Microbial terroir: associations between soil microbiomes and the flavor chemistry of mustard (Brassica juncea)

C Walsh, C Vanderburgh, L Grant, E Katz, DJ Kliebenstein, N Fierer

New Phytologist

Convergently evolved metabolites are new to me but not to my attackers

A Agosto‐Ramos, AJ Muhich, DJ Kliebenstein

New Phytologist

Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea

R Singh, C Caseys, DJ Kliebenstein

Molecular plant pathology 25 (1), e13404

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

L Chen, Q Zeng, J Zhang, C Li, X Bai, F Sun, DJ Kliebenstein, B Li

Journal of Experimental Botany 75 (1), 300-315

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

LE Hibbert, Y Qian, HK Smith, S Milner, E Katz, DJ Kliebenstein, G Taylor

Frontiers in Plant Science 14, 1279823

Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs

SK Kenchanmane Raju, M Lensink, DJ Kliebenstein, C Niederhuth, ...

New Phytologist 240 (3), 1292-1304

Complementing model species with model clades

ME Mabry, RS Abrahams, IA Al-Shehbaz, WJ Baker, S Barak, MS Barker, ...

The Plant Cell, koad260

Specificity and breadth of plant specialized metabolite–microbe interactions

DJ Kliebenstein

Current Opinion in Plant Biology, 102459

Is specialized metabolite regulation specialized?

DJ Kliebenstein

Journal of Experimental Botany 74 (17), 4942-4948

Watercress yield and quality vary depending on both genotype and environment: Results from highly contrasting growing systems of California and UK

Y Qian, LE Hibbert, E Katz, HK Smith, DJ Kliebenstein, G Taylor

Scientia Horticulturae 319, 112154

Mutation bias reflects natural selection in Arabidopsis thaliana (vol 602, pg 101, 2022)

J Monroe, T Srikant, P Carbonell-Bejerano, C Becker, M Lensink, ...

NATURE 620 (7973), E13-E13

Author Correction: Mutation bias reflects natural selection in Arabidopsis thaliana

JG Monroe, T Srikant, P Carbonell-Bejerano, C Becker, M Lensink, ...

Nature 620 (7973), E13-E13

Reply to: Re-evaluating evidence for adaptive mutation rate variation

JG Monroe, KD Murray, W Xian, T Srikant, P Carbonell-Bejerano, ...

Nature 619 (7971), E57-E60

Polygenic pathogen networks influence transcriptional plasticity in the Arabidopsis–Botrytis pathosystem

P Krishnan, C Caseys, N Soltis, W Zhang, M Burow, DJ Kliebenstein

Genetics 224 (3), iyad099

Causes of mutation rate variability in plant genomes

D Quiroz, M Lensink, DJ Kliebenstein, JG Monroe

Annual Review of Plant Biology 74, 751-775

Better living through phytochemistry:“Phytoavengins” and reappraising the production-focused dichotomy for defensive phytochemicals

DJ Kliebenstein, BH Kvitko

Physiological and Molecular Plant Pathology 125, 101978

Polygenic pathogen networks control of host and pathogen transcriptional plasticity in the Arabidopsis-Botrytis pathosystem

P Krishnan, C Caseys, N Soltis, W Zhang, M Burow, DJ Kliebenstein

bioRxiv, 2023.03. 16.533032

Epigenomic divergence underlies sequence polymorphism and the evolutionary fate of duplicate paralogs inA. thaliana

KR SK, M Lensink, DJ Kliebenstein, C Niederhuth, G Monroe

Epigenomic divergence underlies sequence polymorphism and the evolutionary fate of duplicate paralogs in A. thaliana

SK Kenchanmane Raju, M Lensink, DJ Kliebenstein, C Niederhuth, ...

bioRxiv, 2023.03. 02.530917

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

E DeWolf, MT Brock, WJ Calder, DJ Kliebenstein, E Katz, B Li, ...

Molecular Ecology 32 (3), 741-751

Altered defense patterns upon retrotransposition highlights the potential for rapid adaptation by transposable elements

E Aller, C Kanstrup, P Hunziker, DJ Kliebenstein, M Burow

bioRxiv, 2023.12. 20.572632

Genetic variation underlying differential ammonium and nitrate responses in Arabidopsis thaliana

E Katz, A Knapp, M Lensink, CK Keller, J Stefani, JJ Li, E Shane, ...

The Plant Cell 34 (12), 4696-4713

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

P Wang, NM Clark, TM Nolan, G Song, PM Bartz, CY Liao, ...

