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Plant pathogens can decimate crops and render the local cultivation of a species unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital in treating crop diseases, and the use of computer vision for precise disease detection and timing of pesticide application is gaining popularity. Computer vision can reduce labour costs, prevent misdiagnosis of disease, and prevent misapplication of pesticides. Pesticide misapplication is both financially costly and can exacerbate pesticide resistance and pollution. Here, we review the application and development of computer vision and machine learning methods for the detection of plant disease. This review goes beyond the scope of previous works to discuss important technical concepts and considerations when applying computer vision to plant pathology. We present new case studies on adapting standard computer vision methods and review techniques for acquiring training data, the use of diagnostic tools from biology, and the inspection of informative features. In addition to an in‐depth discussion of convolutional neural networks (CNNs) and transformers, we also highlight the strengths of methods such as support vector machines and evolved neural networks. We discuss the benefits of carefully curating training data and consider situations where less computationally expensive techniques are advantageous. This includes a comparison of popular model architectures and a guide to their implementation. [ABSTRACT FROM AUTHOR]

A meta-analysis of multiple published simulations of crop yields predicts aggregate production losses for wheat, rice ( I Oryza sativa i ), and maize in both temperate and tropical regions by 2 °C warming with even greater crop losses in the second half of the 21st century (Challinor et al., 2014). Global emissions of CO SB 2 sb and other greenhouse gases have increased steadily since the pre-industrial era (Pedersen et al., 2021) leading to global temperature increases of >1 °C with most of this increase occurring within the last 50 years (IPCC, 2021). Also focusing on drought and the different molecular mechanisms involved in drought tolerance and drought recovery, Tang and Bassham (2022) address the important process of autophagy and its role in inducing drought tolerance. In their review article, Berrío et al. (2022) discuss several strategies to enhance drought resilience in crops focusing on "growth-centered" and "drought resilience without growth penalty" strategies. [Extracted from the article]

Gall‐inducing insects and their hosts present some of the most intricate plant‐herbivore interactions. Oviposition on the host is often the first cue of future herbivory and events at this early time point can affect later life stages. Many gallers are devastating plant pests, yet little information regarding the plant‐insect molecular interplay exists, particularly following egg deposition. We studied the physiological and transcriptional responses of Eucalyptus following oviposition by the gall‐inducing wasp, Leptocybe invasa, to explore potential mechanisms governing defence responses and gall development. RNA sequencing and microscopy were used to explore a susceptible Eucalyptus‐L. invasa interaction. Infested and control material was compared over time (1–3, 7 and 90 days post oviposition) to examine the transcriptional and morphological changes. Oviposition induces accumulation of reactive oxygen species and phenolics which is reflected in the transcriptome analysis. Gene expression supports phytohormones and 10 transcription factor subfamilies as key regulators. The egg and oviposition fluid stimulate cell division resulting in gall development. Eucalyptus responses to oviposition are apparent within 24 hr. Putative defences include the oxidative burst and barrier reinforcement. However, egg and oviposition fluid stimuli may redirect these responses towards gall development. In the Eucalyptus‐Leptocybe invasa interaction, early gall formation is associated with reactive oxygen species, phenolics, phytohormone signalling and 10 transcriptional factor families, some of which are insect specific responses, revealing key transcription factors regulating the galling trait. [ABSTRACT FROM AUTHOR]

Katherine Denby is taking over as the new Editor in Chief of The Plant Journal (TPJ), following the work of Lee Sweetlove. Denby aims to continue the journal's reputation as a platform for excellent plant science and provide a high-quality publishing experience. TPJ is part-owned by the Society of Experimental Biology (SEB) and supports scientific meetings and early career researchers. The journal publishes original research articles, commissioned reviews, perspectives, technical advances, and resource articles. Denby expresses gratitude to Sweetlove for his leadership and hopes to continue building TPJ's reputation in the changing publishing landscape. [Extracted from the article]

Gall-inducing insects are capable of exerting a high level of control over their hosts' cellular machinery to the extent that the plant's development, metabolism, chemistry, and physiology are all altered in favour of the insect. Many gallers are devastating pests in global agriculture and the limited understanding of their relationship with their hosts prevents the development of robust management strategies. Omics technologies are proving to be important tools in elucidating the mechanisms involved in the interaction as they facilitate analysis of plant hosts and insect effectors for which little or no prior knowledge exists. In this review, we examine the mechanisms behind insect gall development using evidence from omics-level approaches. The secretion of effector proteins and induced phytohormonal imbalances are highlighted as likely mechanisms involved in gall development. However, understanding how these components function within the system is far from complete and a number of questions need to be answered before this information can be used in the development of strategies to engineer or breed plants with enhanced resistance. [ABSTRACT FROM AUTHOR]

Transcriptional reprogramming plays a significant role in governing plant responses to pathogens. The underlying regulatory networks are complex and dynamic, responding to numerous input signals. Most network modelling studies to date have used large-scale expression data sets from public repositories but defence network models with predictive ability have also been inferred from single time series data sets, and sophisticated biological insights generated from focused experiments containing multiple network perturbations. Using multiple network inference methods, or combining network inference with additional data, such as promoter motifs, can enhance the ability of the model to predict gene function or regulatory relationships. Network topology can highlight key signaling components and provides a systems level understanding of plant defence. [ABSTRACT FROM AUTHOR]

