchical manner to contribute to the jasmonate burst. This leads to defense responses with LOX2 playing an important role in plant resistance against caterpillar herb-ivory. In this study, we sought to characterize the impact of AtLOX2 on wound-induced phytohormonal and transcriptional responses to foliar mechanical damage using wildtype (WT) and lox2 mutant plants. Compared with WT, the lox2 mutant had higher constitutive levels of the phytohormone salicylic acid (SA) and enhanced expression of SA-responsive genes. This suggests that AtLOX2 may be involved in the biosynthesis of jasmonates that are involved in the antagonism of SA biosynthesis. As expected, the jasmonate burst in response to wounding was dampened in lox2 plants. Generally, 1 h after wounding, genes linked to jasmonate biosynthesis, jasmonate signaling attenuation and abscisic acid-responsive genes, which are primarily involved in wound sealing and healing, were differentially regulated between WT and lox2 mutants. Twelve h after wounding, WT plants showed stronger expression of genes associated with plant protection against insect herbivory. This study highlights the dynamic nature of jasmonate-responsive gene expression and the contribution of AtLOX2 to this pathway and plant resistance against insects.

Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis

Broccoli (Brassica oleracea var. italica Plenck) is an important vegetable crop, as it is rich in health-beneficial glucosinolates (GSLs). However, the genetic basis of the GSL diversity in Brassicaceae remains unclear. Here we report a chromosome-level genome assembly of broccoli generated using PacBio HiFi reads and Hi-C technology. The final genome assembly is 613.79 Mb in size, with a contig N50 of 14.70 Mb. The GSL profile and content analysis of different B. oleracea varieties, combined with a phylogenetic tree analysis, sequence alignment, and the construction of a 3D model of the methylthioalkylmalate synthase 1 (MAM1) protein, revealed that the gene copy number and amino acid sequence variation both contributed to the diversity of GSL biosynthesis in B. oleracea. The overexpression of BoMAM1 (BolI0108790) in broccoli resulted in high accumulation and a high ratio of C4-GSLs, demonstrating that BoMAM1 is the key enzyme in C4-GSL biosynthesis. These results provide valuable insights for future genetic studies and nutritive component applications of Brassica crops.

A transcriptional regulation of ERF15 contributes to ABA-mediated cold tolerance in tomato

Cold stress is a major meteorological threat to crop growth and yield. Abscisic acid (ABA) plays important roles in plant cold tolerance by activating the expression of cold-responsive genes; however, the underlying transcriptional regulatory module remains unknown. Here, we demonstrated that the cold- and ABA-responsive transcription factor ETHYLENE RESPONSE FACTOR 15 (ERF15) positively regulates ABA-mediated cold tolerance in tomato. Exogenous ABA treatment significantly enhanced cold tolerance in wild-type tomato plants but failed to rescue erf15 mutants from cold stress. Transcriptome analysis showed that ERF15 was associated with the expression of cold-responsive transcription factors such as CBF1 and WRKY6. Further RT-qPCR assays confirmed that the ABA-induced increased in CBF1 and WRKY6 transcripts was suppressed in erf15 mutants when the plants were subjected to cold treatment. Moreover, yeast one-hybrid assays, dual-luciferase assays and electrophoretic mobility shift assays demonstrated that ERF15 activated the transcription of CBF1 and WRKY6 by binding their promoters. Silencing CBF1 or WRKY6 significantly decreased cold tolerance. Overall, our study identified the role of ERF15 in conferring ABA-mediated cold tolerance in tomato plants by activating CBF1 and WRKY6 expression. This study not only broadens our knowledge of the mechanism of ABA-mediated cold tolerance in plants but also highlights ERF15 as an ideal target gene for cold-tolerant crop breeding.

External jasmonic acid isoleucine mediates amplification of plant elicitor peptide receptor (PEPR) and jasmonate-based immune signalling

Jasmonic acid-isoleucine (JA-Ile) is a plant defence hormone whose cellular levels are elevated upon herbivory and regulate defence signalling. Despite their pivotal role, our understanding of the rapid cellular perception of bioactive JA-Ile is limited. This study identifies cell type-specific JA-Ile-induced Ca2+ signal and its role in self-amplification and plant elicitor peptide receptor (PEPR)-mediated signalling. Using the Ca2+ reporter, R-GECO1 in Arabidopsis, we have characterized a monophasic and sustained JA-Ile-dependent Ca2+ signature in leaf epidermal cells. The rapid Ca2+ signal is independent of positive feedback by the JA-Ile receptor, COI1 and the transporter, JAT1. Microarray analysis identified up-regulation of receptors, PEPR1 and PEPR2 upon JA-Ile treatment. The pepr1 pepr2 double mutant in R-GECO1 background exhibits impaired external JA-Ile induced Ca2+ cyt elevation and impacts the canonical JA-Ile responsive genes. JA responsive transcription factor, MYC2 binds to the G-Box motif of PEPR1 and PEPR2 promoter and activates their expression upon JA-Ile treatment and in myc2 mutant, this is reduced. External JA-Ile amplifies AtPep-PEPR pathway by increasing the AtPep precursor, PROPEP expression. Our work shows a previously unknown non-canonical PEPR-JA-Ile-Ca2+ -MYC2 signalling module through which plants sense JA-Ile rapidly to amplify both AtPep-PEPR and jasmonate signalling in undamaged cells.

