Partial disruption of the Arabidopsis 2S seed storage proteins highlights the essential role of redox homeostasis in seed proteome plasticity and rebalancing.

Arabidopsis seeds store most of their amino acids in the 12S and 2S seed storage proteins (SSPs). Elimination of the three most abundant 12S cruciferins (i.e.

Breeding indoor watercress for enhanced crop biofortification: harnessing natural variation of wild germplasm.

We quantified the natural genetic variation of a diverse collection of wild watercress germplasm, consisting of 32 accessions collected from 16 locations in nine countries worldwide and grown in a controlled indoor environment with contrasting blue light regimes. Significant phenotypic diversity was identified for all three categories of traits: morphology and yield varied by 68% across the population (leaf size, biomass production, and stem length), with sensory (sugar content and brix), and nutritional quality (glucosinolates, vitamin C, carotenoids) varying by 45% and 43% respectively. Using two LED light regimes, control and additional blue light exposure, revealed that the watercress nutritional profile is plastic, and that the magnitude and direction of plastic responses vary depending on genotype and trait.

An effluent pump family distributed across plant commensal bacteria conditions host- and organ-specific glucosinolate detoxification.

In nature, plants recruit a diverse microbial community, the plant microbiome, that is distinct from the surrounding soil community. To understand the forces that shape the plant microbiome we need to characterize the microbial traits that contribute to plant colonization. We used barcoded mutant libraries to identify bacterial genes that contribute to the colonization of a monocot and a eudicot host.

Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.

Organisms regulate gene expression in response to environmental cues, a process known as plasticity, to adjust to changing environments. Research into natural variation and the evolution of plasticity frequently studies cis-regulatory elements with theory suggesting they are more important evolutionarily than trans-regulatory elements. Genome-wide association (GWA) studies have supported this idea, observing a predominance of cis-loci affecting plasticity.

Polygenic strategies for host-specific and general virulence of Botrytis cinerea across diverse eudicot hosts.

Diverse qualitative and quantitative genetic architectures can successfully enable fungal virulence and host range. To model the quantitative genetic architecture of a generalist pathogen with an extensive host range, we conducted a genome-wide association study (GWAS) of the lesion area of Botrytis cinerea across 8 hosts. This revealed that it was possible to partition the virulence, as defined by the lesion area, common across all hosts from host-specific virulence.

Molecular evolution of a reproductive barrier in maize and related species.

Three cross-incompatibility loci each control a distinct reproductive barrier in both domesticated maize (Zea mays ssp. mays) and its wild teosinte relatives. These 3 loci, Teosinte crossing barrier1 (Tcb1), Gametophytic factor1 (Ga1), and Ga2, each play a key role in preventing hybridization between incompatible populations and are proposed to maintain the barrier between domesticated and wild subspecies.

Targeted MYC2 stabilization confers citrus Huanglongbing resistance.

Huanglongbing (HLB) is a devastating citrus disease. In this work, we report an HLB resistance regulatory circuit in composed of an E3 ubiquitin ligase, PUB21, and its substrate, the MYC2 transcription factor, which regulates jasmonate-mediated defense responses. A helitron insertion in the promoter introduced multiple MYC2-binding cis-elements to create a regulatory circuit linking the PUB21 activity with MYC2 degradation.

Phylogenetic and genomic mechanisms shaping glucosinolate innovation.

Plants have created an immense diversity of specialized metabolites to optimize fitness within a complex environment. Each plant lineage has created novel metabolites often using the classical duplication/neo-functionalization model, but this is constrained by undersampled genera and an absence of high-quality genomes. Phylogenetically resolved genomes, deeper chemical sampling and mechanistic assessment of glucosinolate diversity in the Brassicales is beginning to fill in a deeper understanding of how chemical novelty arises.

Allopolyploidy expanded gene content but not pangenomic variation in the hexaploid oilseed Camelina sativa.

Ancient whole-genome duplications are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent whole-genome duplications may contribute to evolvability within recent polyploids. Hybridization accompanying some whole-genome duplications may combine divergent gene content among diploid species.

Leaf abaxial and adaxial surfaces differentially affect the interaction of Botrytis cinerea across several eudicots.

Eudicot plant species have leaves with two surfaces: the lower abaxial and the upper adaxial surface. Each surface varies in a diversity of components and molecular signals, resulting in potentially different degrees of resistance to pathogens. We tested how Botrytis cinerea, a necrotroph fungal pathogen, interacts with the two different leaf surfaces across 16 crop species and 20 Arabidopsis genotypes.

Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea.

Unlabelled: Botrytis cinerea Pers. Fr. (teleomorph: Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants.

Making watercress () cropping sustainable: genomic insights into enhanced phosphorus use efficiency in an aquatic crop.

