Arabidopsis Research Roundup: July 27th

Each of the papers in this Arabidopsis Research Roundup involves the response to different stimuli. Giles Johnson at Manchester provides an audio description of work that has discovered a novel mechanism of cold sensing whilst Gordon Simpson and John Brown from Dundee are contributors to work that has interrogated the sugar signaling pathway. Finally is a study from Warwick that has identified novel loci involved in ABA signaling and seed vigour.

Dyson BC, Miller MA, Feil R, Rattray N, Bowsher C, Goodacre R, Lunn JE, Johnson GN (2016) FUM2, a cytosolic fumarase, is essential for acclimation to low temperature in Arabidopsis thaliana Plant Physiology

Open Access


Giles Johnson (Manchester) is the corresponding author on this UK-German collaboration that looks at the mechanisms by which plants sense the low temperatures that cause significant phenotypic changes. GC-MS showed that fumarate is a key component in the cold tolerance response and that the activity of the FUM2 enzyme is responsible for accumulation of fumaric acid. Plants that lack FUM2 activity show significant alteration in gene expression and metabolite profile following a cold treatment and in particularly are unable to acclimate photosynthesis at lower temperatures. Therefore this study introduces a novel component of the temperature sensing apparatus, which might have broad significance for attempts to develop crops with an improved cold response.

Giles kindly provides an audio description of this work, which includes an overview into cold acclimation of photosynthesis. This includes an excellent ‘stress-ball’ analogy! (Apologies for pen-clicks :/).


Carvalho RF, Szakonyi D, Simpson CG, Barbosa IC, Brown JW, Baena-González E, Duque P (2016) The Arabidopsis SR45 Splicing Factor, a Negative Regulator of Sugar Signaling, Modulates SNF1-Related Protein Kinase 1 (SnRK1) Stability The Plant Cell


Gordon Simpson and John Brown (James Hutton Institute) are contributors to this Portuguese-led study that investigates the role of the SR45 splicing factor in sugar signaling. In sr45-1 mutants they show that glucose-feeding causes increased levels of the energy-sensing SNF1-Related Protein Kinase 1 (SnRK1) yet without increasing its gene expression. Concomitantly the hypersensitivity of sr45-1 mutants is rescued in plants with reduced levels of SnRK1. The authors discovered that the mechanistic link between these genes involves SR45-1 regulating the alternative splicing of the 5PTase13 gene, which encodes an inositol polyphosphate 5-phosphatase that interacts with SnRK1 in vivo. In wildtype plants 5PTase13 modulates proteasomal-mediated degradation of SnRK1 and therefore a perturbation of this process in sr45-1 explains this defect in sugar-sensing.

Morris K, Barker GC, Walley PG, Lynn JR, Finch-Savage WE (2016) Trait to gene analysis reveals that allelic variation in three genes determines seed vigour. New Phytol. Open Access

Bill Finch-Savage is the corresponding author on this study from the Warwick University that uses Brassica oleracea natural variation to identify novel loci involved in seed vigour. The discovered QTL was termed Speed of Germination (SOG1) and contained two genes, BoLCVIG2, a homologue of the alternative-splicing regulator (AtPTB1) and BoLCVIG1, which has unknown function. Transfer of these alleles into Arabdopsis causes alterations in seed germination, which is also observed in mutants of the equivalent Arabidopsis genes (At3g01060, At3g01150). Furthermore an additional discovered QTL encodes the Reduced ABscisic Acid 1 (RABA1) gene, which influences ABA content and seed vigour. Therefore this mapping strategy has discovered three genes that promote seed vigour resulting from alterations in ABA content and sensitivity.

Arabidopsis Research Roundup: April 1st.

This weeks Arabidopsis Research Roundup contains an eclectic mix of investigations. Firstly is a study from Peter Unwin that investigates the molecular factors that control interactions between plants and nematode parasites. Secondly is a study led by John Christie that investigates the factors that control hypocotyl curvature. Thirdly is a fascinating proof-of-concept synbio-style study from Rothamstead Research where an algal gene is transferred into Arabidopsis in the hope of developing a phytomediation-based solution to heavy metal contamination. Fourthly is a study from David Bass that catalogues protist species that feed on leaf-microorganisms whilst finally John Carr heads a study that compares RNA-dependent RNA polymerases from Arabidopsis and Potato.

Eves-van den Akker S, Lilley CJ, Yusup HB, Jones JT, Urwin PE (2016) Functional C-terminally encoded plant peptide (CEP) hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis. Mol Plant Pathol.

