Warwick Plant and Crop Sciences

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Plant and crop sciences at the University of Warwick are funded by variety of sources.

www.go.warwick.ac.uk/whri/research/crop

We work closely with industry partners, funding bodies and levy boards to address real issues affecting growers and producers today.

For more information on Warwick Plant and Crop Sciences, visit:

www.go.warwick.ac.uk/plantandcropsciences

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Plant science is a core discipline underpinning crop production and is being driven forward through major advances in areas such as genome sequencing and systems biology. The availability of a complete genome sequence for the “model” plant species Arabidopsis thaliana, was the foundation for the genomic revolution and this has provided knowledge of gene structure and function in plants. The new research challenge is translational biology, whereby scientists use fundamental information from model species to identify and characterise genes that control key processes in crop plants. This enables the targeted approach being used in plant breeding today.

The University of Warwick’s multidisciplinary Plant and Crop Sciences expertise spans several departments linking fundamental research to translational biology in important crop species. Research in plant sciences at Warwick is providing solutions focussed on solving major challenges in crop science such as achieving sustainable crop production with reduced inputs in the face of a changing climate. Our researchers are contributing to the generation of public genome data sets, maintaining genetic diversity collections and extending mapping populations in crop species that enables identification of genes underpinning key traits. Crop systems approaches used at Warwick enable the translation of research into practice.

Innovative technologies will be essential to support UK agriculture and meet future challenges. Investigations into how plants respond at the molecular level to hostile factors including, attacks by pests and disease, as well as extreme weather events, compliment our understanding of how to deploy improved varieties in novel growing systems and will contribute to the development of crops better able to survive and thrive in a changing climate. Warwick Plant Sciences is leading the way in developing predictive models of global gene changes at the whole plant level, using Systems Biology approaches. Advanced genomic analysis such as next generation sequencing and comparative genomics are being used to extend models from lab to field environments.

A key requirement to maintain the UK’s lead in this research area is the provision of skills and training to preserve the people pipeline. Warwick’s doctoral training centres and post-graduate programmes provide state of the art training in plant sciences to support this. To attract the best minds to this vital area of research investment in dynamic, internationally competitive research programmes, is necessary.

Plant and Crop Sciences research at Warwick provides evidence for sound policymaking, ensuring that the UK will provide leadership and solutions to future challenges in order to maintain human and environmental well-being.

Warwick Plant and Crop Sciences Sustainable food production and food security are challenges created by the ever-growing global population and climate change. They require knowledge-intensive solutions, which are reliant upon expertise in plant and crop sciences.

Ecology and Evolution

Robin Allaby, page 22• PlantEvolutionarySystems

and Local Adaptation

Eric Holub, page 22• Ecologicalgeneticsofmicrobesensing

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Plant Development

Vicky Buchanan-Wollaston, page 6• SignallingNetworksinPlantSenescence

Bill Finch-Savage, page 6• SeedDormancyandtheControlof

Germination

Jose Gutierrez-Marcos, page 8• EpigeneticControlof

Plant Development

Steve Jackson, page 8• MolecularControlofFlowering

and Plant Development

Brian Thomas, page 9• EnvironmentalControlofPlant

and Crop Development

Physiology and Metabolism

Isabelle Carré, page 10• PlantCircadianClocks

Peter Eastmond, page 10• RegulationofPlantLipidMetabolism

Lorenzo Frigerio, page 11

• PlantProteinTrafficking

RichardNapier, page 13

• HormonePerception

Lynne Roberts, page 12

• ProteinQualityControlintheSecretoryPathway of Plant Cells

Colin Robinson, page 13

• ChloroplastBiogenesis

Andrew Thompson, page 14

• GeneticControlofWaterUse

• ChemicalGeneticsofApocarotenoidSignalling

Plant-Microbe Interactions

Jim Beynon, page 15

• PlantImmuneResponses

Katherine Denby, page 15• Host-pathogeninteractions

Ari Sadanandom, page 16• UbiquitinandStressSignallinginPlants

Mahmut Tör, page 16• CellularandMolecularPathogenesis

John Walsh, page 17• Plant-VirusInteractions

Systems Biology

Jim Beynon, page 18

• PlantResponsestoEnvironmentalStress(PRESTA)

Vicky Buchanan-Wollaston, page 6

• SignallingNetworksinPlantSenescence

Isabelle Carré, page 10• PlantCircadianClocks

Katherine Denby, page 15• Host-pathogeninteractions

Miriam Gifford, page 19• SystemsBiologyoftheOriginofNodulation

Model Research

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Model Research

Plant Development

Vicky Buchanan-Wollaston, page 6• MappingandAnalysisofGeneticLociControllingQualityTraitsinBroccoli

Bill Finch-Savage, page 7• IdentifyingGenesUnderlyingQTLfor

Seed Vigour in Brassica oleracea

Ken Manning, page 7• FruitDevelopmentandRipening

Jose Gutierrez-Marcos, page 8• EpigeneticControlofPlantDevelopment

Steve Jackson, page 9• ManipulationofBoltingTimefor

ImprovedQualityandGreaterSustainability in Lettuce Production

Brian Thomas, page 9• EnvironmentalControlofPlant

and Crop Development

Physiology and Metabolism

Peter Eastmond, page 11• IncreasingOilYieldinOilseedRape

John Hammond, page 12• PlantMineralNutrition

Andrew Thompson, page 14• GeneticControlofWaterUse

Ecology and Evolution

Robin Allaby, page 22• PlantEvolutionarySystems

and Local Adaptation

Plant-Microbe Interactions and Disease Resistance

Ari Sadanandom, page 16• UbiquitinandStressSignallinginPlants

Mahmut Tör, page 16• CellularandMolecularPathogenesis

John Walsh, page 17• Plant-VirusInteractions

Crop Genetics and Genomics

Guy Barker, page 21• PlantGenomicsandNovelCrops

Paul Hand, page 20• MolecularPlantBreedingof QuantitativeTraits

David Pink, page 20• GeneticsandCropImprovement

Crop Systems

Steve Adams/Debbie Fuller, page 23• CropPhysiologyandAgronomy

Dez Barbara, page 23

• Understanding Plant Diseases

John Clarkson, page 24• IntegratedCropDiseaseManagement

Rosemary Collier, page 24

• Integrated Pest Management

Roy Kennedy, page 25• PredictiveDiseaseResistanceBreeding

Rob Lillywhite, page 25• Environmental Accounting

PaulNeve, page 26

• Weed Ecology

Clive Rahn, page 26

• FertiliserRecommendationSystemsforField Vegetable Crops

Dave Skirvin/Andrew Mead, page 27• Land-use,biodiversityandEcosystem

Services in Crop Systems

Crop Research

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Plant Development

SignallingNetworksinPlantSenescence (led by Vicky Buchanan-Wollaston)

Seed Dormancy and the Control of Germination(led by Bill Finch-Savage)

The aim of our research programme is to understand the internal and external factors that affect plant senescence, which will enable manipulation of the process in crop plants with subsequent improvement of yield, stress tolerance and post harvest quality.