World food security is increasingly dependent on continuous crop improvement and, in particular, the development of crops with increased drought and salinity tolerance. The completed genomic sequence of the model plant Arabidopsis thaliana and the development of whole-genome microarrays, together with increasing repositories of publicly available data and data analysis tools, have opened new avenues to genome-wide systemic analysis of plant stress responses. Here we outline examples of how this full-genome expression profiling can contribute to our understanding of complex stress responses and the identification and evaluation of novel transgenes that could hold the key to the development of commercially viable and sustainable crop plants. [Copyright &y& Elsevier]

Desiccation-tolerance in vegetative tissues of angiosperms has a polyphyletic origin and could be due to 1) appropriation of the seed-specific program of gene expression that protects orthodox seeds against desiccation, and/or 2) a sustainable version of the abiotic stress response. We tested these hypotheses by comparing molecular and physiological data from the development of orthodox seeds, the response of desiccation-sensitive plants to abiotic stress, and the response of desiccation-tolerant plants to extreme water loss. Analysis of publicly-available gene expression data of 35 LEA proteins and 68 anti-oxidant enzymes in the desiccation-sensitive Arabidopsis thaliana identified 13 LEAs and 4 anti-oxidants exclusively expressed in seeds. Two (a LEA6 and 1-cys-peroxiredoxin) are not expressed in vegetative tissues in A. thaliana, hut have orthologues that are specifically activated in desiccating leaves of Xerophyta humilis. A comparison of antioxidant enzyme activity in two desiccation-sensitive species of Eragrostis with the desiccation-tolerant E. nindensis showed equivalent responses upon initial dehydration, but activity was retained at low water content in E. nindensis only. We propose that these antioxidants are housekeeping enzymes and that they are protected from damage in the desiccation-tolerant species. Sucrose is considered an important protectant against desiccation in orthodox seeds, and we show that sucrose accumulates in drying leaves of E. nindensis, but not in the desiccation-sensitive Eragrostis species. The activation of "seed-specific" desiccation protection mechanisms (sucrose accumulation and expression of LEA6 and 1-cys-peroxiredoxin genes) in the vegetative tissues of desiccation-tolerant plants points towards acquisition of desiccation tolerance from seeds. [ABSTRACT FROM AUTHOR]

Microarrays are useful tools to investigate the expression of thousands of genes rapidly. Some researchers remain reluctant to use the technology, however, largely because of its expense. Careful design of a microarray experiment is key to generating cost-effective results. This article explores issues that researchers face when embarking on a microarray experiment for the first time. These include decisions about which microarray platform is available for the organism of interest, the degree of replication (biological and technical) needed and which design (direct or indirect, loop or balanced block) is suitable. [ABSTRACT FROM AUTHOR]

We report the characterization of anArabidopsis thalianamutant,ups1, isolated on the basis of reduced expression of phosphoribosylanthranilate transferase, a tryptophan biosynthetic enzyme.ups1also exhibits defects in a wide range of defence responses. After infection withPseudomonas syringaeorBotrytis cinerea, the expression of genes regulated by both the salicylic acid and jasmonic acid/ethylene pathways is reduced inups1compared with wild type. Camalexin accumulation inups1is greatly reduced after infection with these two pathogens, as well as after amino acid starvation or oxidative stress. Reactive oxygen species (ROS)-mediated gene expression is also compromised inups1indicating that this mutant is defective in signalling pathways activated in response to both biotic and abiotic stress. The fact that all three major defence signalling pathways are disrupted inups1, together with the oxidative stress phenotype, leads us to suggest that UPS1 is involved in ROS signal transduction. [ABSTRACT FROM AUTHOR]

Botrytis cinerea is a major pathogen of fruit and vegetable crops causing both pre- and post-harvest grey mould. We have analysed 16 Arabidopsis thaliana ecotypes for natural variation in B. cinerea susceptibility. Susceptibility was associated with lower camalexin accumulation, and three ecotypes (Cape Verdi Islands (Cvi-0), Slavice (Sav-0) and Kindalville (Kin-0)) showed differential susceptibility to the two B. cinerea isolates used. Subsequently, to better understand the genetic control of grey mould disease, we assayed the Arabidopsis Landsberg erecta (L er) × Columbia (Col-0) recombinant inbred population with the two isolates, and identified multiple small-to-medium-effect quantitative trait loci (QTL) governing susceptibility. Interestingly, the QTL for each isolate are distinct, suggesting that different mechanisms govern defence against these two isolates. Two QTL for each isolate exhibited epistatic interactions with specific allele combinations generating heightened B. cinerea susceptibility. [ABSTRACT FROM AUTHOR]

Examines the signalling pathways underlying disease resistance to specific groups of pathogens in Arabidopsis and discusses the application of the emerging trends to the study of plant pathology in South Africa. Discussion on salicylic acid (SA)-dependent defence responses; SA-independent defence responses; Complexity of disease resistance signalling in Arabidopsis.