The Plant Cell 34 (7), 2594-2614

Improved yield and health benefits of watercress grown in an indoor vertical farm

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

A keystone gene underlies the persistence of an experimental food web

The ease and complexity of identifying and using specialized metabolites for crop engineering

Mutation bias reflects natural selection in Arabidopsis thaliana

Aphid Species and Feeding Location on Canola Influences the Impact of Glucosinolates on a Native Lady Beetle Predator

Differential genetic variation underlying Ammonium and Nitrate responses in Arabidopsis thaliana

A genome‐scale TF–DNA interaction network of transcriptional regulation of Arabidopsis primary and specialized metabolism

A reevaluation of the role of the ASIL trihelix transcription factors as repressors of the seed maturation program

Quantitative interactions: the disease outcome of Botrytis cinerea across the plant kingdom

Appendix A: Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Innovation, conservation, and repurposing of gene function in root cell type development

Genome size evolution is associated with climate seasonality and glucosinolates, but not life history, soil nutrients or range size, across a clade of mustards

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Fine mapping identifies NAD‐ME1 as a candidate underlying a major locus controlling temporal variation in primary and specialized metabolism in Arabidopsis

The Arabidopsis thaliana nucleotide sugar transporter GONST2 is a functional homolog of GONST1

Red-light is an environmental effector for mutualism between begomovirus and its vector whitefly

Plant Responses Underlying Timely Specialized Metabolites Induction of Brassica Crops.

Modeling quantitative interactions: the disease outcome of generalist fungal pathogen across the plant kingdom

flasher, a novel mutation in a glucosinolate modifying enzyme, conditions changes in plant architecture and hormone homeostasis

Plant secondary metabolites as defenses, regulators, and primary metabolites: the blurred functional trichotomy

Diverse allyl glucosinolate catabolites independently influence root growth and development

mGWAS uncovers Gln-Glucosinolate seed-specific interaction and its role in metabolic homeostasis

FRS7 and FRS12 recruit NINJA to regulate expression of glucosinolate biosynthesis genes.

Pathogen Genetic Control of Transcriptome Variation in the Arabidopsis thaliana – Botrytis cinerea Pathosystem

Using networks to identify and interpret natural variation

Epistatic Transcription Factor Networks Differentially Modulate Arabidopsis Growth and Defense

mGWAS Uncovers Gln-Glucosinolate Seed-Speciic Interaction and its Role in Metabolic Homeostasis

Innovation, conservation and repurposing of gene function in plant root cell type development

Genetic diversity increases food-web persistence in the face of climate warming

Quantitative interactions drive Botrytis cinerea disease outcome across the plant kingdom

Identification and stacking of crucial traits required for the domestication of pennycress

PMR 5, an acetylation protein at the intersection of pectin biosynthesis and defense against fungal pathogens

Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels

Plant networks as traits and hypotheses: moving beyond description

Viruses mobilize plant immunity to deter nonvector insect herbivores

Diversity in plant defense genes increases food-web persistence

Questionomics: Using Big Data to Ask and Answer Big Questions

Plant–necrotroph co-transcriptome networks illuminate a metabolic battlefield

The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory

Interactions of Tomato and Botrytis cinerea Genetic Diversity: Parsing the Contributions of Host Differentiation, Domestication, and Pathogen Variation

Progress toward the identification and stacking of crucial domestication traits in pennycress

Regulation of root angle and gravitropism

Transcriptional regulation of nitrogen-associated metabolism and growth

Digital imaging combined with genome-wide association mapping links loci to plant-pathogen interaction traits

Plant nutrient acquisition entices herbivore

Fine mapping and candidate gene analysis for a major locus controlling circadian clock and secondary metabolism in Arabidopsis

The bHLH transcription factor ILR3 modulates multiple stress responses in Arabidopsis

Brassica oleracea: the dog of the plant world

Comparison of the relative potential for epigenetic and genetic variation to contribute to trait stability

Quantitative genetics and genomics of plant resistance to insects

GONST2 transports GDP-Mannose for sphingolipid glycosylation in the Golgi apparatus of Arabidopsis

Combining Digital Imaging and Genome Wide Association Mapping to Dissect Uncharacterized Traits in Plant/Pathogen Interactions

Crop domestication and pathogen virulence: interactions of tomato and Botrytis genetic diversity

A generalist pathogen view of plant evolution

Resequencing and association mapping of the generalist pathogen Botrytis cinerea

Rhizosphere microbes and host plant genotype influence the plant metabolome and reduce insect herbivory