Watercress () is a nutrient-dense salad crop with high antioxidant capacity and glucosinolate concentration and with the potential to contribute to nutrient security as a locally grown outdoor aquatic crop in northern temperate climates. However, phosphate-based fertilizers used to support plant growth contribute to the eutrophication of aquatic habitats, often pristine chalk streams, downstream of farms, increasing pressure to minimize fertilizer use and develop a more phosphorus-use efficient (PUE) crop. Here, we grew genetically distinct watercress lines selected from a bi-parental mapping population on a commercial watercress farm either without additional phosphorus (P-) or under a commercial phosphate-based fertilizer regime (P+), to decipher effects on morphology, nutritional profile, and the transcriptome.

Specificity and breadth of plant specialized metabolite-microbe interactions.

Plant specialized metabolites shape plant interactions with the environment including plant-microbe interactions. While we often group compounds into generic classes, it is the precise structure of a compound that creates a specific role in plant-microbe or-pathogen interactions. Critically, the structure guides definitive targets in individual interactions, yet single compounds are not limited to singular mechanistic targets allowing them to influence interactions across broad ranges of attackers, from bacteria to fungi to animals.

Large-scale identification of novel transcriptional regulators of the aliphatic glucosinolate pathway in Arabidopsis.

Aliphatic glucosinolates are a large group of plant secondary metabolites characteristic of Brassicaceae, including the model plant Arabidopsis. The diverse and complex degradation products of aliphatic glucosinolates contribute to plant responses to herbivory, pathogen attack, and environmental stresses. Most of the biosynthesis genes in the aliphatic glucosinolate pathway have been cloned in Arabidopsis, and the research focus has recently shifted to the regulatory mechanisms controlling aliphatic glucosinolate accumulation.

Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs.

Processes affecting rates of sequence polymorphism are fundamental to the evolution of gene duplicates. The relationship between gene activity and sequence polymorphism can influence the likelihood that functionally redundant gene copies are co-maintained in stable evolutionary equilibria vs other outcomes such as neofunctionalization. Here, we investigate genic variation in epigenome-associated polymorphism rates in Arabidopsis thaliana and consider whether these affect the evolution of gene duplicates.

Is specialized metabolite regulation specialized?

Recent technical and theoretical advances have generated an explosion in the identification of specialized metabolite pathways. In comparison, our understanding of how these pathways are regulated is relatively lagging. This and the relatively young age of specialized metabolite pathways has partly contributed to a default and common paradigm whereby specialized metabolite regulation is theorized as relatively simple with a few key transcription factors and the compounds are non-regulatory end-products.

Polygenic pathogen networks influence transcriptional plasticity in the Arabidopsis-Botrytis pathosystem.

Bidirectional flow of information shapes the outcome of the host-pathogen interactions and depends on the genetics of each organism. Recent work has begun to use co-transcriptomic studies to shed light on this bidirectional flow, but it is unclear how plastic the co-transcriptome is in response to genetic variation in both the host and pathogen. To study co-transcriptome plasticity, we conducted transcriptomics using natural genetic variation in the pathogen, Botrytis cinerea, and large-effect genetic variation abolishing defense signaling pathways within the host, Arabidopsis thaliana.

Causes of Mutation Rate Variability in Plant Genomes.

Mutation is the source of all heritable diversity, the essential material of evolution and breeding. While mutation rates are often regarded as constant, variability in mutation rates has been observed at nearly every level-varying across mutation types, genome locations, gene functions, epigenomic contexts, environmental conditions, genotypes, and species. This mutation rate variation arises from differential rates of DNA damage, repair, and transposable element activation and insertion that together produce what is measured by DNA mutation rates.

The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa.

The rhizosphere microbiome influences many aspects of plant fitness, including production of secondary compounds and defence against insect herbivores. Plants also modulate the composition of the microbial community in the rhizosphere via secretion of root exudates. We tested both the effect of the rhizosphere microbiome on plant traits, and host plant effects on rhizosphere microbes using recombinant inbred lines (RILs) of Brassica rapa that differ in production of glucosinolates (GLS), secondary metabolites that contribute to defence against insect herbivores.

Integrated omics reveal novel functions and underlying mechanisms of the receptor kinase FERONIA in Arabidopsis thaliana.

The receptor kinase FERONIA (FER) is a versatile regulator of plant growth and development, biotic and abiotic stress responses, and reproduction. To gain new insights into the molecular interplay of these processes and to identify new FER functions, we carried out quantitative transcriptome, proteome, and phosphoproteome profiling of Arabidopsis (Arabidopsis thaliana) wild-type and fer-4 loss-of-function mutant plants. Gene ontology terms for phytohormone signaling, abiotic stress, and biotic stress were significantly enriched among differentially expressed transcripts, differentially abundant proteins, and/or misphosphorylated proteins, in agreement with the known roles for FER in these processes.