Leaf senescence is an active process and is controlled by novel gene expression. Functional analysis of senescence enhanced regulatory genes has identified genes that control gene expression during senescence and shown specific pathways

that are important in normal developmental senescence. Detailed time course microarray analysis has revealed many clusters of genes that change in expression during senescence and we are using statistical modelling of these to reveal key senescence control pathways. We are using systems biology techniques to produce and test predictive models of the transcriptional networks that underpin plant responses to different types of environmental stress.

Dormancy defines the environmental conditions in which the seed is able to germinate. It is not a constant, but cycles in response to environmental signals that are seasonally characteristic and integrated by the seed over time. In this way, seeds gear themselves to germinate and establish in a favourable habitat and climate space. We are using molecular techniques in an ecophysiological context to improve understanding of this process. In continuing work we are characterising cycling behaviour in the dormant accession Cvi under both controlled laboratory and variable field conditions. Microarray analysis has been used to obtain transcriptional profiles for key states induced by different environmental signals. We have identified similarity underlying these states and core gene sets that change in a quantitative manner with depth of dormancy apparently driven by a dynamic hormonal balance of both synthesis and catabolism (Figure). In parallel work we are

developing models to describe this dormancy cycling in response to variable environmental signals.

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Plant Development

Post harvest yellowing in green vegetables such as broccoli has similarity to stress induced senescence in leaves and we have shown that many of the same genes and signalling pathways are involved. Currently we are exploiting natural variation to identify genes and metabolites that are linked to good shelf life in broccoli (with David Pink). Translation of knowledge gained from Arabidopsis to generate trait improvements in crop species is our key target.

Mapping and Analysis of Genetic LociControllingQualityTraitsinBroccoli (led by Vicky Buchanan-Wollaston)

Genetic variation in shelf life, 3 days post harvest

Regulation of dormancy (Finch-Savage and Leubner-Metzger(2006)NewPhytologist171:501-523)

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IdentifyingGenesUnderlyingQTLfor Seed Vigour in Brassica oleracea (led by Bill Finch-Savage)

Fruit Development and Ripening (led by Ken Manning)

Seed vigour is essential for successful crop establishment and this is the cornerstone of sustainable crop production, but understanding of the genetic basis for seed vigour differences is limited. We have adopted a trait-led approach, using natural variation in Brassica oleracea, to identifyafine-mappedseedvigourQTLandmarkersforplant breeding. Colinearity with the Arabidopsis genome has aided the identification of underlying candidate genes, which we are currently investigating in both Arabidopsis and B. oleracea.

Germination in B. oleracea

Fruits are essential for a healthy diet, contributing valuable minerals, vitamins and health-promoting phytochemicals. Understanding the control of fruit ripening will allow modulation of these components to enhance crop quality. Tomato is the model system of choice to study the ripening process and the strategy we have been using is to identify regulatory genes by characterisation of non-ripening mutants. One of these mutants, named Colourless non-ripening (Cnr), exhibits an extreme non-ripening phenotype with marked changes in cell wall properties, pigments and flavour. In collaboration with Graham Seymour (UniversityofNottingham)wehaveusedpositional cloning to identify the gene underlying this mutation as an SBP-box transcription factor, SlySPL-CNR.Wediscoveredthatthemutationresulted from an epigenetic change leading to hypermethylationoftheCNRpromoteranddown regulation of the gene. Knocking out this genedemonstratesCNRhasacriticalroleinfruitdevelopment.

CNRhasbeenrevealedasakeycomponentoftheripening transcriptional network and is therefore an important link in the genetic control of factors associated with fruit quality attributes. Our work also hints at the possible role of epigenetics during normal ripening and in the natural phenotypic variation of tomato and other fruits. Furthermore, CNRislikelytoberegulatedposttranscriptionally

bysmallRNAs.WehaveidentifiedapotentialmicroRNA(miRNA)bindingsiteintheCNRtranscript and in a recent collaboration with Tamas Dalmay (University of East Anglia) we have useddeepsequencingtoclonethismiRNA.ThecorrespondingcleavagesiteintheCNRmRNAhassubsequently been validated. We are exploring howthisandothernewlydiscoveredmicroRNAsfunction in fruit development. Future research will focus on elucidating both downstream and upstream(withYiguoHong)componentsofthetranscriptionalwebsurroundingCNRandthisknowledge will be integrated with information aboutmiRNAsandepigeneticcontroltobetterunderstand the ripening process in relation to crop quality.

TheSlySPL-CNRtranscriptionfactorgeneisessentialfor ripening as demonstrated by VIGS suppression (A), compared with control fruit (B)

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Plant Development

Flowering is an essential process in the life-cycle of plants, and the time of flowering in crop plants is extremely important economically as this determines the time of seed and fruit production. Several molecular pathways controlling flowering time have been described in the model plant Arabidopsis, and we have discovered a new gene that plays a critical role in this process called DayNeutralFlowering(DNF). The DNF gene acts in the photoperiodic pathway to repress the expression of CONSTANS in short days, and thus prevents the induction of early flowering in short days. In the dnf mutant, flowering occurs at the same time in short days as it normally does in long days. The DNFgene is thus essential for Arabidopsis to be able to have a photoperiodic

Molecular Control of Flowering and Plant Development (led by Steve Jackson)

Epigenetic Control of Plant Development(led by Jose Gutierrez-Marcos)

We are interested in understanding how plant growth and development is epigenetically regulated and the impact that the environment plays on the formation of new epigenetic traits. We are particularly interested in heterosis, or hybrid vigour, a phenomenon that leads to the increased performance of a hybrid in relation to its parents. The challenge is to decipher how possible changes in transcriptional/regulatory activity are governed by epigenetic interactions between parental alleles. Our main aim is to increase our understanding of how epigenetic mechanisms contribute to heterosis. This analysis may provide pivotal information about how novel beneficial allelic combinations in certain hybrids contribute to heterotic phenotypic effects, and thus improve crop performance.

We are also interested in the regulation of seed endosperm development. Alongside the embryo, the endosperm forms within the seed as a result of a double fertilisation process that is unique to the flowering plants. The endosperm plays a pivotal placenta-like function in that not only is it necessary for nurturing the embryo, but it also plays a crucial role in regulating embryogenesis

through a series of complex genetic and epigenetic interactions. While both the embryo and endosperm inherit the same genetic information, the developmental fates of these two structures differ greatly. The mechanisms that regulate this extraordinary developmental transition are not yet well understood. We aim to identify regulators of early endosperm development in plants by using a collection of maize and Arabidopsis thaliana mutants to identify genes that regulate this process.

Free-nuclear development of a maize seed

Mutant lines altered in the photoperiodic response

response. Interestingly, the effect of the dnf mutation is temperature conditional, being reversed at lower temperatures, the reason for this is currently being investigated.

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We are utilising the knowledge gained from research into the control of flowering time in Arabidopsis in our lab and others around the world, to try and manipulate the flowering time of crop plants such as lettuce. When lettuce is induced to flower (or bolt), bitter tasting secondary metabolites are produced in the leaves which render the crop unmarketable and the plants have to be ploughed back into the field. We are producing and characterising lettuce lines that carry late flowering alleles of specific flowering time genes. These lines can then be used in breeding programmes to develop late-bolting commercial lettuce lines through non-GM means.