Network-guided discovery of extensive epistasis between transcription factors involved in aliphatic glucosinolate biosynthesis

An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway

An integrated RNAseq-1H NMR metabolomics approach to understand soybean primary metabolism regulation in response to Rhizoctonia foliar blight disease

Initiation of ER body formation and indole glucosinolate metabolism by the plastidial retrograde signaling metabolite, MEcPP

Plastic Transcriptomes Stabilize Immunity to Pathogen Diversity: The Jasmonic Acid and Salicylic Acid Networks within the Arabidopsis/Botrytis Pathosystem

Epistasis × environment interactions among Arabidopsis thaliana glucosinolate genes impact complex traits and fitness in the field

Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

A novel Filamentous Flower mutant suppresses brevipedicellus developmental defects and modulates glucosinolate and auxin levels

A global coexpression network approach for connecting genes to specialized metabolic pathways in plants

Quantitative resistance: more than just perception of a pathogen

Observability of plant metabolic networks Is reflected in the correlation of metabolic profiles

An integrative genetic study of rice metabolism, growth and stochastic variation reveals potential C/N partitioning loci

Genome wide association mapping in Arabidopsis thaliana identifies novel genes involved in linking allyl glucosinolate to altered biomass and defense

Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense

False idolatry of the mythical growth versus immunity tradeoff in molecular systems plant pathology

The defense metabolite, allyl glucosinolate, modulates Arabidopsis thaliana biomass dependent upon the endogenous glucosinolate pathway

The Defense Metabolite, Allyl Glucosinolate, Modulates Arabidopsis thaliana Biomass Dependent upon the Endogenous Glucosinolate Pathway

Expansive Phenotypic Landscape of Botrytis cinerea Shows Differential Contribution of Genetic Diversity and Plasticity

Molecular mechanisms governing differential robustness of development and environmental responses in plants

Isolate Dependency of Brassica rapa Resistance QTLs to Botrytis cinerea

The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics

Pectin Biosynthesis Is Critical for Cell Wall Integrity and Immunity in Arabidopsis thaliana

Nonlinear selection and a blend of convergent, divergent and parallel evolution shapes natural variation in glucosinolates

Metabolism: Evolution retraces its steps to advance

Keeping the rhythm: light/dark cycles during postharvest storage preserve the tissue integrity and nutritional content of leafy plants

Natural variation of plant metabolism: genetic mechanisms, interpretive caveats, and evolutionary and mechanistic insights

Macroevolutionary patterns of glucosinolate defense and tests of defense‐escalation and resource availability hypotheses

Overexpression of three glucosinolate biosynthesis genes in Brassica napus identifies enhanced resistance to Sclerotinia sclerotiorum and Botrytis cinerea

The Plant Cell Introduces Breakthrough Reports: A New Forum for Cutting-Edge Plant Research

Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity

Investigation of the multifunctional gene AOP3 expands the regulatory network fine-tuning glucosinolate production in Arabidopsis

Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis

Transcriptional networks governing plant metabolism

The glucosinolate biosynthetic gene AOP2 mediates feed-back regulation of jasmonic acid signaling in Arabidopsis

Quantitative Variation in Responses to Root Spatial Constraint within Arabidopsis thaliana

Reassess the t Test: Interact with All Your Data via ANOVA

Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses

The conserved transcription factors, MYB115 and MYB118, control expression of the newly evolved benzoyloxy glucosinolate pathway in Arabidopsis thaliana

In planta variation of volatile biosynthesis: an alternative biosynthetic route to the formation of the pathogen-induced volatile homoterpene DMNT via triterpene degradation in …

Genetic variation in the nuclear and organellar genomes modulates stochastic variation in the metabolome, growth, and defense

Plant Physiology Preview. Published on August 13, 2015, as DOI: 10.1104/pp. 15.01108

FOCUS ON METABOLISM

Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness

An Arabidopsis gene regulatory network for secondary cell wall synthesis

Promoter-based integration in plant defense regulation

Meta-analysis of metabolome QTLs in Arabidopsis: trying to estimate the network size controlling genetic variation of the metabolome

Response of turnip to Botrytis cinerea infection and their relationship with glucosinolate profiles

The AT-hook motif-encoding gene METABOLIC NETWORK MODULATOR 1 underlies natural variation in Arabidopsis primary metabolism

Synthetic biology of metabolism: using natural variation to reverse engineer systems

Interview with Daniel Kliebenstein.