Drought responses and population differentiation of Calohypnum plumiforme inferred from comparative transcriptome analysis

Bryophytes, known as poikilohydric plants, possess vegetative desiccation-tolerant (DT) ability to withstand water deficit stress. Consequently, they offer valuable genetic resources for enhancing resistance to water scarcity stress. In this research, we examined the physiological, phytohormonal, and transcriptomic changes in DT mosses Calohypnum plumiforme from two populations, with and without desiccation treatment. Comparative analysis revealed population differentiation at physiological, gene sequence, and expression levels. Under desiccation stress, the activities of superoxide dismutase (SOD) and peroxidase (POD) showed significant increases, along with elevation of soluble sugars and proteins, consistent with the transcriptome changes. Notable activation of the bypass pathway of JA biosynthesis suggested their roles in compensating for JA accumulation. Furthermore, our analysis revealed significant correlations among phytohormones and DEGs in their respective signaling pathway, indicating potential complex interplays of hormones in C plumiforme. Protein phosphatase 2C (PP2C) in the abscisic acid signaling pathway emerged as the pivotal hub in the phytohormone crosstalk regulation network. Overall, this study was one of the first comprehensive transcriptome analyses of moss C. plumiforme under slow desiccation rates, expanding our knowledge of bryophyte transcriptomes and shedding light on the gene regulatory network involved in response to desiccation, as well as the evolutionary processes of local adaptation across moss populations.

Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression

The Southern green shield bug, Nezara viridula, is an invasive piercing and sucking pest insect that feeds on crop plants and poses a threat to global food production. Given that insects are known to live in a close relationship with microorganisms, our study provides insights into the community composition and function of the N. viridula-associated microbiota and its effect on host-plant interactions. We discovered that N. viridula hosts both vertically and horizontally transmitted microbiota throughout different developmental stages and their salivary glands harbor a thriving microbial community that is transmitted to the plant while feeding. The N. viridula microbiota was shown to aid its host with the detoxification of a plant metabolite, namely 3-nitropropionic acid, and repression of host plant defenses. Our results demonstrate that the N. viridula-associated microbiota plays an important role in interactions between insects and plants and could therefore be considered a valuable target for the development of sustainable pest control strategies.

Integrative transcriptomics reveals association of abscisic acid and lignin pathways with cassava whitefly resistance

BACKGROUND

Whiteflies are a global threat to crop yields, including the African subsistence crop cassava (Manihot esculenta). Outbreaks of superabundant whitefly populations throughout Eastern and Central Africa in recent years have dramatically increased the pressures of whitefly feeding and virus transmission on cassava. Whitefly-transmitted viral diseases threaten the food security of hundreds of millions of African farmers, highlighting the need for developing and deploying whitefly-resistant cassava. However, plant resistance to whiteflies remains largely poorly characterized at the genetic and molecular levels. Knowledge of cassava-defense programs also remains incomplete, limiting characterization of whitefly-resistance mechanisms. To better understand the genetic basis of whitefly resistance in cassava, we define the defense hormone- and Aleurotrachelus socialis (whitefly)-responsive transcriptome of whitefly-susceptible (COL2246) and whitefly-resistant (ECU72) cassava using RNA-seq. For broader comparison, hormone-responsive transcriptomes of Arabidopsis thaliana were also generated.

RESULTS

Whitefly infestation, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) transcriptome responses of ECU72 and COL2246 were defined and analyzed. Strikingly, SA responses were largely reciprocal between the two cassava genotypes and we suggest candidate regulators. While susceptibility was associated with SA in COL2246, resistance to whitefly in ECU72 was associated with ABA, with SA-ABA antagonism observed. This was evidenced by expression of genes within the SA and ABA pathways and hormone levels during A. socialis infestation. Gene-enrichment analyses of whitefly- and hormone-responsive genes suggest the importance of fast-acting cell wall defenses (e.g., elicitor recognition, lignin biosynthesis) during early infestation stages in whitefly-resistant ECU72. A surge of ineffective immune and SA responses characterized the whitefly-susceptible COL2246's response to late-stage nymphs. Lastly, in comparison with the model plant Arabidopsis, cassava's hormone-responsive genes showed striking divergence in expression.

CONCLUSIONS

This study provides the first characterization of cassava's global transcriptome responses to whitefly infestation and defense hormone treatment. Our analyses of ECU72 and COL2246 uncovered possible whitefly resistance/susceptibility mechanisms in cassava. Comparative analysis of cassava and Arabidopsis demonstrated that defense programs in Arabidopsis may not always mirror those in crop species. More broadly, our hormone-responsive transcriptomes will also provide a baseline for the cassava community to better understand global responses to other yield-limiting pests/pathogens.

Changing turn-over rates regulate abundance of tryptophan, GS biosynthesis, IAA transport and photosynthesis proteins in Arabidopsis growth defense transitions

BACKGROUND

Shifts in dynamic equilibria of the abundance of cellular molecules in plant-pathogen interactions need further exploration. We induced PTI in optimally growing Arabidopsis thaliana seedlings for 16 h, returning them to growth conditions for another 16 h.