ManipulationofBoltingTimeforImprovedQualityand Greater Sustainability in Lettuce Production (led by Steve Jackson)

Environmental Control of Plant and Crop Development (led by Brian Thomas)

We are investigating the mechanisms by which light quantity, quality and duration regulates development and how this information can be applied to enhance crop performance and quality. Current research includes a multidisciplinary study of the control of juvenility defined as the early phase of development, where flowering cannot be induced. Work includes fundamental studies with Arabidopsis and translational studies with Antirrhinum, an ornamental species where flowering is photoperiod-sensitive and Brassica where flowering is temperature-dependent. We have identified both environmental and genetic

factors controlling the length of the juvenile phase. These are being characterised along with the mechanisms involved. A second interest is in the genetic components of day length induction of flowering and how these are involved in the photoperiodic bulbing in Allium. We have isolated Allium homologues of photoperiod response genes from Arabidopsis and identified differences in expression patterns in different daylength response types. This information will help in breeding high quality flower and vegetable crops with minimal waste through reliable scheduling against a background of climate change.

Lettuce plants growing in the field

Transfer experiment with Antirrhinum, showing the length of the juvenile phase

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Physiology and Metabolism

24-h biological clocks, also known as circadian clocks, enable organisms to fine-tune their physiology and behaviour in anticipation of the varying demands of the day/night cycle. These clocks are particularly important for plants, which are sessile and incapable of evading changes in their natural environment. Thus, understanding of how the clock controls various aspects of plant physiology is expected to open up new avenues for improvement of crop productivity. Our current work aims to investigate the regulation of rhythmic transcription by the clock and how the clock can generate a wide range of rhythmic gene expression patterns using a relatively small number of oscillator components. We are focusing onatranscriptionfactorcalledLHY,whichisoneofthe central components of the clock. The rhythmic expressionpatternofLHYisknowntounderlieoscillatory expression of a large number of target genes, which are expressed with a variety of phases. We will test whether different on- and off-rates ofbindingofLHYtodifferenttargetpromoterscan account for their different temporal pattern of activation. We will identify co-factors that modulatetheeffectofLHYonitstargetpromoters

andalsotestthecontributionofmRNAdegradationratestothetimingofmRNAaccumulation.Novelanalysis tools and mathematical models will be produced to understand the regulatory logic underlying different gene expression patterns. This multidisciplinary project is carried out by a team of biologists, bioinformaticans, mathematicians and statisticians.

Plant Circadian Clocks(led by Isabelle Carré)

We are investigating the regulation of plant lipid metabolism using Arabidopsis as a model. Lipids are a diverse family of chemicals with many functions. Certain lipids form membranes that define the cell and compartmentalise all the biochemical processes within it. Other lipids act as messengers controlling growth, development and responses to the environment, while others act as a major reservoir for chemical energy.

The capacity to store energy as oil is critical for the life cycle of many plants since it enables their seeds to germinate and become seedlings. We have recently identified the lipase that initiates oil breakdown in Arabidopsis seeds (A) and this discovery is enabling us to study how the process is regulated. We are also interested in understanding how membrane biogenesis is controlled in plants and how it is coordinated with growth. We have

isolated an Arabidopsis mutant that over-produces membrane lipids (B) and we are using this mutant as a tool to uncover the regulatory mechanisms.

Regulation of Plant Lipid Metabolism(led by Peter Eastmond)

(B) Membrane biogenesis in overdrive

(A) Lipase on the oil droplet surface

LHYtargetgenesexhibitawiderangeofcircadianexpression patterns

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PlantProteinTrafficking (led by Lorenzo Frigerio)

Most plant proteins of interest for human and animal nutrition, or of biotechnological value are located in, or travel through, the secretory pathway. We are interested in three major processes that regulate the plant secretory system:

Sorting of proteins to storage vacuoles: we are studying the function of a class of vacuolar sorting receptors (VSR) and their role in the transport of storage proteins to seed vacuoles. We have recently generated a panel of fluorescent reporter proteins targeted to the vacuolar lumen or the vacuolar membrane. These are being used to study vacuolar biogenesis and targeting in developing Arabidopsis seeds. We are also studying the intracellular targeting and fate of recombinant proteins of medical importance, in particular monoclonal antibodies and HIV antigens.

Plant Reticulons: Reticulons have been described as major regulators of endoplasmic reticulum (ER) shape in animal and yeast cells. The Arabidopsis genome contains many more (21) members of the reticulon family than mammalian genomes. We arestudyingaseed-specificisoform,RTNLB13.Wefound that its expression modulates the capacity of the ER to form tubules, thus affecting diffusion of soluble and membrane proteins in the ER lumen. We are now assessing the effect of reticulon overexpression or knock-down on the function of the plant secretory pathway. We are also studying the tissue-specificity of expression of the other members of the reticulon family by confocal microscopy.

Qualitycontrolandproteindegradation: how does the plant endoplasmic reticulum dispose of proteins that fail to fold or assemble correctly? In collaboration with Prof. Lynne Roberts, these questions are addressed in vivo by studying the intracellular fate of model secretory proteins, such as the plant toxin ricin. Our studies employ biochemistry, cell biology, genetics and in vivo imaging.

Confocal Image of protein storage vacuoles (blue) in Arabidopsis seeds

IncreasingOilYieldinOilseedRape (led by Peter Eastmond)

From a human perspective, the ability of plants to convert solar energy to oil is of considerable value. Using Arabidopsis, we have identified several genes that can enhance this process. For example, blocking the lipase shifts the balance between oil synthesis and breakdown during seed development, resulting in over-accumulation of oil. We are working with industry to translate these technologies to crops.

Lipase-deficient oilseed rape

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Physiology and Metabolism

PlantMineralNutrition(led by John Hammond)

Plants require over 20 mineral elements to complete their life cycle. We aim to optimise the deliveryoftheseelementstoincreaseefficiency,safeguard quality and protect the environment. Our work incorporates classical genetic, molecular-biological, physiological, agronomic and modelling techniques in collaboration with Philip White (SCRI) andMartinBroadley(UniversityofNottingham).We focus on the management of crop phosphorus fertilisation and the transcriptional responses of plants to nutrient deficiencies and toxicities. These include (i) applied agronomic solutions to reducing fertiliser inputs, such as the placement of fertiliser into the rooting zone of the crop, trials of renewable sources of phosphorus as alternatives to non-renewable inorganic phosphate fertilisers, such as struvite, and identifying crop varieties that use fertilisersmoreefficiently,focusingonroottraitsfor improved capture of nutrients from the soil, (ii) basic research into the genetic responses of various species to mineral deficiencies and toxicities using transcriptional profiling and phylogenetic variation in plant mineral traits both within and between species and (iii) research to inform decisions on national and international policy issues, such as the EU Water Framework Directive.

A significant component of our work utilises microarray technology to investigate the changes in the gene expression of plants subjected to different nutrient regimes. This work has involved developing

techniques,incollaborationtheNottinghamArabidopsis Stock Centre, to use microarrays designed for model organisms to monitor the transcriptome of organisms for which the arrays were not originally designed. We have recently used this technique to provide evidence for a neutral theory of evolution for plant transcriptomes.