This study is a collaboration between researchers at the Universities of Dundee and Leeds, led by Peter Unwin. The focus of the paper is the interaction of Plant-Parasitic Nematodes (PPNs) with their plant hosts. PPNs stimulate redifferentiation of vascular tissues to form ‘feeding structures’ that benefit the parasite. This process is mediated by a diverse family of effector proteins termed C-terminally Encoded Peptide plant hormone mimics (CEPs). This study investigates the CEPs from the nematode Rotylenchulus reniformis and suggests that these peptides evolved de novo in this organism. They show that the activity of a synthetic peptide corresponding to RrCEPs causes a reduction in primary root elongation whilst upregulating a set of genes including the nitrate transporter AtNRT2.1. The authors propose that CEPs evolved in R. reniformis to allow sustained biotrophy by upregulating a specific set of feeding-responsive genes and by limiting the size of the feeding site produced. This study represents an exciting introduction to a currently under-researched area within plant-pathogen interactions.

Sullivan S, Hart JE, Rasch P, Walker CH, Christie JM (2016) Phytochrome A Mediates Blue-Light Enhancement of Second-Positive Phototropism in Arabidopsis. Front Plant Sci. 7:290 Open AccessFrontiersPHOT1

John Christie (Glasgow) is the corresponding author on this investigation into the role of the blue-light receptor phototropin 1 (phot1) during hypocotyl phototropism. Curvature of this organ is enhanced by treatment by red-light mediated by the phytochromeA receptor. However this study shows that pre-treatment with blue-light can also enhance this hypocotyl curvature although this did not occur at higher light intensities. In addition phototropic enhancement was also lacking when PHOT1 is expressed only in the hypocotyl epidermis. Therefore the study shows that the phyA impact on phot1 signaling is restricted to low light intensities and in tissues other than the epidermis.

Zhong Tang, Yanling Lv, Fei Chen, Wenwen Zhang, Barry P. Rosen, and Fang-Jie Zhao (2016) Arsenic Methylation in Arabidopsis thaliana Expressing an Algal Arsenite Methyltransferase Gene Increases Arsenic Phytotoxicity J. Agric. Food Chem. Open Access ArsM

This synthetic biology-focused study is led by Fang-Jie Zhao at Rothamstead Research. The authors take an algal gene (arsM) that allows the transformation of inorganic arsenic to a more volatile methylated version. The biological activity of this enzyme was successfully transferred to two different Arabidopsis ecotypes. However interestingly these transgenic plants became more sensitive to arsenic in growth media suggesting that the new methylated arsenic intermediate is more phytotoxic than inorganic arsenic. Therefore this study demonstrates a negative consequence of this project that attempted to engineer arsenic tolerance in plants. Once again this demonstrates that nature rarely acts predictably and any great ideas usually need to be tested in vivo.

Ploch S, Rose L, Bass D, Bonkowski M (2016) High Diversity Revealed in Leaf Associated Protists (Rhizaria: Cercozoa) of Brassicaceae J Eukaryot Microbiol.

After a fantastic opening line in the abstract, ‘The largest biological surface on earth is formed by plant leaves’, this study includes the work of David Bass from the Natural History Museum in London. They investigate the abundance of protists that associate with leaf-inhabiting microorganisms, the “phyllosphere microbiome“. Their findings demonstrate that protists should be considered an important part of the diversity of plant-interacting microbial organisms.

Hunter LJ, Brockington SF, Murphy AM, Pate AE, Gruden K, MacFarlane SA, Palukaitis P, Carr JP (2016) RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases Sci Rep. 6:23082 Open Access

John Carr (Cambridge) is the UK-lead on this collaboration with Slovenian and Korean researchers. They primarily investigate the role of the RDR1 RNA-dependent RNA polymerase (RDRs) in potato. In Arabidopsis the RDR1 gene contributes to basal viral resistance but potato plants deficient in StRDR1 do not show altered susceptibility to three different plant viruses. In addition they perform a phylogenetic analysis on the RDR genes and identify a novel RDR7 gene that is only found in Rosids (but not Arabidopsis.