METHODS

Turn-over and abundance of 99 flg22 responding proteins were measured chronologically using a stable heavy nitrogen isotope partial labeling strategy and targeted liquid chromatography coupled to mass spectrometry (PRM LC-MS). These experiments were complemented by measurements of mRNA and phytohormone levels.

RESULTS

Changes in synthesis and degradation rate constants (Ks and Kd) regulated tryptophane and glucosinolate, IAA transport, and photosynthesis-associated protein (PAP) homeostasis in growth/PTI transitions independently of mRNA levels. Ks values increased after elicitation while protein and mRNA levels became uncorrelated. mRNA returned to pre-elicitation levels, yet protein abundance remained at PTI levels even 16 h after media exchange, indicating protein levels were robust and unresponsive to transition back to growth. The abundance of 23 PAPs including FERREDOXIN-NADP( +)-OXIDOREDUCTASE (FNR1) decreased 16 h after PAMP exposure, their depletion was nearly abolished in the myc234 mutant. FNR1 Kd increased as mRNA levels decreased early in PTI, its Ks decreased in prolonged PTI. FNR1 Kd was lower in myc234, mRNA levels decreased as in wild type.

CONCLUSIONS

Protein Kd and Ks values change in response to flg22 exposure and constitute an additional layer of protein abundance regulation in growth defense transitions next to changes in mRNA levels. Our results suggest photosystem remodeling in PTI to direct electron flow away from the photosynthetic carbon reaction towards ROS production as an active defense mechanism controlled post-transcriptionally and by MYC2 and homologs. Target proteins accumulated later and PAP and auxin/IAA depletion was repressed in myc234 indicating a positive effect of the transcription factors in the establishment of PTI.

Regulation of hormone pathways in wheat infested by Blumeria graminis f. sp. tritici

BACKGROUND

Wheat powdery mildew is an obligate biotrophic pathogen infecting wheat, which can pose a serious threat to wheat production. In this study, transcriptome sequencing was carried out on wheat leaves infected by Blumeria graminis f. sp. tritici from 0 h to 7 d.

RESULTS

KEGG and GO enrichment analysis revealed that the upstream biosynthetic pathways and downstream signal transduction pathways of salicylic acid, jasmonic acid, and ethylene were highly enriched at all infection periods. Trend analysis showed that the expressions of hormone-related genes were significantly expressed from 1 to 4 d, suggesting that 1 d-4 d is the main period in which hormones play a defensive role. During this period of time, the salicylic acid pathway was up-regulated, while the jasmonic acid and ethylene pathways were suppressed. Meanwhile, four key modules and 11 hub genes were identified, most of which were hormone related.

CONCLUSION

This study improves the understanding of the dynamical responses of wheat to Blumeria graminis f. sp. tritici infestation at the transcriptional level and provides a reference for screening core genes regulated by hormones.

A transcription factor ZmGLK36 confers broad resistance to maize rough dwarf disease in cereal crops

Maize rough dwarf disease (MRDD), caused by maize rough dwarf virus (MRDV) or rice black-streaked dwarf virus (RBSDV), seriously threatens worldwide production of all major cereal crops, including maize, rice, wheat and barley. Here we report fine mapping and cloning of a previously reported major quantitative trait locus (QTL) (qMrdd2) for RBSDV resistance in maize. Subsequently, we show that qMrdd2 encodes a G2-like transcription factor named ZmGLK36 that promotes resistance to RBSDV by enhancing jasmonic acid (JA) biosynthesis and JA-mediated defence response. We identify a 26-bp indel located in the 5' UTR of ZmGLK36 that contributes to differential expression and resistance to RBSDV in maize inbred lines. Moreover, we show that ZmDBF2, an AP2/EREBP family transcription factor, directly binds to the 26-bp indel and represses ZmGLK36 expression. We further demonstrate that ZmGLK36 plays a conserved role in conferring resistance to RBSDV in rice and wheat using transgenic or marker-assisted breeding approaches. Our results provide insights into the molecular mechanisms of RBSDV resistance and effective strategies to breed RBSDV-resistant cereal crops.

Autophagy promotes jasmonate-mediated defense against nematodes

Autophagy, as an intracellular degradation system, plays a critical role in plant immunity. However, the involvement of autophagy in the plant immune system and its function in plant nematode resistance are largely unknown. Here, we show that root-knot nematode (RKN; Meloidogyne incognita) infection induces autophagy in tomato (Solanum lycopersicum) and different atg mutants exhibit high sensitivity to RKNs. The jasmonate (JA) signaling negative regulators JASMONATE-ASSOCIATED MYC2-LIKE 1 (JAM1), JAM2 and JAM3 interact with ATG8s via an ATG8-interacting motif (AIM), and JAM1 is degraded by autophagy during RKN infection. JAM1 impairs the formation of a transcriptional activation complex between ETHYLENE RESPONSE FACTOR 1 (ERF1) and MEDIATOR 25 (MED25) and interferes with transcriptional regulation of JA-mediated defense-related genes by ERF1. Furthermore, ERF1 acts in a positive feedback loop and regulates autophagy activity by transcriptionally activating ATG expression in response to RKN infection. Therefore, autophagy promotes JA-mediated defense against RKNs via forming a positive feedback circuit in the degradation of JAMs and transcriptional activation by ERF1.