Brassica oleracea plants with low (A) and high (B) phosphorususeefficiency,correlatedwithimprovedlateral growth rate and length

ProteinQualityControlintheSecretoryPathway of Plant Cells (led by Lynne Roberts)

Protein homeostasis is essential and involves a complex, regulated network of folding and degradative systems. A large number of proteins are handled within the plant cell endoplasmic reticulum (ER) where an elaborate array of chaperones and enzymes function to ensure the correct folding, assembly and disulphide bond formation of proteins entering the secretory pathway. Secretory proteins that fail to fold correctly in the endoplasmic reticulum are ultimately degraded. In plant cells, the location of this disposal was at one time considered the exclusive province of vacuoles.

However, the operation of additional quality control pathways has recently been uncovered. Using orphan toxin subunits as our primary tools, we are investigating the factors and requirements for protein disposal by the ER-

associated degradation (ERAD) pathway and potentially, by secretory pathway proteases. The ERAD pathway involves substrate recognition, retrotranslocation across the ER membrane, extraction by cytosolic machineries or chaperones, and ultimately degradation by proteasomes. In addition to the ER-cytosol disposal pathway, aggregation and degradation within the secretory pathway itself is also under study in our laboratory. The players involved in both these proteolytic systems and the overall role and impact of these pathways relative to protein turnover within vacuoles is not known at present. ERAD and the secretory pathway turnover of proteins is likely to be of physiological relevance, not only for routine housekeeping, but in relation to hormone and stress responses, pathogens and in plant development.

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Hormone Perception(ledbyRichardNapier)

Chloroplast Biogenesis (led by Colin Robinson)

Biosensor development:

Biosensors are commonplace tools in some areas of science, but not in plant biology. We are developing new biosensor platforms in order to gain quantitative and time-resolved data about analyte concentrations in real-time. We work with both Biacore and fluorescence technologies. These new tools will help test current systems models of hormone flux and help monitor movements of phytohormone stimuli around plants.

Auxin receptor interaction analysis:

Selectivity in auxin perception, a joint project with Dr Stefan Kepinski (University of Leeds) and Dr Tim Hawkes (Syngenta). We are expressing the auxin receptor TIR1 in order to examine the kinetics of its interactions with both ligand (auxin) and substrate (Aux/IAA transcription factors) and other partners in the TIR1SCF complex. Using both SPR Biacore and other techniques we will determine the basis of specificity for different auxin phenotypes and examine the biophysical basis to the concept that auxin acts as ‘molecular glue’ in its receptor binding pocket.

Chloroplasts carry out the critical processes of light capture, photosynthetic electron transport and ATP synthesis in plants. They are structurally complex organelles that contain a double membrane envelope, a major internal soluble phase (the stroma) and a complex interconnected thylakoid membrane network. Thousands of proteins are imported post-translationally across the chloroplast envelope using distinct protein transporters in the outer and inner envelope membranes. We are interested in the mechanisms involved; there is evidence that proteins are transporters in an unfolded state, and the two translocases appear to act in concert, but many questions remain unresolved. We use bioimaging approaches to study the translocation of green fluorescent protein (GFP) tagged chloroplast proteins in vivo, combined with biochemical approaches to probe the mechanisms by which proteins are imported into intact chloroplasts. After import into the stroma, a subset of proteins undergo further targeting into the thylakoid network. Of these, many are transported completely across the membrane into the lumenal space inside. Two distinct protein transporters carry out these processes, using very different mechanisms. The Sec system uses ATP hydrolysis to thread substrate proteins through a pore in an unfolded state, while the Tat system has the unique ability to transport fully folded proteins across the thylakoid membrane. We use a variety of techniques to study the Tat system, whose unusual properties have attracted considerable interest. A variety of in vitro import assays have been

devised to probe the translocation mechanism; isolated thylakoids import Tat substrates very efficiently,whichmeansthattheenergeticsand operating mechanism can be studied with relative ease. In addition, we use bioimaging to study the targeting of Tat substrates in transiently transfected protoplasts. GFP-tagged Tat substrates can be imaged in chloroplasts and these studies have demonstrated an unexpected property of the system: ‘quality control’. It transpires that a proportion of imported Tat substrates interact with the Tat translocon, and even undergo partial translocation, but are then returned to the stroma. We believe that this reflects an inherent ‘proofreading’ activity of the Tat system, which is predisposed to transport only correctly folded substrate molecules. This combination of in vivo and in vitro techniques provides a variety of studies that can address many areas of interest associated with the biogenesis of this organelle.

GFP-tagged protein within the chloroplast stroma

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Physiology and Metabolism

Genetic Control of Water Use(led by Andrew Thompson)

The most important factor limiting crop production worldwide is water, and many have questioned whether our fresh water resources will be able to sustain crop production for the 9-10 billion people who will inhabit the Earth by 2050. Improvements inwateruseefficiency(WUE)areessentialforfoodsecurity.

ABA is a phytohormone of fundamental importance to WUE and drought resistance produced via cleavage of carotenoids by the rate-limiting enzyme 9-cis-epoxycarotenoiddioxygenase(NCED).Wehave shown that transgenic increases in ABA biosynthesis dramatically increase WUE, but that excessive increases can have profound effects on growth. We are using both Arabidopsis and tomato as model plants to understand the complex pleiotropic effects on whole plant physiology; we are optimising WUE by fine-tuning transgene expression in target crops.

WUE is a complex quantitative trait and we have used recombinant inbred line populations and association mapping in Arabidopsis to define loci that influence WUE, and its component traits. Expertise in population genetics and biometrics will now enable more powerful association analysis using recently expanded genotype data sets. We have identified loci that influence WUE in the vegetable Brassicas, and that control the ability of tomato roots to access soil water at depth, and we are now attempting to discover the genes underlyingtheseQTL.Weaimtotransferthisknowledge to other crops, including potato, the most water-hungry crop in the UK.

“Over-guttating” high ABA tomato plant

Arabidopsis WUE experiment

Chemical Genetics of Apocarotenoid Signalling (led by Andrew Thompson)

NCEDisamemberofthecarotenoidcleavage dioxygenase (CCD) family, enzymes that produce a diversity of apocarotenoid signalling molecules. We have taken a chemical genetics approach to develop inhibitors of different classes of CCD. These provide tools to investigate biological functions of apocarotenoids (e.g. the poorly understood strigolactones), and to probe enzyme mechanisms. They also provide leads to develop agrochemicals that control several plant developmental processes including branching.

Design of CCD inhibitors

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Plant Microbe

Hyaloperonospora arabidopsidis (downy mildew)

Plants possess a wide range of defence responses to prevent or limit infection by pathogens. We are investigating how these host defence responses are activated using the interaction between Arabidopsis and the fungal pathogen, Botrytis cinerea, an economically important pathogen. We have identified several Arabidopsis genes that influence the outcome of a B. cinerea infection and are now elucidating how these, and other regulatory components, are inter-connected in a network. Having this “systems” understanding will be crucial for exploitation of the defence network in crops.