Our food system is giving rise to a growing social, health and environmental crisis. Much of the food consumed in the United Kingdom is cheap, nutrient‐poor and highly processed, leading to under‐consumption of essential foods such as grains, beans, vegetables and fruit. This has contributed to a rise in diet‐related diseases, with approximately 22% of primary school leavers being overweight or obese. Food production is unsustainable with agriculture responsible for 10% of the UK's greenhouse gas emissions and intensive farming practices have led to a significant loss of soil carbon and a decline in biodiversity. COVID‐19 increased inequalities in our food system. Therefore, there is an urgent need for interventions to counteract these adverse social, health and environmental impacts. Education can play a crucial role as an intervention to address challenges in the food system. We tested an innovative school initiative using portable aquaponic pods and aligned to the national curriculum, to engage pupils in food production and foster learning about sustainability, climate change and healthy eating. The evaluation, based on teacher surveys, aquapod chart data, student blogs and postcards and feedback from the development team, revealed positive impacts on students’ environmental awareness, as well as sustainability and practical food production knowledge. However, the programme encountered logistical challenges and we therefore highlight future improvements to produce a curriculum programme that can be delivered at scale to enhance food education and empower pupils to drive the agenda on tackling food sustainability and climate change. [ABSTRACT FROM AUTHOR]

This paper provides an outline of a new interdisciplinary project called FixOurFood, funded through UKRI's 'Transforming UK food systems' programme. FixOurFood aims to transform the Yorkshire food system to a regenerative food system and will work to answer two main questions: (1) What do regenerative food systems look like? (2) How can transformations be enabled so that we can achieve a regenerative food system? To answer these questions, FixOurFood will work with diverse stakeholders to change the Yorkshire food system and use the learning to inform change efforts in other parts of the UK and beyond. Our work will focus on shifting trajectories towards regenerative dynamics in three inter‐related systems of: healthy eating for young children, hybrid food economies and regenerative farming. We do this by a set of action‐orientated interventions in schools and the food economy, metrics, policies and deliverables that can be applied in Yorkshire and across the UK. This article introduces the FixOurFood project and concludes by assessing the potential impact of these interventions and the importance we attach to working with stakeholders in government, business, third sector and civil society. [ABSTRACT FROM AUTHOR]

Key message: We demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling. Lactuca sativa L. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance to B. cinerea and S. sclerotiorum in lettuce. We demonstrated genetic variation for quantitative resistance to B. cinerea and S. sclerotiorum in a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F6 mapping population derived from a Lactuca serriola (wild relative) × lettuce cross, which each explained 5–10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci. [ABSTRACT FROM AUTHOR]

Deciphering the networks that underpin complex biological processes using experimental data remains a significant, but promising, challenge, a task made all the harder by the added complexity of host-pathogen interactions. The aim of this article is to review the progress in understanding plant immunity made so far by applying network modeling algorithms and to show how this computational/mathematical strategy is facilitating a systems view of plant defense. We review the different types of network modeling that have been used, the data required, and the type of insight that such modeling can provide. We discuss the current challenges in modeling the regulatory networks that underlie plant defense and the future developments that may help address these challenges. [ABSTRACT FROM AUTHOR]

We propose a semiparametric Bayesian model, based on penalized splines, for the recovery of the time-invariant topology of a causal interaction network from longitudinal data. Our motivation is inference of gene regulatory networks from low-resolution microarray time series, where existence of nonlinear interactions is well known. Parenthood relations are mapped by augmenting the model with kinship indicators and providing these with either an overall or gene-wise hierarchical structure. Appropriate specification of the prior is crucial to control the flexibility of the splines, especially under circumstances of scarce data; thus, we provide an informative, proper prior. Substantive improvement in network inference over a linear model is demonstrated using synthetic data drawn from ordinary differential equation models and gene expression from an experimental data set of the Arabidopsis thaliana circadian rhythm. [ABSTRACT FROM PUBLISHER]

The article reports on plants' evolved systems of immunity such as the pathogen-associated molecular patterns (PAMP) detection, which serve as a warning for the presence of pathogens. PAMP binds to pattern recognition receptor resulting to the induction of basal defense systems. Pathogens fight back with evolved effectors resulting to evolution of cultivar-specific resistance in plants as a defense.

Numerous studies have suggested that plant/pathogen interactions are partially mediated via plant secondary metabolite production and corresponding pathogen tolerance. However, there are inconsistent reports on the ability of particular compounds to provide resistance to a pathogen. Most of these studies have focused on individual isolates of a given pathogen, suggesting that pathogens vary in their sensitivity to plant-produced toxins. We tested variability in virulence among pathogen isolates, and the impact on this by plant production of, and pathogen tolerance to, secondary metabolites. Botrytis cinerea isolates showed differing sensitivity to purified camalexin, and camalexin-sensitive isolates produced larger lesions on camalexin-deficient Arabidopsis genotypes than on the wild type. In contrast, the camalexin-insensitive isolate produced lesions of similar size on wild-type and camalexin-deficient Arabidopsis. Additional analysis with Arabidopsis secondary metabolite biosynthetic mutants suggests that Botrytis also has variable sensitivity to phenylpropanoids and glucosinolates. Furthermore, Botrytis infection generates a gradient of secondary metabolite responses emanating from the developing lesion, with the Botrytis isolate used determining the accumulation pattern. Collectively, our results indicate that Arabidopsis/ Botrytis interactions are influenced at the metabolic level by variations in toxin production in the host and sensitivity in the pathogen. [ABSTRACT FROM AUTHOR]