Biosynthesis of Betalains Elicited by Methyl Jasmonate in Two Species of Alternanthera Genus: Antagonistic Regulations Result in Increase of Pigments

Natural pigments are components very important in the dye industry. The betalains are pigments found in plants from Caryophyllales order and are relevant in the food manufacturing. The main source of betalains is beetroot, which has unfavorable aftertaste. Therefore, the demand for alternative species producing betalains has increased. Elicitor molecules such as methyl jasmonate (MeJA) induce metabolic reprogramming acting in the biosynthesis of specialized metabolites and can enhance pigment concentrations. Here, we used this strategy to identify if treatment with MeJA at 100 µM can promote the accumulation of betalains and other bioactive compounds in Alternanthera philoxeroides and Alternanthera sessilis. We performed the gene expression, concentration of betalains, phenols, flavonoids, amino acids (phenylalanine and tyrosine), and antioxidant activity. The results showed that MeJA treatment increased betalains and other bioactive compounds in the two Alternanthera species but A. sessilis had a better performance. One key factor in this pathway is related to the phenylalanine and tyrosine concentration. However, the species have distinct metabolic regulation: in A. philoxeroides, high concentrations of betalain pigments increase the tyrosine concentration and gene expression (include ADH) under MeJA and in A. sessilis, high concentrations of betalain pigments reduce the gene expression and tyrosine concentration after 2 days under MeJA. This study brings new questions about betalain biosynthesis and sheds light on the evolution of this pathway in Caryophyllales.

The spatiotemporal profile of Dendrobium huoshanense and functional identification of bHLH genes under exogenous MeJA using comparative transcriptomics and genomics

Introduction

Alkaloids are one of the main medicinal components of Dendrobium species. Dendrobium alkaloids are mainly composed of terpene alkaloids. Jasmonic acid (JA) induce the biosynthesis of such alkaloids, mainly by enhancing the expression of JA-responsive genes to increase plant resistance and increase the content of alkaloids. Many JA-responsive genes are the target genes of bHLH transcription factors (TFs), especially the MYC2 transcription factor.

Methods

In this study, the differentially expressed genes involved in the JA signaling pathway were screened out from Dendrobium huoshanense using comparative transcriptomics approaches, revealing the critical roles of basic helix-loop-helix (bHLH) family, particularly the MYC2 subfamily.

Results and discussion

Microsynteny-based comparative genomics demonstrated that whole genome duplication (WGD) and segmental duplication events drove bHLH genes expansion and functional divergence. Tandem duplication accelerated the generation of bHLH paralogs. Multiple sequence alignments showed that all bHLH proteins included bHLH-zip and ACT-like conserved domains. The MYC2 subfamily had a typical bHLH-MYC_N domain. The phylogenetic tree revealed the classification and putative roles of bHLHs. The analysis of cis-acting elements revealed that promoter of the majority of bHLH genes contain multiple regulatory elements relevant to light response, hormone responses, and abiotic stresses, and the bHLH genes could be activated by binding these elements. The expression profiling and qRT-PCR results indicated that bHLH subgroups IIIe and IIId may have an antagonistic role in JA-mediated expression of stress-related genes. DhbHLH20 and DhbHLH21 were considered to be the positive regulators in the early response of JA signaling, while DhbHLH24 and DhbHLH25 might be the negative regulators. Our findings may provide a practical reference for the functional study of DhbHLH genes and the regulation of secondary metabolites.

Full Bayesian identification of linear dynamic systems using stable kernels

System identification learns mathematical models of dynamic systems starting from input-output data. Despite its long history, such research area is still extremely active. New challenges are posed by identification of complex physical processes given by the interconnection of dynamic systems. Examples arise in biology and industry, e.g., in the study of brain dynamics or sensor networks. In the last years, regularized kernel-based identification, with inspiration from machine learning, has emerged as an interesting alternative to the classical approach commonly adopted in the literature. In the linear setting, it uses the class of stable kernels to include fundamental features of physical dynamical systems, e.g., smooth exponential decay of impulse responses. Such class includes also unknown continuous parameters, called hyperparameters, which play a similar role as the model discrete order in controlling complexity. In this paper, we develop a linear system identification procedure by casting stable kernels in a full Bayesian framework. Our models incorporate hyperparameters uncertainty and consist of a mixture of dynamic systems over a continuum spectrum of dimensions. They are obtained by overcoming drawbacks related to classical Markov chain Monte Carlo schemes that, when applied to stable kernels, are proved to become nearly reducible (i.e., unable to reconstruct posteriors of interest in reasonable time). Numerical experiments show that full Bayes frequently outperforms the state-of-the-art results on typical benchmark problems. Two real applications related to brain dynamics (neural activity) and sensor networks are also included.