We have generated a high-resolution time series of Arabidopsis gene expression profiles following B. cinerea infection. Collaboration with mathematicians and statisticians has enabled us to infer gene regulatory network models operating in the leaf during infection. These models identify novel key regulators as well as predicting gene-gene interactions. Importantly,

predicting key regulators via network modelling has greatly increased the proportion of genes tested that show altered susceptibility to B. cinerea when knocked out or overexpressed. We are currently validating the network models using an iterative process of biological experiments and re-training of the model with the new data.

Plants and their pathogens are involved in a constant battle in which the plant develops immunity which the pathogen needs to defeat. We are analysing the interaction between the oomycete pathogen Hyaloperonospora arabidopsidis (downy mildew) and its host Arabidopsis. To overcome host immunity the pathogen produces an arsenal of proteins, called effectors, that are delivered to the host cell. We identified a motif (RXLR) in the amino acids of these effectors that is responsible for delivery into the host cell. This has been shown to be functionally equivalent to the RXL motif used by the malarial parasite to deliver effectors to human cells. We have sequenced the genome of H.arabidopsidis and have identified over 200 effectors. As these proteins are designed to allow the pathogen to grow in the hostile environment of the plant they represent an amazing set of tools with which to reveal the host immune system. Hence, we are using yeast two hybrid techniques to determine with which host proteins the effectors interact, revealing multiple targets. We are also determining the location of the effectors in the host cells using fluorescent labeling methods and are able to show co-localisation with host proteins. The host proteins are components of the host that the pathogen needs to compromise and will represent candidates for developing novel means to produce durable disease resistance in crops.

Plant Immune Responses(led by Jim Beynon)

Host-Pathogen Interactions(led by Katherine Denby)

Botrytis cinerea hyphae emanating from disease lesion on Arabidopsis leaf

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Cellular and Molecular Pathogenesis (led by Mahmut Tör)

A highly evolved surveillance system in plants is able to detect a broad range of signals originating from pathogens, damaged tissues, or altered developmental processes, initiating sophisticated molecular mechanisms that result in defense, wound healing, and development. Microbe associated molecular pattern molecules (MAMPs), damage associated molecular pattern molecules (DAMPs), virulence factors, secreted proteins and processed peptides can be recognized directly or indirectly by this surveillancesystem.Nucleotidebinding-leucinerichrepeatproteins(NB-LRR)areintracellularreceptors and have been targeted by breeders for decades to elicit resistance to crop pathogens in the field. Receptor-like kinases (RLKs) and receptor like proteins (RLPs) are membrane bound signalling molecules with an extracellular receptor domain. They provide an early warning

system for the presence of potential pathogens and activate the protective immune pathways in plants. We have been investigating the role of cytoplasmic and membrane bound Arabidopsis receptors in the recognition of downy mildew pathogen. We have identified several RLK-type receptors that may play a significant role in the detection of this pathogen. We are investigating these further by genetic, molecular and biochemical approaches. We have established an assay to study MAMPs and apoplastic effectors of oomycete pathogens, which may aid the identification of the ligands for the orphan receptors. In addition, we have also been investigating the role of non-RXLR effectors that may possibly be recognized by RLK-type receptors. Part of our studies also address how new effectors are born and whether they are subject to the surveillance system of the plant.

Ubiquitin and Stress Signalling in Plants(led by Ari Sadanandom )

Plant diseases are major limiting factors to the production of food worldwide. Understanding the mechanisms by which pathogens invade plants and the means by which plants perceive the invasion is very important to developing novel control strategies in the future. The control of protein degradation through the ubiquitin-proteasome system (UPS) is a central modifier of signalling in animals and plants. An emerging paradigm in biology is the pathogen mediated targeting of the UPS to suppress host immunity but how pathogens achieve this is not known.

We have identified key regulatory factors of host UPS that could act as targets for defence suppression by plant pathogens. Using Arabidopsis and tomato as model hosts we employ a cross disciplinary approach including genetic, molecular and biochemical techniques to identify components that are specifically ubiquitinated by bacterial and fungal pathogens to undermine plant immunity.

How plant pathogens suppress the plant immune system is of great scientific importance particularly as it may inform on how one aspect of our own immune system may operate. Using the mechanistic conservation between plant and human UPS as a tool, we have developed a synthetic biology model for understanding ubiquitin mediating signalling in human cancers.

Eukaryotes also possess other small proteins that are related in amino acid sequence to ubiquitin and are involved in protein modification. In recent years the small ubiquitin-like modifier (SUMO) has emerged as a very influential regulator of stress signalling in plants and animals. High salinity is a major stress factor limiting worldwide agriculture as nearly all crops are predominantly salt sensitive. Our work on post translational modification of proteins has shown for the first time in plants that specific signalling proteins are SUMOylated as part of plant’s survival strategy during salt stress. We have developed a novel experimental method to specifically quantify and identify SUMOylated proteins in plants. Understanding how cellular SUMOylation is regulated will have huge implications for agriculture as this knowledge will be crucial to generating stress resistant crops.

Plant Microbe

GFP labelling of ubiquitin signalling in the cell

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Plant-Virus Interactions (led by John Walsh)

In our group we are using Arabidopsis and Turnip mosaic virus (TuMV) to study plant – virus interactions from a number of angles. TuMV is best adapted to Arabidopsis and is a member of the Potyviridae, the largest group of plant viruses in the world, causing some of the most important crop diseases. We have a large collection of TuMV isolates representating the genetic and phenotypic diversity from around the world. We also have full-lengthinfectiousDNAclonesofthevirus,allowingvery precise dissection of host – virus responses. We are collaborating with a number of colleagues from around the world, including Spain, Japan, Canada and China, looking at TuMV diversity and evolution, viral symptom determinants in Arabidopsis and TuMV resistance in brassicas. We are also using Arabidopsis to study the interaction between TuMV and genes from crop plants.

We have mapped a series of single dominant R genes in brassicas (TuRB01 – TuRB06). Some confer

extreme resistance / immunity to TuMV, whereas others give rise to a hypersensitive response. We have mapped two further brassica genes, one recessive (retr01) and one dominant (ConTR01) which together, appear to confer broad-spectrum resistance to a diverse range of TuMV isolates. So far we have not found a TuMV isolate capable of overcoming this resistance. The genes retr01 and ConTR01 are coincident with the eukaryotic initiation factor 4E (eIF4E) or the isoform (eIF(iso)4E). Candidate genes have been cloned and their involvement in the broad-spectrum resistance is currently being investigated. Further sources of broad-spectrum resistence have been identified and are being characterised. We have identified the viral determinants (avirulence genes) for most of the TuRB0 genes in brassicas; they cluster in two of the viral proteins. Additionally we have been investigating co-evolution between wild brassica plants and TuMV.

A healthy brassica leaf (left) and a brassica leaf infected by an infectious clone of TuMV expressing GFP (right) (TGM leaf only inverted and flipped)

18

Systems Biology

Plant Responses to Environmental Stress in Arabidopsis (PRESTA) (led by Jim Beynon)

Sustainable food production and food security are being threatened by our ever-expanding world population and the effects of climate change. To help address this problem we have brought together leading plant biologists, theoreticians and bioinformaticians from the Universities of Essex, Exeter and Warwick to understand how plants modulate their response to environmental challenges such as drought and pathogen attack.