SUMMARY: The photosynthetic capacity of mature leaves increases after several days' exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast‐level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL‐dependent changes in transcript abundance of 3844 genes in a 0–6 h time‐series transcriptomics experiment. It was hypothesized that among such genes were those that contribute to the initiation of HL acclimation. By focusing on differentially expressed transcription (co‐)factor genes and applying dynamic statistical modelling to the temporal transcriptomics data, a regulatory network of 47 predominantly photoreceptor‐regulated transcription (co‐)factor genes was inferred. The most connected gene in this network was B‐BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants overexpressing BBX32 were strongly impaired in acclimation to HL and displayed perturbed expression of photosynthesis‐associated genes under LL and after exposure to HL. These observations led to demonstrating that as well as regulation of chloroplast‐level acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA‐105 are important. In addition, the BBX32‐centric gene regulatory network provides a view of the transcriptional control of acclimation in mature leaves distinct from other photoreceptor‐regulated processes, such as seedling photomorphogenesis. Significance Statement: Identifying genes that control plants' intrinsic photosynthetic capacity would provide opportunities for increasing crop productivity. Photosynthetic capacity in mature leaves increases after several days' exposure to episodes of high‐light intensity (HL), which is defined as HL acclimation. Using temporal transcriptomics data and dynamic modelling, we inferred a BBX32‐centric 47‐member Gene Regulatory Network, members of which control, in the first hours of HL exposure, cellular processes that result in enhanced photosynthetic capacity 5 days later. [ABSTRACT FROM AUTHOR]

Summary: Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over‐reliant on a small number of internationally traded crops. Traditional crops are typically well‐adapted to local agro‐ecological conditions and many are nutrient‐dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate‐resilient and biodiverse agriculture. Using short‐read, long‐read and phased sequencing technologies, we generated a high‐quality chromosome‐level genome assembly for Amaranthuscruentus, an under‐researched crop with micronutrient‐ and protein‐rich leaves and gluten‐free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a related species, Amaranthushypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus‐specific genes with a likely role in phytic acid synthesis (an anti‐nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much‐needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity. [ABSTRACT FROM AUTHOR]

Hyaloperonospora arabidopsidis (Hpa) is an oomycete pathogen causing Arabidopsis downy mildew. Effector proteins secreted from the pathogen into the plant play key roles in promoting infection by suppressing plant immunity and manipulating the host to the pathogen's advantage. One class of oomycete effectors share a conserved 'RxLR' motif critical for their translocation into the host cell. Here we characterize the interaction between an RxLR effector, HaRxL21 (RxL21), and the Arabidopsis transcriptional co-repressor Topless (TPL). We establish that RxL21 and TPL interact via an EAR motif at the C-terminus of the effector, mimicking the host plant mechanism for recruiting TPL to sites of transcriptional repression. We show that this motif, and hence interaction with TPL, is necessary for the virulence function of the effector. Furthermore, we provide evidence that RxL21 uses the interaction with TPL, and its close relative TPL-related 1, to repress plant immunity and enhance host susceptibility to both biotrophic and necrotrophic pathogens. Author summary: Disease in plants depends on the outcome of interaction between the pathogen and the host plant. Pathogens use effector proteins to aid colonization by suppression of the host immune system. Identification of effector targets can pinpoint key components of plant defence in addition to aiding our understanding of how pathogens manipulate their hosts. Here, we see a downy mildew effector mimicking a plant transcriptional repression motif and interacting with a transcriptional co-repressor in order to manipulate the plant immunity transcriptional response and susceptibility to both a biotrophic and a necrotrophic pathogen. [ABSTRACT FROM AUTHOR]

Phytohormones mediate most diverse processes in plants, ranging from organ development to immune responses. Receptor protein complexes perceive changes in intracellular phytohormone levels and trigger a signaling cascade to effectuate downstream responses. The in planta analysis of elements involved in phytohormone signaling can be achieved through transient expression in mesophyll protoplasts, which are a fast and versatile alternative to generating plant lines that stably express a transgene. While promoter-reporter constructs have been used successfully to identify internal or external factors that change phytohormone signaling, the range of available marker constructs does not meet the potential of the protoplast technique for large scale approaches. The aim of our study was to provide novel markers for phytohormone signaling in the Arabidopsis mesophyll protoplast system. We validated 18 promoter::luciferase constructs towards their phytohormone responsiveness and specificity and suggest an experimental setup for high-throughput analyses. We recommend novel markers for the analysis of auxin, abscisic acid, cytokinin, salicylic acid and jasmonic acid responses that will facilitate future screens for biological elements and environmental stimuli affecting phytohormone signaling. [ABSTRACT FROM AUTHOR]

Climate change represents a serious threat to global agriculture, necessitating the development of more environmentally resilient crops to safeguard the future of food production. The effects of climate change are appearing to include a higher frequency of extreme weather events and increased day-to-day weather variability. As such, crops which are able to cope with short-term environmental stress, in addition to those that are tolerant to longer term stress conditions are required . It is becoming apparent that the hitherto relatively little studied process of post-stress plant recovery could be key to optimizing growth and production under fluctuating conditions with intermittent transient stress events. Developing more durable crops requires the provision of genetic resources to identify useful traits through the development of screening protocols. Such traits can then become the objective of crop breeding programmes. In this study, we discuss these issues and outline example research in leafy vegetables that is investigating resilience to short-term abiotic stress. [ABSTRACT FROM AUTHOR]

Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. To advance our understanding of the architecture and dynamic regulation of the JA gene regulatory network, we performed a high-resolution RNA-seq time series of methyl JA -treated Arabidopsis thaliana at 15 time points over a 16-h period. Computational analysis showed that methyl JA (MeJA) induces a burst of transcriptional activity, generating diverse expression patterns over time that partition into distinct sectors of the JA response targeting specific biological processes. The presence of transcription factor (TF) DNA binding motifs correlated with specific TF activity during temporal MeJA -induced transcriptional reprogramming. Insight into the underlying dynamic transcriptional regulation mechanisms was captured in a chronological model of the JA gene regulatory network. Several TFs, including MYB59 and bHLH27, were uncovered as early network components with a role in pathogen and insect resistance. Analysis of subnetworks surrounding the TFs ORA47, RAP2.6L, MYB59, and ANAC055, using transcriptome profiling of overexpressors and mutants, provided insights into their regulatory role in defined modules of the JA network. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints and validates previously unknown regulators, and provides a valuable resource for functional studies on JA signaling components in plant defense and development. [ABSTRACT FROM AUTHOR]

To feed humanity, while maintaining a stable and diverse biosphere, crop science needs to adapt to an open research environment where genetic resources and the data demonstrating the environments in which they are effective are freely shared. The challenge faced is to expand crop production on a reduced land area, due to environmental degradation caused by human encroachment and climate change, while maintaining biodiversity. Individual researchers are discovering alleles and genetic combinations that are effective in certain environments but not in others. These data and alleles are useful globally to speed progress in breeding for similar environments while not wasting time on ineffective genotypes. However, currently, there are significant barriers to the sharing of genetic resources and their underpinning data, which must be overcome if we are to sustain the planet for future generations. [ABSTRACT FROM AUTHOR]

In Arabidopsis, jasmonate (JA)-signaling plays a key role in mediating Fusarium oxysporum disease outcome. However, the roles of JASMONATE ZIM-domain (JAZ) proteins that repress JA-signaling have not been characterized in host resistance or susceptibility to this pathogen. Here, we found most JAZ genes are induced following F. oxysporum challenge, and screening T-DNA insertion lines in Arabidopsis JAZ family members identified a highly disease-susceptible JAZ7 mutant (jaz7-1D). This mutant exhibited constitutive JAZ7 expression and conferred increased JA-sensitivity, suggesting activation of JA-signaling. Unlike jaz7 loss-of-function alleles, jaz7-1D also had enhanced JA-responsive gene expression, altered development and increased susceptibility to the bacterial pathogen Pst DC3000 that also disrupts host JA-responses. We also demonstrate that JAZ7 interacts with transcription factors functioning as activators (MYC3, MYC4) or repressors (JAM1) of JA-signaling and contains a functional EAR repressor motif mediating transcriptional repression via the co-repressor TOPLESS (TPL). We propose through direct TPL recruitment, in wildtype plants JAZ7 functions as a repressor within the JA-response network and that in jaz7-1D plants, misregulated ectopic JAZ7 expression hyper-activates JA-signaling in part by disturbing finely-tuned COI1-JAZ-TPL-TF complexes. [ABSTRACT FROM AUTHOR]

The circadian clock, an internal time-keeping mechanism, allows plants to anticipate regular changes in the environment, such as light and dark, and biotic challenges such as pathogens and herbivores. Here, we demonstrate that the plant circadian clock influences susceptibility to the necrotrophic fungal pathogen, Botrytis cinerea. Arabidopsis plants show differential susceptibility to B. cinerea depending on the time of day of inoculation. Decreased susceptibility after inoculation at dawn compared with night persists under constant light conditions and is disrupted in dysfunctional clock mutants, demonstrating the role of the plant clock in driving time-of-day susceptibility to B. cinerea. The decreased susceptibility to B. cinerea following inoculation at subjective dawn was associated with faster transcriptional reprogramming of the defence response with gating of infection-responsive genes apparent. Direct target genes of core clock regulators were enriched among the transcription factors that responded more rapidly to infection at subjective dawn than subjective night, suggesting an influence of the clock on the defence-signalling network. In addition, jasmonate signalling plays a crucial role in the rhythmic susceptibility of Arabidopsis to B. cinerea with the enhanced susceptibility to this pathogen at subjective night lost in a jaz6 mutant. [ABSTRACT FROM AUTHOR]

Plant biology is rapidly entering an era where we have the ability to conduct intricate studies that investigate how a plant interacts with the entirety of its environment. This requires complex, large studies to measure how plant genotypes simultaneously interact with a diverse array of environmental stimuli. Successful interpretation of the results from these studies requires us to transition away from the traditional standard of conducting an array of pairwise t tests toward more general linear modeling structures, such as those provided by the extendable ANOVA framework. In this Perspective, we present arguments for making this transition and illustrate how it will help to avoid incorrect conclusions in factorial interaction studies (genotype × genotype, genotype × treatment, and treatment × treatment, or higher levels of interaction) that are becoming more prevalent in this new era of plant biology. [ABSTRACT FROM AUTHOR]

Summary: Every year, a large number of novel algorithms are introduced to the scientific community for a myriad of applications, but using these across different research groups is often troublesome, due to suboptimal implementations and specific dependency requirements. This does not have to be the case, as public cloud computing services can easily house tractable implementations within self-contained dependency environments, making the methods easily accessible to a wider public. We have taken 14 popular methods, the majority related to expression data or promoter analysis, developed these up to a good implementation standard and housed the tools in isolated Docker containers which we integrated into the CyVerse Discovery Environment, making these easily usable for a wide community as part of the CyVerse UK project. [ABSTRACT FROM AUTHOR]