The MYB59 transcription factor negatively regulates salicylic acid- and jasmonic acid-mediated leaf senescence

Leaf senescence is the final stage of leaf development and is affected by various exogenous and endogenous factors. Transcriptional regulation is essential for leaf senescence, however, the underlying molecular mechanisms remain largely unclear. In this study, we report that the transcription factor MYB59, which was predominantly expressed in early senescent rosette leaves, negatively regulates leaf senescence in Arabidopsis (Arabidopsis thaliana). RNA sequencing revealed a large number of differentially expressed genes involved in several senescence-related biological processes in myb59-1 rosette leaves. Chromatin immunoprecipitation and transient dual-luciferase reporter assays demonstrated that MYB59 directly repressed the expression of SENESCENCE ASSOCIATED GENE 18 and indirectly inhibited the expression of several other senescence-associated genes to delay leaf senescence. Moreover, MYB59 was induced by salicylic acid (SA) and jasmonic acid (JA). MYB59 inhibited SA production by directly repressing the expression of ISOCHORISMATE SYNTHASE 1 and PHENYLALANINE AMMONIA-LYASE 2 and restrained JA biosynthesis by directly suppressing the expression of LIPOXYGENASE 2, thus forming two negative feedback regulatory loops with SA and JA and ultimately delaying leaf senescence. These results help us understand the novel function of MYB59 and provide insights into the regulatory network controlling leaf senescence in Arabidopsis.

Combination of bacterial N-acyl homoserine lactones primes Arabidopsis defenses via jasmonate metabolism

N-acyl homoserine lactones (AHLs) are important players in plant-bacteria interactions. Different AHL-producing bacteria can improve plant growth and resistance against plant pathogens. In nature, plants may host a variety of AHL-producing bacteria and frequently experience numerous AHLs at the same time. Therefore, a coordinated response to combined AHL molecules is necessary. The purpose of this study was to explore the mechanism of AHL-priming using combined AHL molecules including N-(3-oxo-hexanoyl)-L-homoserine lactone, N-3-oxo-octanoyl-L-homoserine lactone, N-3-oxo-dodecanoyl-L-homoserine lactone, and N-3-oxo-tetradecanoyl-L-homoserine lactone and AHL-producing bacteria including Serratia plymuthica HRO-C48, Rhizobium etli CFN42, Burkholderia graminis DSM17151, and Ensifer meliloti (Sinorhizobium meliloti) Rm2011. We used transcriptome analysis, phytohormone measurements, as well as genetic and microbiological approaches to assess how the combination of structurally diverse AHL molecules influence Arabidopsis (Arabidopsis thaliana). Our findings revealed a particular response to a mixture of AHL molecules (AHL mix). Different expression patterns indicated that the reaction of plants exposed to AHL mix differs from that of plants exposed to single AHL molecules. In addition, different content of jasmonic acid (JA) and derivatives revealed that jasmonates play an important role in AHL mix-induced priming. The fast and stable decreased concentration of COOH-JA-Ile after challenge with the flagellin-derived peptide flg22 indicated that AHL mix modifies the metabolism of jasmonates. Study of various JA- and salicylic acid-related Arabidopsis mutants strengthened the notion that JA homeostasis is involved in AHL-priming. Understanding how the combination of AHLs primes plants for enhanced resistance has the potential to broaden our approaches in sustainable agriculture and will help to effectively protect plants against pathogens.

Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways

Cross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors and thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. In addition, a group of MITOGEN-ACTIVATED PROTEIN KINASES (MPKs) were identified as potential key points of cross-regulation between multiple hormones. Accordingly, the loss of function of one of these (MPK6) disrupted the global proteome, phosphoproteome and transcriptome during hormone responses. Lastly, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression.

A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

Gene regulation is central to all aspects of organism growth, and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking. In this study, we constructed a wheat integrative gene regulatory network (wGRN) by combining an updated genome annotation and diverse complementary functional datasets, including gene expression, sequence motif, transcription factor (TF) binding, chromatin accessibility, and evolutionarily conserved regulation. wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127 439 target genes, which were further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies. In addition, wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks. We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions. Finally, we developed an interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), for the community to explore gene regulation and discover trait-associated genes. Collectively, this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

Evaluation of the mechanism of action of Bacillus spp. to manage Meloidogyne incognita with split root assay, RT-qPCR and qPCR