Traditionally scientists work to elucidate specific pathways that regulate the expression of a single characteristic of a plant, for instance disease resistance, leaf shape or flowering time. However, it is now clear that such pathways do not exist in simple terms but are part of complex networks of proteins that result in a specific outcome depending on the environment within which the plant is grown. In the natural environment crop plants are exposed to a variety of stresses simultaneously, for instance disease and water shortage. Therefore, when exposed to multiple stresses plants must adapt their response by using a combination of networks that result in the best strategy for survival.

This project aims to elucidate the networks of transcriptional pathways and underlying regulatory mechanisms that control developmental senescence, responses to pathogens, high light and drought stresses in the Arabidopsis leaf. By combining high resolution time course assays with mathematical modelling techniques we are identifying key regulatory genes and their downstream targets. This will allow both common and unique features that govern responses to different stresses to be identified. The common regulatory components will represent targets for improving crop robustness to environmental stress.

Using data from developmental senescence, following infection by Botrytis cinerea, Pseudomonas syringae and Hyaloperonospora arabidopsidis, and by imposing drought and high intensity light on the plants we aim to:

• build a mathematical model of how the plant leaf switches between alternative responses during environmental challenges

• elucidate the network of transcriptional pathways and underlying regulatory mechanisms controlling plant stress responses

• develop and apply novel mathematical/statistical tools aimed at inferring global networks, parameterising local networks and predicting the optimal subsequent experiments

• identify regulatory regions containing transcription factor binding sites (TFBS) responsible for controlling gene expression in plants

• use this information to generate hypotheses for testing by experiment and to feed into gene regulatory network models

• TFBS are known to be short degenerate sequences, therefore determining them precisely is non-trivial. Our approach utilises information derived from the comparison of homologous sequences that reduces the search space to informative regions of conserved sequence alignment that we term regulatory modules

• develop a new software platform, “Analysis of Plant Promoter-Linked Elements” (APPLES), which aims to enable sophisticated and biologically meaningful queries surrounding the understanding of transcriptional regulation.

The PRESTA project is a collaboration between Warwick Plant and Crop Sciences, the Warwick Systems Biology Centre, the University of Exeter and the University of Essex.Example gene regulatory network inferred from expression

data from B. cinerea infected Arabidopsis leaves

19

SystemsBiologyoftheOriginofNodulation(led by Miriam Gifford)

Plants are keenly sensitive to the environment and adapt their body plans in response to their surroundings. Two quintessential examples are the development of specialised organs that obtain nutrients; lateral roots in higher plants and nodules in legumes. The ability to nodulate arose several times in legumes. Recent developments in cell-specific genomic profiling technologies enable us to test the received hypothesis that the pre-existing lateral root ‘blueprint’wasco-optedfornodulation.Nodulesand lateral roots are both formed by reactivation of cell division in differentiated cells, however while lateral roots arise from division in the pericycle, the majority of nodule tissue originates from the inner cortex. This suggests a cell-type switch occurred during co-option. Although regulators of nodulation and lateral root development have been characterised, molecular components underlying the proposed co-option have not been uncovered.

Systems-level understanding of nodulation at the cell-specific level:

We are taking a comparative systems approach combining whole-genome profiling of single cells with bioinformatic analysis to compare nitrogen and nodulation responses in Medicago to nitrogen responses in Arabidopsis. One goal is to gain new insight into the evolutionary origin of nodulation by identifying which molecular networks involved in ‘core’ root developmental nitrogen responses in Medicago and Arabidopsis are also regulated during nodulation in Medicago and thus could have been co-opted. Another long-term goal is to identify the minimal program needed to transform non-leguminous crops into nodulating plants. This work will lead to new perspectives on how the environment controls development in plants with broad applications for agriculture through impacts on nutrition and the environment.

Other Plant and Crop Science projects using a Systems Biology approach are:

Vicky Buchanan-Wollaston •SignallingNetworksinPlantSenescencepage,6

Isabelle Carré •PlantCircadianClocks,page10

Katherine Denby •Host-PathogenInteractions,page15

Cell-specific genomic profiling is combined with modelling data in our systems approach

20

Example gene regulatory network inferred from expression data from B. cinerea infected Arabidopsis leaves.

Crop Genetics

Genetics and Crop Improvement(led by David Pink)

We are developing tools and resources to facilitate the genetic improvement of quantitative traits of agronomic interest in a range of crops particularly brassica and lettuce. Significant effort is being put in to developing Diversity Sets based upon the collections held in the Warwick HRI gene bank; these are strategic resources in research to exploit natural allelic variation within the genepool. Currently we have Diversity Fixed Foundation Sets of Brassica napus, Brassica oleracea and 90 gene bank accessions representing 14 wild C genome Brassica species as well as diversity sets for lettuce and onion. The diversity sets include parents of mapping populations; currently we have mapping populations and associated linkage maps for B.oleracea, B. napus. B rapa and lettuce. In addition wehavedevelopedaTILLINGpopulationinlettuce.Current target traits in brassica are resistance to the insect pests Brevicoryne brassicae, Delia radicum

and Plutella xylostella, and the bacterial pathogen Xanthomonas campestris pv campestris (with Paul Hand)nitrogenuseefficiencyandpostharvestshelflife (with Vicky Buchanan-Wollaston), in lettuce target traits are quantitative field resistance to Bremia lactucae, reducing nitrate content, post harvest discolouration and the interaction with human bacterial pathogens (with Paul Hand) .

MolecularPlantBreedingofQuantitativeTraits(led by Paul Hand)

Conventional plant breeding is struggling to deliver the demands of modern consumers and growers for sustainably produced high quality products. We are therefore developing genetic mapsandmolecularmarkerstoidentifyQTL(quantitative trait loci) for pest and disease resistance and quality traits in lettuce and Brassica.WehavealreadyidentifiedQTLforresistance to downy mildew and peach-potato aphid in lettuce and this work is being taken forward in collaboration with the breeding industry. Recent interdisciplinary collaboration with colleagues in Applied Microbial Sciences demonstrated the role of plant genetic variation in microbial population structure and dynamics on the lettuce phyllosphere. In collaboration with Gad Frankel (Imperial) we are characterising the genetic components of the interaction between lettuce genotypes and human pathogens. We are currently producing alettuceTILLINGpopulationasaresourcetoallow reverse genetics in this species.

Our work in Brassicas has included mapping resistance to the important Brassica bacterial pathogen Xanthomonas campestris pv. campestris, the causal agent of black rot. Further characterisation and fine mapping of this resistance are under way in a collaborative

BBSRC/DfID funded SARID project (with Eric Holub and Dave Pink). This brings a new international development aspect to the research programme. As part of a wider strategy to exploit natural diversity, we are working on the genetic characterisation of a wild species Brassica Differential Fixed Foundation Set (DFFS) which is being developed at Warwick HRI (with Dave Pink). Future research will exploit the emerging genomics resources in lettuce and Brassica and synteny at the sequence level between these crop species and Arabidopsis to determine ‘genes for traits’ and gain an understanding of how allelic variation in key traits could be exploited in molecular plant breeding.