The Arabidopsis constitutive induced resistance 1 (cir1) mutant displays salicylic acid (SA)-dependent constitutive expression of defence genes and enhanced resistance to biotrophic pathogens. To further characterise the role of CIR1 in plant immunity we conducted epistasis analyses with two key components of the SA-signalling branch of the defence network, ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4). We demonstrate that the constitutive defence phenotypes of cir1 require both EDS1 and PAD4, indicating that CIR1 lies upstream of the EDS1-PAD4 regulatory node in the immune signalling network. In light of this finding we examined EDS1 expression in cir1 and observed increased protein, but not mRNA levels in this mutant, suggesting that CIR1 might act as a negative regulator of EDS1 via a post-transcriptional mechanism. Finally, as environmental temperature is known to influence the outcome of plant-pathogen interactions, we analysed cir1 plants grown at 18, 22 or 25°C. We found that susceptibility to Pseudomonas syringae pv. tomato (Pst) DC3000 is modulated by temperature in cir1. Greatest resistance to this pathogen (relative to PR-1:LUC control plants) was observed at 18°C, while at 25°C no difference in susceptibility between cir1 and control plants was apparent. The increase in resistance to Pst DC3000 at 18°C correlated with a stunted growth phenotype, suggesting that activation of defence responses may be enhanced at lower temperatures in the cir1 mutant. [ABSTRACT FROM AUTHOR]

• Describes impact of Maf1 depletion by RNAi and mutagenesis in Arabidopsis. • Selective increases in expression of specific tRNAs on Maf1 depletion. • Significantly enhanced plant growth after Maf1 depletion. • No evidence of increased vulnerability to a common pathogen. • Growth enhancement by Maf1 depletion retained during drought and salt stress. Maf1 is a transcription factor that is conserved in sequence and structure between yeasts, animals and plants. Its principal molecular function is also well conserved, being to bind and repress RNA polymerase (pol) III, thereby inhibiting synthesis of tRNAs and other noncoding RNAs. Restrictions on tRNA production and hence protein synthesis can provide a mechanism to preserve resources under conditions that are suboptimal for growth. Accordingly, Maf1 is found in some organisms to influence growth and/or stress survival. Because of their sessile nature, plants are especially vulnerable to environmental changes and molecular adaptations that enhance growth under benign circumstances can increase sensitivity to external challenges. We tested if Maf1 depletion in the model plant Arabidopsis affects growth, pathogen resistance and tolerance of drought or soil salinity, a common physiological challenge that imposes both osmotic and ionic stress. We find that disruption of the Maf1 gene or RNAi-mediated depletion of its transcript is well-tolerated and confers a modest growth advantage without compromising resistance to common biotic and abiotic challenges. [ABSTRACT FROM AUTHOR]

Motivation: Identification of modules of co-regulated genes is a crucial first step towards dissecting the regulatory circuitry underlying biological processes. Co-regulated genes are likely to reveal themselves by showing tight co-expression, e.g. high correlation of expression profiles across multiple time series datasets. However, numbers of up- or downregulated genes are often large, making it difficult to discriminate between dependent co-expression resulting from co-regulation and independent co-expression. Furthermore, modules of co-regulated genes may only show tight co-expression across a subset of the time series, i.e. show condition-dependent regulation.Results: Wigwams is a simple and efficient method to identify gene modules showing evidence for co-regulation in multiple time series of gene expression data. Wigwams analyzes similarities of gene expression patterns within each time series (condition) and directly tests the dependence or independence of these across different conditions. The expression pattern of each gene in each subset of conditions is tested statistically as a potential signature of a condition-dependent regulatory mechanism regulating multiple genes. Wigwams does not require particular time points and can process datasets that are on different time scales. Differential expression relative to control conditions can be taken into account. The output is succinct and non-redundant, enabling gene network reconstruction to be focused on those gene modules and combinations of conditions that show evidence for shared regulatory mechanisms. Wigwams was run using six Arabidopsis time series expression datasets, producing a set of biologically significant modules spanning different combinations of conditions.Availability and implementation: A Matlab implementation of Wigwams, complete with graphical user interfaces and documentation, is available at: warwick.ac.uk/wigwams.Contact: k.j.denby@warwick.ac.ukSupplementary Data: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

A model is presented describing the gene regulatory network surrounding three similar NAC transcription factors that have roles in Arabidopsis leaf senescence and stress responses. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1-hybrid analysis and modelling using gene expression time course data has been applied to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modelling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions. Gene expression analysis in mutants of ANAC019 and ANAC055 at different times during leaf senescence has revealed a distinctly different role for each of these genes. Yeast 1-hybrid analysis is shown to be a valuable tool that can distinguish clades of binding proteins and be used to test and quantify protein binding to predicted promoter motifs. [ABSTRACT FROM AUTHOR]

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana , papaya [ Carica papaya ], poplar [ Populus trichocarpa ], and grape [ Vitis vinifera ]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research. [ABSTRACT FROM AUTHOR]