The goal of this research is to determine the mechanism of action of two Bacillus spp. that can manage Meloidogyne incognita population density in cotton. The overall objectives are 1) determine the efficacy and direct antagonistic capabilities of the Bacillus spp. and 2) determine the systemic capabilities of the Bacillus spp. The greenhouse in planta assay indicated B. amyloliquefaciens QST713 and B. firmus I-1582 could manage M. incognita similarly to the chemical standard fluopyram. An in vitro assay determined that B. firmus I-1582 and its extracted metabolites were able to directly manage M. incognita second stage juveniles by increasing mortality rate above 75%. A split root assay, used to determine systemic capabilities of the bacteria, indicated B. amyloliquefaciens QST713 and B. firmus I-1582 could indirectly decrease the nematode population density. Another species, B. mojavensis strain 2, also demonstrated systemic capabilities but was not a successful biological control agent because it supported a high population density in greenhouse in planta assay and in the split root assay. A RT-qPCR assay was used to confirm any systemic activity observed in the split root assay. At 24 hours both B. amyloliquefaciens QST713 and B. firmus I-1582 upregulated one gene involved in the initial stages of JA synthesis pathway but not another gene involved in the later stages of JA synthesis. These results point to a JA intermediate molecule, most likely OPDA, stimulated by the bacteria rather than JA in a short-term systemic response. After 1 week, the Bacillus spp. stimulated a SA-responsive defense related gene. The long-term systemic response to the Bacillus spp. indicates salicylic acid also plays a role in defense conferred by these bacteria. The final assay was a qPCR to determine the concentration of the bacteria on the cotton roots after 24 days. Bacillus amyloliquefaciens QST713 and B. firmus I-43 1582 were able to colonize the root successfully, with the concentration after 24 days not significantly differing from the concentration at inoculation. This study identifies two bacteria that work via systemic resistance and will help aid in implementing these species in an integrated management system.

Coexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress Responses

Dynamic gene expression changes are primary cellular reactions in response to most stresses and developmental cues in all organisms, including plants. With the ever-decreasing cost and increasing access, high-throughput transcriptome analyses have become a significant research tool to understand a wide spectrum of complex gene regulatory mechanisms. However, it is still challenging to understand the complete picture of gene responses because of the interactive and dynamic nature of gene expression in biological networks. Coexpression network analyses followed by network mapping are being increasingly applied to overcome this challenge. In this chapter, we will introduce detailed instructions for performing a weighted coexpression network analysis (WGCNA) and network visualization using a transcriptome dataset obtained during recovery from endoplasmic reticulum (ER) stress in Arabidopsis thaliana. The streamlined workflow described here allows biologists to identify and visualize coexpression interactions among genes, accessing a comprehensive landscape of dynamic gene expression changes for further downstream analyses using their datasets.

2,3-Butanediol from the leachates of pine needles induces the resistance of Panax notoginseng to the leaf pathogen Alternaria panax

Compared with the use of monocultures in the field, cultivation of medicinal herbs in forests is an effective strategy to alleviate disease. Chemical interactions between herbs and trees play an important role in disease suppression in forests. We evaluated the ability of leachates from needles of Pinus armandii to induce resistance in Panax notoginseng leaves, identified the components via gas chromatography-mass spectrometry (GC-MS), and then deciphered the mechanism of 2,3-Butanediol as the main component in the leachates responsible for resistance induction via RNA sequencing (RNA-seq). Prespraying leachates and 2,3-Butanediol onto leaves could induce the resistance of P. notoginseng to Alternaria panax. The RNA-seq results showed that prespraying 2,3-Butanediol onto leaves with or without A. panax infection upregulated the expression of large number of genes, many of which are involved in transcription factor activity and the mitogen-activated protein kinase (MAPK) signaling pathway. Specifically, 2,3-Butanediol spraying resulted in jasmonic acid (JA) -mediated induced systemic resistance (ISR) by activating MYC2 and ERF1. Moreover, 2,3-Butanediol induced systemic acquired resistance (SAR) by upregulating pattern-triggered immunity (PTI)- and effector-triggered immunity (ETI)-related genes and activated camalexin biosynthesis through activation of WRKY33. Overall, 2,3-Butanediol from the leachates of pine needles could activate the resistance of P. notoginseng to leaf disease infection through ISR, SAR and camalexin biosynthesis. Thus, 2,3-Butanediol is worth developing as a chemical inducer for agricultural production.

Long-lasting memory of jasmonic acid-dependent immunity requires DNA demethylation and ARGONAUTE1

Stress can have long-lasting impacts on plants. Here we report the long-term effects of the stress hormone jasmonic acid (JA) on the defence phenotype, transcriptome and DNA methylome of Arabidopsis. Three weeks after transient JA signalling, 5-week-old plants retained induced resistance (IR) against herbivory but showed increased susceptibility to pathogens. Transcriptome analysis revealed long-term priming and/or upregulation of JA-dependent defence genes but repression of ethylene- and salicylic acid-dependent genes. Long-term JA-IR was associated with shifts in glucosinolate composition and required MYC2/3/4 transcription factors, RNA-directed DNA methylation, the DNA demethylase ROS1 and the small RNA (sRNA)-binding protein AGO1. Although methylome analysis did not reveal consistent changes in DNA methylation near MYC2/3/4-controlled genes, JA-treated plants were specifically enriched with hypomethylated ATREP2 transposable elements (TEs). Epigenomic characterization of mutants and transgenic lines revealed that ATREP2 TEs are regulated by RdDM and ROS1 and produce 21 nt sRNAs that bind to nuclear AGO1. Since ATREP2 TEs are enriched with sequences from IR-related defence genes, our results suggest that AGO1-associated sRNAs from hypomethylated ATREP2 TEs trans-regulate long-lasting memory of JA-dependent immunity.