LettuceTILLINGlines

Kale diversity plot

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PlantGenomicsandNovelCrops(led by Guy Barker)

We are interested in the genomic organisation and the genetics of the Brassicas which are among the most diverse species within the plant kingdom, with Brassica oleracea being one of the most diverse of all crop types. We have developed a large number of reference doubled haploid (DH) populations and have integrated these with a range of genomic resources and sequence data to look at genomic organisation and its impact e.g. for isolating genes underlying traits of interest. Activities include participation in the Multinational Brassica Genome Project,SNPdiscoveryandutilisationofspeciesbiodiversityfor the production of new varieties of Brassica to produce oils in the UK for use as a feedstock to replace mineral oil and as an alternative crop for production of compounds for industrial use.

Other interests include isolation of various novel plant products and the development of integrated bio-refineries. In collaboration with the Warwick Medical School we are also looking at metabolite analysis, nutrition and its impact on human health.

The Genomics Resource Centre (GRC): In house state-of-the-art technologiessuchasgenomesequencingandSNPgenotyping

22

Plant Evolutionary Systems and Local Adaptation(led by Robin Allaby)

Our research focus is to understand the evolution of plants important to man during the Holocene. Our approach is highly interdisciplinary involving wet lab archaeogenetic and modogenetic techniques, bioinformatics and computational biology. We are interested in the evolutionary system associated with the domestication process and local adaptation on several levels of organization: the gene, the genome, the population and the selective environment in which the population exists. We utilize genetic information directly from both modern and archaeological samples from sites suchasQasrIbrimworkingcloselywiththearchaeology community, and applying the latest palaeogenomic techniques. We are interested, for instance, in the basis of how barley could have adapted to drought conditions in ancient civilizations through local adaptation, and whether that trait could be translated to modern crops.

To study local adaptation in modern plants we use an ecological genomics approach with wild populations of Arabidopsis in which genome wide diversity is associated with selection pressures. We also develop bioinformatic approaches for high throughput analysis , which we release as downloads such as FiPoDs and TreeMos. Using

computational biology we study the complex evolutionary system which gives rise to the patterns of genetic diversity we observe. Using this in vitro and in silico two-pronged approach we wish to answer questions about where crops come from, and how plants such as crops become locally adapted to environmental conditions. Such information may help us in the future to produce crops which are better adapted to a wider range of conditions: the key to a sustainable future is to understand the past.

Ecological Genetics of Microbe Sensing (led by Eric Holub)

Arabidopsis thaliana is the reference species for modern plant breeding and genetic conservation of leafy vegetables, seed crops and even trees. Lab-based research has provided a vast catalog of molecularly characterized and informative genes that crop scientists can use as templates to identify analogous genes in crop species or directly via genetic engineering. Breeders in turncantapthisDNA-basedknowledgeandthe new biological resources to improve crops using marker-assisted selection, especially for applications in crop production where water availability, nutrition and weed/pest/pathogen levels can be managed within affordable limits. Deep genome-wide knowledge of natural variation in A. thaliana will also provide an important reference for ex situ conservation of biodiversity in other species. However, further ecological genetics will be vital to understand and predict a plant population’s ability to adapt in variable habitats across the geographic range of a species. Breeders refer to this local adaptation

as “genotype x environment interactions.” Genetic knowledge will be increasingly useful to sustain productivity of low input agriculture in changeable environments. Landraces may, for example, already contain environmentally resilient traits, which can readily be lost through generations of breeding for other traits, without the use of selectable molecular markers (ideally designed from the essential genes) to maintain thevaluedtraitsinnewcultivars.Naturalvariation in the key proteins that govern plant-microbe interactions provides compelling case studies for addressing this important challenge, to pursue molecular genetics research of local adaptation in the real world of changeable environments. We are pursuing this challenge using state-of-the-art genomic approaches, “open-air” laboratories for recurring A. thaliana in natural UK habitat, public engagement, and comparative research with US and European partners.

Ecology and Evolution

Archaeobotanical samples of barley and cottonfromQasrIbrim

23

Crop Systems

Crop Physiology and Agronomy(led by Steve Adams & Debbie Fuller )

Effective crop management is essential for the sustainable production of horticultural commodities. The industry is being constantly stretched by increasing production costs (for example fuel, fertilisers, packaging and labour), and the need to minimise environmental impact and mitigate against climate change.

We focus on the physiology and agronomy of crops. We mainly work on projects funded either by industry (predominantly HDC) or by Defra, these cover a wide range of commercially relevant edible and ornamental species that are grown with or without protection. Ongoing and recent projects have included:

• Theeffectsoftemperatureoncropgrowthand development so as to enable growers to save energy without compromising crop quality or scheduling. Improvements in energy efficiencyinglasshousecropshavebeenachieved using variable temperature regimes, targeted humidity control, the use of thermal screens and novel engineering solutions.

• Commercialsurvivalinhorticultureincreasingly depends on growers being able to schedule crops with precision to meet stringent retail demands for continuity of high

quality product. In the ornamentals sector this often involves being able to predict and manipulate flowering. The environmental triggers for flowering (temperature, light quality, light quantity and daylength) have been investigated in a number of species.

• Environmentalfactorsrelatingtocropquality/yield, including summer stress and air quality.

• Regulationofnutritiontomanipulateshootgrowth and adventitious rooting.

Understanding Plant Diseases (led by Dez Barbara)

Plant diseases are still important constraints on crop production. We are interested in reducing their impact through broadening our understanding of plant pathogens and from this developing more effective approaches to control. Over the years we have worked on a wide spectrum of pathogens from viroids to fungi by way of viruses and phytoplasmas to fungi and studied many things from molecular taxonomy through to practical control in the field by way of epidemiology and developing diagnostics. A major interest has been in soil-borne fungal pathogens and we have worked extensively on Verticillium wilts and on cavity spot of carrots. Defra funded work on the Pythium species associated with cavity spot is changing our understanding of how it interacts with other soil microbiota and brought the realisation that the key to control is through managing that interaction. Work on Verticillium is moving into a new phase as wilt of oilseed rape has recently arrived in the UK; we will be collaborating with ADAS on this

new threat to a major crop. Experimentally our work stretches from being collaborators in genome sequencing (of Verticillium species) through to field trials of possible disease management techniques.

Field trial examining growth of Pythium violae on carrots

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Crop Systems

Integrated Pest Management(led by Rosemary Collier )

Pest insects account for a considerable proportion of crop losses world-wide. Environmental change will alter the status of many pests and lead to invasions by new species. Our research focuses on the control of the pest insects of crops through an understanding of their biology and behaviour. We have studied the ecology and phenology of key species and used the information to develop mathematical models to forecast the timing of pest insect attacks. We are interested in developing methods of pest insect control which exploit detailed knowledge of insect biology and behaviour. For example, we have been undertaking detailed studies of the behaviour of pest insects of brassicaceous plants to understand how increased plant diversity within a crop affects insect behaviour and this has given us greater insight into the cues that phytophagous insects use to select their host plants. We have used this knowledge to evaluate and refine a control method, companion planting, based on this phenomenon.

Genetic variability amongst the wild and cultivated members of plant families offers the opportunity to search for sources of resistance to pest insects. Working with crop geneticists, our aim is to identify sources of resistance and understand the mechanisms by which pest insect numbers are reduced.