The PHYTOCHROME AND FLOWERING TIME1 gene encoding the MEDIATOR25 (MED25) subunit of the eukaryotic Mediator complex is a positive regulator of jasmonate (JA)-responsive gene expression in Arabidopsis (Arabidopsis thaliana). Based on the function of the Mediator complex as a bridge between DNA-bound transcriptional activators and the RNA polymerase II complex, MED25 has been hypothesized to function in association with transcriptional regulators of the JA pathway. However, it is currently not known mechanistically how MED25 functions to regulate JA-responsive gene expression. In this study, we show that MED25 physically interacts with several key transcriptional regulators of the JA signaling pathway, including the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factors OCTADECANOID-RESPONSWE ARABIDOPSIS AP2/ERF59 and ERF1 as well as the master regulator MYC2. Physical interaction detected between MED25 and four group IX AP2/ERF transcription factors was shown to require the activator interaction domain of MED25 as well as the recently discovered Conserved Motif IX-1/EDLL transcription activation motif of MED25-interacting AP2/ERFs. Using transcriptional activation experiments, we also show that OCTADECANOIDRESPONSIVE ARABIDOPSIS AP2/ERF59- and ERF1-dependent activation of PLANT DEFENSIN1.2 as well as MYC2- dependent activation of VEGETATIVE STORAGE PROTEIN1 requires a functional MED25. In addition, MED25 is required for MYC2-dependent repression of pathogen defense genes. These results suggest an important role for MED25 as an integrative hub within the Mediator complex during the regulation of JA-associated gene expression. [ABSTRACT FROM AUTHOR]

Motivation: The generation of time series transcriptomic datasets collected under multiple experimental conditions has proven to be a powerful approach for disentangling complex biological processes, allowing for the reverse engineering of gene regulatory networks (GRNs). Most methods for reverse engineering GRNs from multiple datasets assume that each of the time series were generated from networks with identical topology. In this study, we outline a hierarchical, non-parametric Bayesian approach for reverse engineering GRNs using multiple time series that can be applied in a number of novel situations including: (i) where different, but overlapping sets of transcription factors are expected to bind in the different experimental conditions; that is, where switching events could potentially arise under the different treatments and (ii) for inference in evolutionary related species in which orthologous GRNs exist. More generally, the method can be used to identify context-specific regulation by leveraging time series gene expression data alongside methods that can identify putative lists of transcription factors or transcription factor targets.Results: The hierarchical inference outperforms related (but non-hierarchical) approaches when the networks used to generate the data were identical, and performs comparably even when the networks used to generate data were independent. The method was subsequently used alongside yeast one hybrid and microarray time series data to infer potential transcriptional switches in Arabidopsis thaliana response to stress. The results confirm previous biological studies and allow for additional insights into gene regulation under various abiotic stresses.Availability: The methods outlined in this article have been implemented in Matlab and are available on request.Contact: d.l.wild@warwick.ac.ukSupplementary Information: Supplementary data is available for this article. [ABSTRACT FROM PUBLISHER]

Summary In Arabidopsis, resistance to the necrotrophic fungus Botrytis cinerea is conferred by ethylene via poorly understood mechanisms. Metabolomic approaches compared the responses of the wild-type, the ethylene-insensitive mutant etr1-1, which showed increased susceptibility, and the constitutively active ethylene mutants ctr1-1 and eto2 both exhibited decreased susceptibility to B. cinerea. Fourier transform-infrared (FT-IR) spectroscopy demonstrated reproducible biochemical differences between treatments and genotypes. To identify discriminatory mass-to-charge ratios ( m/ z) associated with resistance, discriminant function analysis was employed on spectra derived from direct injection electrospray ionisation-mass spectrometry on the derived principal components of these data. Ethylene-modulated m/z were mapped onto Arabidopsis biochemical pathways and many were associated with hydroxycinnamate and monolignol biosynthesis, both linked to cell wall modification. A high-resolution linear triple quadrupole-Orbitrap hybrid system confirmed the identity of key metabolites in these pathways. The contribution of these pathways to defence against B. cinerea was validated through the use of multiple Arabidopsis mutants. The FT-IR microspectroscopy indicated that spatial accumulation of hydroxycinnamates and monolignols at the cell wall to confine disease was linked ot ethylene. These data demonstrate the power of metabolomic approaches in elucidating novel biological phenomena, especially when coupled to validation steps exploiting relevant mutant genotypes. [ABSTRACT FROM AUTHOR]

Motivation: Identifying regulatory modules is an important task in the exploratory analysis of gene expression time series data. Clustering algorithms are often used for this purpose. However, gene regulatory events may induce complex temporal features in a gene expression profile, including time delays, inversions and transient correlations, which are not well accounted for by current clustering methods. As the cost of microarray experiments continues to fall, the temporal resolution of time course studies is increasing. This has led to a need to take account of detailed temporal features of this kind. Thus, while standard clustering methods are both widely used and much studied, their shared shortcomings with respect to such temporal features motivates the work presented here. [ABSTRACT FROM PUBLISHER]

Expression of the Arabidopsis Oxidative Signal-Inducible1 (OXI1) serine/threonine protein kinase gene (At3g25250) is induced by oxidative stress. The kinase is required for root hair development and basal defence against the oomycete pathogen Hyaloperonospora parasitica, two separate H2O2-mediated processes. In this study, the role of OXI1 during pathogenesis was characterized further. Null oxi1 mutants are more susceptible to both virulent and avirulent strains of the biotrophic bacterial pathogen Pseudomonas syringae compared with the wild type, indicating that OXI1 positively regulates both basal resistance triggered by the recognition of pathogen-associated molecular patterns, as well as effector-triggered immunity. The level of OXI1 expression appears to be critical in mounting an appropriate defence response since OXI1 overexpressor lines also display increased susceptibility to biotrophic pathogens. The induction of OXI1 after P. syringae infection spatially and temporally correlates with the oxidative burst. Furthermore, induction is reduced in atrbohD mutants and after application of DPI (an inhibitor of NADPH oxidases) suggesting that reactive oxygen species produced through NADPH oxidases drives OXI1 expression during this plant–pathogen interaction. [ABSTRACT FROM PUBLISHER]