Orchestration of plant defense systems: genes to populations

Promoter-Based Integration in Plant Defense Regulation1 [W][OPEN]

Natural genetic variation in growth and metabolite regulatory roles of Allyl glucosinolate in Arabidopsis thaliana

Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

Fatty acids and early detection of pathogens

Postharvest circadian entrainment enhances crop pest resistance and phytochemical cycling

Hierarchical Nuclear and Cytoplasmic Genetic Architectures for Plant Growth and Defense within Arabidopsis

Identification of novel loci regulating interspecific variation in root morphology and cellular development in tomato

Conducting Genome‐Wide Association Mapping of Metabolites

New synthesis—regulatory evolution, the veiled world of chemical diversification

Making new molecules—evolution of structures for novel metabolites in plants

Natural enemies drive geographic variation in plant defenses

Exploring the shallow end; estimating information content in transcriptomics studies

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

Making new molecules–evolution of pathways for novel metabolites in plants

Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes

Plant defense compounds: systems approaches to metabolic analysis

What can causal networks tell us about metabolic pathways?

Model misinterpretation within biology: phenotypes, statistics, networks, and inference

Making new molecules-evolution of structures for novel metabolites in plants

An ecological genomic approach challenging the paradigm of differential plant responses to specialist versus generalist insect herbivores

Genomic analysis of QTLs and genes altering natural variation in stochastic noise

Using knockout mutants to reveal the growth costs of defensive traits

Biosynthesis and Defensive Function of N  Δ-Acetylornithine, a Jasmonate-Induced Arabidopsis Metabolite

Cofactome analyses reveal enhanced flux of carbon into oil for potential biofuel production

The quantitative genetics of phenotypic error or uniformity

Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana

Chemically mediated tritrophic interactions: opposing effects of glucosinolates on a specialist herbivore and its predators

Genetic and functional modularity: how does an organism solve a nearly infinite genetic/environmental problem space?

Intronic T-DNA Insertion Renders Arabidopsis opr3 a Conditional Jasmonic Acid-Producing Mutant

Arctic mustard flower color polymorphism controlled by petal-specific downregulation at the threshold of the anthocyanin biosynthetic pathway

Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis

Quantitative genomics of natural variation in plant metabolism: the illusion of simplicity

The complex genetic architecture of the metabolome

A new method for measuring relative growth rate can uncover the costs of defensive compounds in Arabidopsis thaliana

Understanding the Evolution of Defense Metabolites in Arabidopsis thaliana Using Genome-wide Association Mapping

Using network biology to identify quantitative genetic variation altering signaling in both plant host and generalist pathogens

Regulatory networks of glucosinolates shape Arabidopsis thaliana fitness

A complex interplay of three R2R3 MYB transcription factors determines the profile of aliphatic glucosinolates in Arabidopsis

Deficiencies in jasmonate-mediated plant defense reveal quantitative variation in Botrytis cinerea pathogenesis

All mold is not alike: the importance of intraspecific diversity in necrotrophic plant pathogens

Systems biology uncovers the foundation of natural genetic diversity

Flavin monooxygenases and transcription factors involved in glucosinolate biosynthesis

MODIFIED VACUOLE PHENOTYPE1 is an Arabidopsis myrosinase-associated protein involved in endomembrane protein trafficking

Advancing genetic theory and application by metabolic quantitative trait loci analysis

Anti-rust antitrust

Use of secondary metabolite variation in crop improvement

Quantification of variation in expression networks

Competition, herbivory and genetics interact to determine the accumulation and fitness consequences of a defence metabolite

The genetic basis of constitutive and herbivore-induced ESP-independent nitrile formation in Arabidopsis

A quantitative genetics and ecological model system: understanding the aliphatic glucosinolate biosynthetic network via QTLs

The chromatin remodeler SPLAYED regulates specific stress signaling pathways

A novel 2-oxoacid-dependent dioxygenase involved in the formation of the goiterogenic 2-hydroxybut-3-enyl glucosinolate and generalist insect resistance in Arabidopsis

Complex Genetics Control Natural Variation in Arabidopsis thaliana Resistance to Botrytis cinerea

Determination of the absolute configuration of the glucosinolate methyl sulfoxide group reveals a stereospecific biosynthesis of the side chain

Subclade of flavin-monooxygenases involved in aliphatic glucosinolate biosynthesis

Genetic networks controlling structural outcome of glucosinolate activation across development

Differential levels of insect herbivory in the field associated with genotypic variation in glucosinolates in Arabidopsis thaliana

Ecological costs of biotrophic versus necrotrophic pathogen resistance, the hypersensitive response and signal transduction

