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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]

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]

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]

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]

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]

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]

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]