Conserved hierarchical gene regulatory networks for drought and cold stress response in Myrica rubra

Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (Myrica rubra). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses. Drought- and cold-responsive GRNs, which have been built according to the timing of transcription under both abiotic stresses, have a conserved trans-regulator and a common regulatory network. In both GRNs, basic helix-loop-helix family transcription factor (bHLH) serve as central nodes. MrbHLHp10 transcripts exhibited continuous increase in the two abiotic stresses and acts upstream regulator of ASCORBATE PEROXIDASE (APX) gene. To examine the potential biological functions of MrbHLH10, we generated a transgenic Arabidopsis plant that constitutively overexpresses the MrbHLH10 gene. Compared to wild-type (WT) plants, overexpressing transgenic Arabidopsis plants maintained higher APX activity and biomass accumulation under drought and cold stress. Consistently, RNAi plants had elevated susceptibility to both stresses. Taken together, these results suggested that MrbHLH10 mitigates abiotic stresses through the modulation of ROS scavenging.

A Tea Plant (Camellia sinensis) FLOWERING LOCUS C-like Gene, CsFLC1, Is Correlated to Bud Dormancy and Triggers Early Flowering in Arabidopsis

Flowering and bud dormancy are crucial stages in the life cycle of perennial angiosperms in temperate climates. MADS-box family genes are involved in many plant growth and development processes. Here, we identified three MADS-box genes in tea plant belonging to the FLOWERING LOCUS C (CsFLC) family. We monitored CsFLC1 transcription throughout the year and found that CsFLC1 was expressed at a higher level during the winter bud dormancy and flowering phases. To clarify the function of CsFLC1, we developed transgenic Arabidopsis thaliana plants heterologously expressing 35S::CsFLC1. These lines bolted and bloomed earlier than the WT (Col-0), and the seed germination rate was inversely proportional to the increased CsFLC1 expression level. The RNA-seq of 35S::CsFLC1 transgenic Arabidopsis showed that many genes responding to ageing, flower development and leaf senescence were affected, and phytohormone-related pathways were especially enriched. According to the results of hormone content detection and RNA transcript level analysis, CsFLC1 controls flowering time possibly by regulating SOC1, AGL42, SEP3 and AP3 and hormone signaling, accumulation and metabolism. This is the first time a study has identified FLC-like genes and characterized CsFLC1 in tea plant. Our results suggest that CsFLC1 might play dual roles in flowering and winter bud dormancy and provide new insight into the molecular mechanisms of FLC in tea plants as well as other plant species.

JAZ is essential for ligand specificity of the COI1/JAZ co-receptor

Jasmonates are phytohormones that regulate defense and developmental processes in land plants. Despite the chemical diversity of jasmonate ligands in different plant lineages, they are all perceived by COI1/JAZ co-receptor complexes, in which the hormone acts as a molecular glue between the COI1 F-box and a JAZ repressor. It has been shown that COI1 determines ligand specificity based on the receptor crystal structure and the identification of a single COI1 residue, which is responsible for the evolutionary switch in ligand binding. In this work, we show that JAZ proteins contribute to ligand specificity together with COI1. We propose that specific features of JAZ proteins, which are conserved in bryophytes and lycophytes, enable perception of dn-OPDA ligands regardless the size of the COI1 binding pocket. In vascular plant lineages beyond lycophytes, JAZ evolved to limit binding to JA-Ile, thus impeding dn-OPDA recognition by COI1.

Herbivore-induced Ca2+ signals trigger a jasmonate burst by activating ERF16-mediated expression in tomato

Herbivory severely affects plant growth, posing a threat to crop production. Calcium ion (Ca²⁺ ) signaling and accumulation of jasmonates (JAs) are activated in plant response to herbivore attack, leading to the expression of defense pathways. However, little is known about how the Ca²⁺ signal modulates JA biosynthesis. We used diverse techniques, including CRISPR/Cas9, UPLC-MS/MS and molecular biology methods to explore the role of ETHYLENE RESPONSE FACTOR 16 in Ca²⁺ signal-triggered JA burst during herbivore defense in tomato. Here we show that simulated herbivory induces GLUTAMATE RECEPTOR LIKE3.3/3.5 (GLR3.3/3.5)-dependent increases in electrical activity, Ca²⁺ influx and increases the abundance of CALMODULIN2 (CaM2) and ERF16 transcripts in tomato. The interaction between CaM2 and ERF16 promotes JA biosynthesis by enhancing the transcriptional activity of ERF16, which increases the activation of ERF16 expression and causes expression of LIPOXYGENASE D (LOXD), AOC and 12-OXO-PHYTODIENOIC ACID REDUCTASE 3 (OPR3), the key genes in JA biosynthesis. Mutation of CaM2 results in decreased JA accumulation, together with the expression of JA biosynthesis-related genes, leading to reduced resistance to the cotton bollworm Helicoverpa armigera. These findings reveal a molecular mechanism underpinning the Ca²⁺ signal-initiated systemic JA burst and emphasize the pivotal role of Ca²⁺ signal/ERF16 crosstalk in herbivore defense.