Genotype, age, tissue, and environment regulate the structural outcome of glucosinolate activation

Biochemical Networks and Epistasis Shape the Arabidopsis thaliana Metabolome

A role for gene duplication and natural variation of gene expression in the evolution of metabolism

ESP and ESM1 mediate indol-3-acetonitrile production from indol-3-ylmethyl glucosinolate in Arabidopsis

Identifying the molecular basis of QTLs: eQTLs add a new dimension

Research Area: Biochemical Processes and Macromolecular Structures

The Chromatin Remodeler SPLAYED Regulates Specific Stress Signaling

A systems biology approach identifies a R2R3 MYB gene subfamily with distinct and overlapping functions in regulation of aliphatic glucosinolates

Elevated Genetic Variation Within Virulence-Associated Botrytis cinerea Polygalacturonase Loci

Characterization of seed‐specific benzoyloxyglucosinolate mutations in Arabidopsis thaliana

Linking Metabolic QTLs with Network and cis-eQTLs Controlling Biosynthetic Pathways

Natural Variation among Arabidopsis thaliana Accessions for Transcriptome Response to Exogenous Salicylic Acid

Identification of a flavin‐monooxygenase as the S‐oxygenating enzyme in aliphatic glucosinolate biosynthesis in Arabidopsis

Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis

Metabolomics and Plant Quantitative Trait Locus Analysis–The optimum genetical genomics platform?

Convergence, constraint and the role of gene expression during adaptive radiation: floral anthocyanins in Aquilegia

Identification of QTLs controlling gene expression networks defined a priori

Glucosinolate survey of cultivated and feral mashua (Tropaeolum tuberosum Ruíz & Pavón) in the Cuzco Region of Peru

The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and influences Trichoplusia ni herbivory (vol 13, pg 2793, 2001)

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis

The Gene Controlling the Quantitative Trait Locus EPITHIOSPECIFIER MODIFIER1 Alters Glucosinolate Hydrolysis and Insect Resistance in Arabidopsis

Genomic Survey of Gene Expression Diversity in Arabidopsis thaliana

A UV-B-specific signaling component orchestrates plant UV protection

Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity

Geographic and evolutionary diversification of glucosinolates among near relatives of Arabidopsis thaliana (Brassicaceae)

A constitutive PR‐1::luciferase expression screen identifies Arabidopsis mutants with differential disease resistance to both biotrophic and necrotrophic pathogens

Substrate-dependent isothiocyanate toxicity

Secondary metabolites and plant/environment interactions: a view through Arabidopsis thaliana tinged glasses

Identification of Botrytis cinerea susceptibility loci in Arabidopsis thaliana

" Present address: Department of Vegetable Crops, University of California

Chapter five Glucosinolate hydrolysis and its impact on generalist and specialist insect herbivores

Arabidopsis UVR8 Regulates Ultraviolet-B Signal Transduction and Tolerance and Contains Sequence Similarity to Human Regulator of Chromatin Condensation 1

Disarming the mustard oil bomb

Genetic Architecture of Plastic Methyl Jasmonate Responses in Arabidopsis thaliana

Comparative Analysis of Quantitative Trait Loci Controlling Glucosinolates, Myrosinase and Insect Resistance in Arabidopsis thaliana

Benzoic acid glucosinolate esters and other glucosinolates from Arabidopsis thaliana

Comparative analysis of insect resistance QTL and QTL controlling the myrosinase/glucosinolate system in Arabidopsis thaliana

The Arabidopsis Epithiospecifier Protein Promotes the Hydrolysis of Glucosinolates to Nitriles and Influences Trichoplusia ni Herbivory

Comparative Quantitative Trait Loci Mapping of Aliphatic, Indolic and Benzylic Glucosinolate Production in Arabidopsis thaliana Leaves and Seeds

Genetic control of natural variation in Arabidopsis glucosinolate accumulation

Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate–dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis

LSD1 regulates salicylic acid induction of copper zinc superoxide dismutase in Arabidopsis thaliana

Arabidopsis superoxide dismutase

Superoxide dismutase in Arabidopsis: an eclectic enzyme family with disparate regulation and protein localization

Arabidopsis mutants altered in antioxidant enzyme accumulation.

Destabilization ofrbcS sense transcripts by antisense RNA

Antisense RNA inhibition of Rubisco activase expression

MECHANISM OF ANTISENSE INHIBITION IN TOBACCO ANTISENSE MUTANTS

ANTISENSE MESSENGER-RNA INHIBITION OF RUBISCO ACTIVASE EXPRESSION