Diamondback moth caterpillar

Integrated Crop Disease Management(led by John Clarkson )

Crop diseases caused by fungal soilborne plant pathogens present problems for effective managementbecausetheyaredifficulttotargetwith agrochemicals and often persist for long periods of time. We are taking an integrated approach to the control of those which form long-lived sclerotia (survival structures) through disease forecasting, screening crop diversity sets for resistance and biological control. We have developed a disease forecasting model for Sclerotinia sclerotiorum based on the environmental conditions required for germination of sclerotia which is now being evaluated for a variety of Sclerotinia susceptible crops such as lettuce, carrot and oilseed rape. The importance of variation within key biological traits which may influence disease management strategies such as the ability of sclerotia to germinate and aggressiveness of infection is also being assessed by studying the diversity of UK S. sclerotiorum populations. At the same time, this work will identify appropriate genetically characterised isolates which will be deployed for resistance screening of brassica diversity sets associated with the Oilseed Rape GeneticImprovementNetwork(OREGIN).

Warwick HRI’s research on biological control of plant pathogens has contributed to the registration of Coniothyrium minitans for control of S. sclerotiorum in the UK and the use of Trichoderma viride for control of S. cepivorum, which causes Allium white rot disease. Current work is now developing a more effective approach which combines T. viride with green waste compost resulting in enhanced levels of disease control and added value for use of a waste product.

Sclerotinia-infected lettuce

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Environmental Accounting (led by Rob Lillywhite )

Increased food production and the impact of climate change has focused attention on the environmental impact of land use. The conflicting need to provide food, fibre and fuel, for an increasing population, can have unintended consequences for sustainable production, greenhouse gas emissions and pollution. These problems, and possible solutions, are best understood by quantifying the environmental impact of production.

Our work uses different, but complimentary, methods of environmental accounting, for example, life cycle assessment, carbon footprinting (PAS2050), water footprinting, mass and energy balances to describe and quantify the environmental impacts of crop production systems. The results provide a baseline for future investigation and allow the inputs, and burdens, of production to be understood.

Recent work has included:

• Environmentalfootprinting(carbonandwater footprints plus an assessment of pesticide toxicity, eutrophication and acidification) of selected arable and horticultural crops.

• Waterfootprintingofagriculturalproductsand an assessment of the effect that UK agricultural has on water resources.

• Greenhousegasassessmentofgrowingmedia materials.

• MassbalanceofnitrogenintheUK.

Population change by downy mildews within leafy vegetable crops is an important model for investigating the durability of R genes. Molecular genetics describing the behaviour of Hyaloperonospora arabidopsidis (Arabidopsis downy mildew) and Bremia lactucae (lettuce downy mildew) in plants is a developing area of research. Factors in populations which influence a rapid turn over of pathogen variants are not clearly understood, especially under glasshouse or field conditions. Crops or single plants often support large numbers of infections by a range of downy mildew pathogen isolates or pathotypes. Conventionally it has been assumed (from animal models) that multiple infection of a single host, with different pathotypes, selects for those with high reproductive rates and high death rates (aggressiveness). Recently this view has been challenged based on results from crop systems. We are using genetic variability in RXLR proteins to develop molecular markers for experimental systems in lettuce and brassica, to

investigate the pathogen population responses to cultivars. Strategic research links have been established with Professor Richard Michelmore at UCD Davis to investigate this approach in other oomycete pathogens.

Predictive Disease Resistance Breeding(led by Roy Kennedy)

Brassica downy mildew

26

Crop Systems

Weed Ecology (ledbyPaulNeve)

The major focus of weeds research at the University of Warwick is to understand the ecological and evolutionary processes that underpin the establishment and persistence of ‘weedy’ plants in agricultural and natural ecosystems. Weeds thrive on disturbance and escalating rates of environmental and climate change will likely create more ecological niches into which weedy plant species will invade and persist. Also, in the future, as changes to pesticide legislation further limit herbicide use for weed control, greater knowledge of weed biology will be essential for integrated weed management. The development of process-based and simulation models to understand key life history processes in weeds is a central theme of our research. These models can be used to predict the ecological and evolutionary consequences of agricultural and environmental change for weed species.

Current projects and interests focus on:

• Modellingevolutionofresistancetoherbicides in cropping systems

• Modellingweedpopulationdynamics

• Experimentalevolutionofresistancetoherbicides in Chlamydomonas reinhardtii

• Fitnesscostsofevolvedresistancetoherbicides

• Ecologyofweedgerminationandseedlingrecruitment

• Weedecologyandadaptationinachangingclimate

Anagallis arvensis

Fertiliser Recommendation Systems for Field Vegetable Crops (led by Clive Rahn )

Putting on the right amount of nitrogen fertiliser to field vegetable crops has a dramatic effect on marketable yield. It is very tempting to over fertilise to achieve maximum yield but this does not always lead to the desired effect and can lead to significant lossesofNtoairandwater.WarwickHRIhasalong history in the development of decision support systemstooptimisesuchNuse.Acomputerbasedsystem,WELL_Nhasbeenavailableforgrowerusesince 1994. In 2008 Warwick HRI led the revision of the national fertiliser recommendations (RB209) for field vegetable crops with ADAS.

Field vegetable crops can leave large amounts of residue nitrogen, in some cases large enough for the needs of following crops to be fully met. Nitrogeninputsforintensivelygrownfieldvegetable crops should be managed rotationally. Warwick HRI led a team of European researchers to developEU-Rotate_Nwhichcanbeusedtoplanthemanagement of nitrogen inputs in conventional and organic rotations. The model enabling a balancing of environmental and economic objectives.

ValuableNforthenextcrop

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Land-Use, Biodiversity and Ecosystem Services in Crop Systems (led by Andrew Mead and Dave Skirvin)

Environmental change is a major factor influencing the spatial arrangement of cropping systems within the UK. The mosaic of crop and non-crop land parcels in the UK potentially has a major impact on biodiversity and ecosystem services, such as pollination and pest control, within the landscape. Our research approach combines population, spatial, economic and statistical modelling with experimental methods to determine how changes in land-use will affect biodiversity and ecosystem services within crop systems. We focus on determining the spatial and temporal scales at which species respond to land-use changes and how the connectivity of the landscape influences the ecosystem services provided by different species. We are investigating how environmental, economic, political and social factors can influence land-use change decisions, and the impacts of these decisions on biodiversity and ecosystem services.

A framework for the assessment of land-use change on biodiversity

Naturalenemiesinawildflowerstrip

Recent research suggests that manipulating habitats within crop systems may be beneficial to pest control through increased provision of natural enemies. We are investigating the mechanisms by which habitat manipulations, such as wildflower strips, intercropping, set-aside vegetation and beetle banks, increase natural enemy abundance

and enhance control of pest populations. Our main focus is on how manipulated habitats influence the spatial and temporal population dynamics of natural enemy species within the mosaic of natural and manipulated habitats that comprise the agricultural landscape.

The impacts of increased biodiversity in crop systems

The impacts of land-use change on crop systems

Enquires welcome. Please contact Centre Secretariat: plantandcropinfo@warwick.ac.uk

www.go.warwick.ac.uk/plantandcropsciences

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