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Summary: The plant immune system involves detection of pathogens via both cell‐surface and intracellular receptors. Both receptor classes can induce transcriptional reprogramming that elevates disease resistance. To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP‐I). We designed and synthesized biotinylated single‐strand RNA bait libraries targeted to a subset of defense genes, and generated sequence capture data from 99 RNA‐seq libraries. We built a data processing pipeline to quantify the RNA‐CAP‐I‐seq data, and visualize differential gene expression. Sequence capture in combination with quantitative RNA‐seq enabled cost‐effective assessment of the expression profile of a specified subset of genes. Quantitative sequence capture is not limited to RNA‐seq or any specific organism and can potentially be incorporated into automated platforms for high‐throughput sequencing. [ABSTRACT FROM AUTHOR]

Expansion of gene families facilitates robustness and evolvability of biological processes but impedes functional genetic dissection of signalling pathways. To address this, quantitative analysis of single cell responses can help characterize the redundancy within gene families. We developed high‐throughput quantitative imaging of stomatal closure, a response of plant guard cells, and performed a reverse genetic screen in a group of Arabidopsis mutants to five stimuli. Focussing on the intersection between guard cell signalling and the endomembrane system, we identified eight clusters based on the mutant stomatal responses. Mutants generally affected in stomatal closure were mostly in genes encoding SNARE and SCAMP membrane regulators. By contrast, mutants in RAB5 GTPase genes played specific roles in stomatal closure to microbial but not drought stress. Together with timed quantitative imaging of endosomes revealing sequential patterns in FLS2 trafficking, our imaging pipeline can resolve non‐redundant functions of the RAB5 GTPase gene family. Finally, we provide a valuable image‐based tool to dissect guard cell responses and outline a genetic framework of stomatal closure. High‐throughput imaging at cellular and subcellular scales enables genetic dissection of plant physiological responses to biotic and abiotic stresses. We developed the software tool StomataMeasurer allowing the identification and measurements of stomatal apertures in an automated fashion. Using Arabidopsis mutant screening, we demonstrate that StomataMeasurer is suitable to analyse stomatal patterning and behaviours in response to five stimuli. [ABSTRACT FROM AUTHOR]

Summary: The tomato PROCERA gene encodes a DELLA protein, and loss‐of‐function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERADELLA domain, and recovered several loss‐of‐function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin. Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes. [ABSTRACT FROM AUTHOR]

High throughput confocal imaging poses challenges in the computational image analysis of complex subcellular structures such as the microtubule cytoskeleton. Here, we developed CellArchitect, an automated image analysis tool that quantifies changes to subcellular patterns illustrated by microtubule markers in plants. We screened microtubule-targeted herbicides and demonstrate that high throughput confocal imaging with integrated image analysis by CellArchitect can distinguish effects induced by the known herbicides indaziflam and trifluralin. The same platform was used to examine 6 other compounds with herbicidal activity, and at least 3 different effects induced by these compounds were profiled. We further show that CellArchitect can detect subcellular patterns tagged by actin and endoplasmic reticulum markers. Thus, the platform developed here can be used to automate image analysis of complex subcellular patterns for purposes such as herbicide discovery and mode of action characterisation. The capacity to use this tool to quantitatively characterize cellular responses lends itself to application across many areas of biology. [ABSTRACT FROM AUTHOR]

1. Herbivory often induces systemic plant responses that affect the host choice of subsequent herbivores, either deterring or attracting them, with implications for the performance of both herbivore and host plant. Combining measures of herbivore movement and consumption can efficiently provide insights into the induced plant responses that are most important for determining choice behaviour. 2. The preferences of two frugivorous stink bug species, Nezara viridula and Euschistus servus between cotton plants left undamaged or damaged by Helicoverpa zea and Heliothis virescens larvae were investigated. A novel consumer movement model was used to investigate if attraction rates or leaving rates determined preferences. Stink bug consumption rates were measured using salivary sheath flanges. Finally, the systemic induction of selected phenolic-based and terpenoid secondary metabolites were measured from heliothine herbivory on developing cotton bolls, to investigate if they explained stink bug feeding responses. 3. Heliothine herbivory did not affect the N. viridula feeding preference. However, we found opposing effects of H. zea and H. virescens herbivory on the behaviour of E. servus. Avoidance of H. zea-damaged plants is not obviously related to phenolic or terpenoid induction in cotton bolls; whereas a preference for H. virescens-damaged plants may be related to reductions in chlorogenic acid in boll carpel walls. 4. The present results highlight the inferential power of measuring both consumer movement and consumption in preference experiments and combining behavioural responses with phytochemical responses. Furthermore, while plant-mediated interactions among herbivorous insects are well studied, interactions among frugivorous species specifically have been poorly documented. [ABSTRACT FROM AUTHOR]

RenSeq is a NB- LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB- LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB- LRRs and can be accessed through a genome browser that we provide. We compared these NB- LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB- LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii ( Rpi-ber2) and S. ruiz-ceballosii ( Rpi-rzc1), we were able to apply Ren Seq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]

This study investigated the effects of exposure to waterborne perfluorooctane sulfonate (PFOS) on oxidative stress and reproductive endpoints in fish. Exposures utilized species commonly used in toxicological testing, including the fathead minnow (Pimephales promelas) and rainbow trout (Oncorhynchus mykiss), as well as relatively insensitive taxa such as creek chub (Semotilus atromaculatus), spottail shiner (Notropis hudsonius), and white sucker (Catostomus commersoni). In all fish species, short-term (14-28 d) exposure to PFOS produced only modest mortality at concentrations consistent with environmental spill scenarios. However, PFOS consistently increased hepatic fatty acyl--CoA oxidase activity and increased oxidative damage, as quantified using the 2-thiobarbituric acid--reactive substances assay. Plasma testosterone, 11-ketotestosterone, and 17ß-estradiol titers were often elevated with PFOS exposure. Vitellogenin, the egg yolk precursor protein, was occasionally altered in the plasma with PFOS exposure, but responses varied with maturity. Oviposition frequency and egg deposition in fathead minnow were not significantly impaired with PFOS exposure, despite a trend toward progressive impairment with increasing exposure concentrations. Although short-term PFOS exposure produced significant impacts on biochemical and reproductive endpoints in fish at concentrations consistent with environmental spills, the impact of long-term exposure to environmentally relevant concentrations of PFOS is unclear. [ABSTRACT FROM AUTHOR]