Constitutive expression of JASMONATE RESISTANT 1 induces molecular changes that prime the plants to better withstand drought

In this study, we investigated Arabidopsis thaliana plants with altered levels of the enzyme JASMONATE RESISTANT 1 (JAR1), which converts jasmonic acid (JA) to jasmonoyl-l-isoleucine (JA-Ile). Analysis of a newly generated overexpression line (35S::JAR1) revealed that constitutively increased JA-Ile production in 35S::JAR1 alters plant development, resulting in stunted growth and delayed flowering. Under drought-stress conditions, 35S::JAR1 plants showed reduced wilting and recovered better from desiccation than the wild type. By contrast, jar1-11 plants with a strong reduction in JA-Ile content were hypersensitive to drought. RNA-sequencing analysis and hormonal profiling of plants under normal and drought conditions provided insights into the molecular reprogramming caused by the alteration in JA-Ile content. Especially 35S::JAR1 plants displayed changes in expression of developmental genes related to growth and flowering. Further transcriptional differences pertained to drought-related adaptive systems, including stomatal density and aperture, but also reactive oxygen species production and detoxification. Analysis of wild type and jar1-11 plants carrying the roGFP-Orp1 sensor support a role of JA-Ile in the alleviation of methyl viologen-induced H₂ O₂ production. Our data substantiate a role of JA-Ile in abiotic stress response and suggest that JAR1-mediated increase in JA-Ile content primes Arabidopsis towards improved drought stress tolerance.

Integrative omics approaches for biosynthetic pathway discovery in plants

Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.

Induced Resistance Combined with RNA Interference Attenuates the Counteradaptation of the Western Flower Thrips

The western flower thrips, Frankliniella occidentalis Pergande, is an invasive pest that damages agricultural and horticultural crops. The induction of plant defenses and RNA interference (RNAi) technology are potent pest control strategies. This study investigated whether the anti-adaptive ability of F. occidentalis to jasmonic acid (JA)- and methyl jasmonate (MeJA)-induced defenses in kidney bean plants was attenuated after glutathione S-transferase (GST) gene knockdown. The expression of four GSTs in thrips fed JA- and MeJA-induced leaves was analyzed, and FoGSTd1 and FoGSTs1 were upregulated. Exogenous JA- and MeJA-induced defenses led to increases in defensive secondary metabolites (tannins, alkaloids, total phenols, flavonoids, and lignin) in leaves. Metabolome analysis indicated that the JA-induced treatment of leaves led to significant upregulation of defensive metabolites. The activity of GSTs increased in second-instar thrips larvae fed JA- and MeJA-induced leaves. Co-silencing with RNAi simultaneously knocked down FoGSTd1 and FoGSTs1 transcripts and GST activity, and the area damaged by second-instar larvae feeding on JA- and MeJA-induced leaves decreased by 62.22% and 55.24%, respectively. The pupation rate of second-instar larvae also decreased by 39.68% and 39.89%, respectively. Thus, RNAi downregulation of FoGSTd1 and FoGSTs1 reduced the anti-adaptive ability of F. occidentalis to JA- or MeJA-induced defenses in kidney bean plants.

Comparison of the pathway structures influencing the temporal response of salicylate and jasmonate defence hormones in Arabidopsis thaliana

Defence phytohormone pathways evolved to recognize and counter multiple stressors within the environment. Salicylic acid responsive pathways regulate the defence response to biotrophic pathogens whilst responses to necrotrophic pathogens, herbivory, and wounding are regulated via jasmonic acid pathways. Despite their contrasting roles in planta, the salicylic acid and jasmonic acid defence networks share a common architecture, progressing from stages of biosynthesis, to modification, regulation, and response. The unique structure, components, and regulation of each stage of the defence networks likely contributes, in part, to the speed, establishment, and longevity of the salicylic acid and jasmonic acid signaling pathways in response to hormone treatment and various biotic stressors. Recent advancements in the understanding of the Arabidopsis thaliana salicylic acid and jasmonic acid signaling pathways are reviewed here, with a focus on how the structure of the pathways may be influencing the temporal regulation of the defence responses, and how biotic stressors and the many roles of salicylic acid and jasmonic acid in planta may have shaped the evolution of the signaling networks.

Specialist root herbivore modulates plant transcriptome and downregulates defensive secondary metabolites in a brassicaceous plant

Plants face attackers aboveground and belowground. Insect root herbivores can lead to severe crop losses, yet the underlying transcriptomic responses have rarely been studied. We studied the dynamics of the transcriptomic response of Brussels sprouts (Brassica oleracea var. gemmifera) primary roots to feeding damage by cabbage root fly larvae (Delia radicum), alone or in combination with aboveground herbivory by cabbage aphids (Brevicoryne brassicae) or diamondback moth caterpillars (Plutella xylostella). This was supplemented with analyses of phytohormones and the main classes of secondary metabolites; aromatic, indole and aliphatic glucosinolates. Root herbivory leads to major transcriptomic rearrangement that is modulated by aboveground feeding caterpillars, but not aphids, through priming soon after root feeding starts. The root herbivore downregulates aliphatic glucosinolates. Knocking out aliphatic glucosinolate biosynthesis with CRISPR-Cas9 results in enhanced performance of the specialist root herbivore, indicating that the herbivore downregulates an effective defence. This study advances our understanding of how plants cope with root herbivory and highlights several novel aspects of insect-plant interactions for future research. Further, our findings may help breeders develop a sustainable solution to a devastating root pest.