A complex signal transduction network involving salicylic acid, jasmonic acid and ethylene underlies disease resistance inArabidopsis. To understand this defence signalling network further, we identified mutants that expressed the marker genePR-1::luciferasein the absence of pathogen infection. Thesecirmutants all display constitutive expression of a suite of defence-related genes but exhibit different disease resistance profiles to two biotrophic pathogens,Pseudomonas syringaepv.tomatoandPeronospora parasiticaNOCO2, and the necrotrophic pathogenBotrytis cinerea. We further characterizedcir3, which displays enhanced resistance only to the necrotrophic pathogen.Cir3-mediated resistance toB. cinereais dependent on accumulated salicylic acid and a functional EIN2 protein. [ABSTRACT FROM AUTHOR]

Xerophyta humilis (Bak.) Dur and Schinz is an indigenous Southern African resurrection plant which is able to protect itself from the stresses associated with extreme dehydration. For the purpose of analysing global patterns of gene expression in response to desiccation and recovery on rehydration, we have generated a normalized 10 900 library, representing genes from root and leaf tissue that are expressed during the dehydration-rehydration cycle. For the small-scale microarray analysis described here, 424 cDNAs were sequenced, annotated, arrayed and hybridized with hydrated and dehydrated, leaf-specific RNA. Reverse Northern blots were used as an alternative method to compare the expression results. A total of 55 dehydration-inducible cDNAs were identified combining the results of both methods. Northern blot analysis of 14 of the 55 the dehydration-upregulated cDNAs verified the expression status of all 14 genes. Dehydration-upregulated cDNAs included those homologous to known dehydration stress-responsive genes encoding metallothioneins, galactinol synthases, an aldose reductase and a glyoxalase. A large number of genes encoding late embryonic abundant proteins (LEAs), dehydrins and desiccation-related proteins were also identified, suggesting that proteins that provide mechanical and antioxidant protection against water loss dominate the mRNA population in desiccated X. humilis leaf tissue. Dehydration-upregulated genes identified in this study, and not previously implicated in the dehydration response, include cDNAs encoding a putative chloroplast RNA-binding protein and a protein containing SNF2/helicase domains. Comparisons with microarray data, which profile the dehydration response in desiccation-sensitive plants, reveal differences in expression patterns between X. humilis and Arabidopsis and rice that could provide clues as to the mechanisms underlying desiccation-tolerant and -sensitive phenotypes. The X. humilis library promises to be a useful resource for transcript profiling the dehydration and rehydration response in a desiccation‐tolerant plant. [ABSTRACT FROM AUTHOR]

A guanylyl cyclase has been recently identified in Arabidopsis but, despite the use of pharmacological inhibitors to infer roles of the second messenger 3′,5′-cyclic guanosine monophosphate (cGMP), very few measurements of actual cGMP levels in plants are available. Here, we demonstrate that cGMP levels in Arabidopsis seedlings increase rapidly (⩽5 s) and to different degrees after salt and osmotic stress, and that the increases are prevented by treatment with LY, an inhibitor of soluble guanylyl cyclases. In addition, we provide evidence to suggest that salt stress activates two cGMP signalling pathways – an osmotic, calcium-independent pathway and an ionic, calcium-dependent pathway. [Copyright &y& Elsevier]

Seed dormancy is an adaptive trait defining where and when plants are established. Diverse signals from the environment are used to decide when to initiate seed germination, a process driven by the expansion of cells within the embryo. How these signals are integrated and transduced into the biomechanical changes that drive embryo growth remains poorly understood. Using Arabidopsis seeds, we demonstrate that cell-wall-loosening EXPANSIN (EXPA) genes promote gibberellic acid (GA)-mediated germination, identifying EXPA s as downstream molecular targets of this developmental phase transition. Molecular interaction screening identified transcription factors (TFs) that bind to both EXPA promoter fragments and DELLA GA-response regulators. A subset of these TFs is targeted each by nitric oxide (NO) and the phytochrome-interacting TF PIL5. This molecular interaction network therefore directly links the perception of an external environmental signal (light) and internal hormonal signals (GA and NO) with downstream germination-driving EXPA gene expression. Experimental validation of this network established that many of these TFs mediate GA-regulated germination, including TCP14/15 , RAP2.2/2.3/2.12 , and ZML1. The reduced germination phenotype of the tcp14 tcp15 mutant seed was partially rescued through ectopic expression of their direct target EXPA9. The GA-mediated control of germination by TCP14/15 is regulated through EXPA -mediated control of cell wall loosening, providing a mechanistic explanation for this phenotype and a previously undescribed role for TCPs in the control of cell expansion. This network reveals the paths of signal integration that culminate in seed germination and provides a resource to uncover links between the genetic and biomechanical bases of plant growth. • The network linking integration of environmental signals to seed growth is mapped • EXPANSIN gene expression is redundantly regulated and promotes GA-mediated germination • The TCP14 transcription factor directly regulates EXPANSIN9 expression • The tcp14/15 germination phenotype is complemented by EXPANSIN9 expression Seeds use a range of environmental cues to decide when to commence germination. Xu et al. report the molecular interaction network used to integrate inputs into growth-promoting EXPANSIN gene expression. Functional validation defines EXPANSIN s as downstream factors driving germination and TCP14/15 as transcription factors mediating their expression. [ABSTRACT FROM AUTHOR]