Brassica Research Report: 2015

The Arabidopsis Research Roundup has been put to bed for 2015 so in the leadup to the Christmas we’ll take a look at some of the papers that have been published in 2015 by UK researchers working ondifferent plants.
Today we focus on Brassica species and by looking at papers from throughout 2015 this selection touches on a broad selection of research areas. Chronologically first is a study from Nottingham University that looks at the ability of Brassica rapa to take up specific elements, such as Zn, Ca and Mg. Secondly is a study that documents the parameters that make different cultivars of Brassica napus useful in biorefining. Thirdly we highlight where Brassica oleracea has been used both in preference to, and alongside Arabidopsis in a study that investigates meiotic recombination. Next is a study that investigates the relationship between leaf colour and insect herbivory. Finally we highlight a recent publication from the John Innes Centre that demonstrates the ability to generate gene-edited B.oleracea.
The varieties of Brassica

Blasco B, Graham NS, Broadley MR (2015) Antioxidant response and carboxylate metabolism in Brassica rapa exposed to different external Zn, Ca, and Mg supply.
J Plant Physiol. 176:16-24
Martin Broadley and Neil Graham from Nottingham University lead this study that investigates antioxidant response and carboxylate metabolism in Brassica rapa. The authors looked at these parameters in the presence of varying amounts of zinc, calcium or magnesium in experiments that aimed to simulate the response to deficiency or toxicity of these elements. Plants grown with high concentrations of these elements showed increased shoot biomass, hydrogen peroxide, total ascorbate and increasing activity of enzymes involved in removal of antioxidants. This indicates that B.rapa is particularly sensitive to high levels of these elements. The information provided in this study represents important baseline measurements that will aid the future characterisation of B.rapa TILLING lines, generated by the RevGenUK service at the JIC.


Wood IP, Wellner N, Elliston A, Wilson DR, Bancroft I, Waldron KW (2015) Effect of Brassica napus cultivar on cellulosic ethanol yield. Biotechnol Biofuels. 8:99. Open Access
Keith Waldron (Institute of Food Research, JIC) leads this collaboration with the University of York that investigates how the sugar composition of Brassica napus alters its ability to be used as a source for biorefining. They found significant differences in the saccharification and fermentation yields after the processing of straw obtained from 17 different B.napus cultivars. Surprisingly glucan-rich straw was not correlated with higher saccharification or ethanol yields but rather the non-cellulosic components were more reliable indicators of substrate quality, with the amount of pectins and arabinogalactans having the greatest impact on saccharification. Ultimately this study finds that pectin concentration is most likely to determine to effectiveness of the cultivar in the production of bioethanol. This is important information for the future development of different dicot species for use in this aspect of biorefining.


Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372 Open Access

Immunolocalisation of proteins during meiotic recombination in Brassica.
Immunolocalisation of proteins during meiotic recombination in Brassica.

Chris Franklin (Birmingham) is the leader on the UK-US-Austrian collaboration that looks at the role of the PCH2 protein during meiotic recombination. Although much of this study uses Arabidopsis mutant plants, the initial immunoprecipitations that led to identification of novel factors were performed using pollen mother cells from Brassica oleracea. Subsequently some important imaging also takes place in B.oleracea. The authors use structured illumination microscopy (SIM) to investigation the localisation of synaptonemal complex formation during meiosis and the close relationship between Arabidopsis and B.oleracea allowed the authors to use to same reagents fo these experiments. This paper was featured in an Arabidopis Research Roundup earlier in the year.


Green JP, Foster R, Wilkins L, Osorio D, Hartley SE (2015) Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea). PLoS One 10(9):e0136884 Open Access

This collaboration between York and Sussex Universitites is led by Sue Hartley and Daniel Osorio and look into the role that leaf colour plays in the defence response in wild cabbage. This aspect of plant physiology has been proposed as being important in defence against insect herbivory but this is the first instance where real data from wild populations has been obtained on this topic. The authors found that variation in leaf colour and brightness corresponded to particular glucosinolate levels as well as of the ability of certain herbivores to colonise the leaves. As might be predicted, leaves with lower levels of glucosinolate coincided with faster growth rates of lepidopteran larvae. However in a controlled experiment neither adult butterflies or adult aphids showed a preference for leaves of different colours. This therefore might suggest that although in the field herbivores may benefit from colonising leaves with lower defence chemicals (and an altered colour), the adults do not have the ability to select for these particular leaves, indicating that selection of leaves is either down to chance or other uninvestigated parameters.


Lawrenson T, Shorinola O, Stacey N, Li C, Østergaard L, Patron N, Uauy C, Harwood W (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease Genome Biol. 16:258. Open Access

An example of successfully gene edited Brassica. From Genome Biology
An example of successfully gene edited Brassica. From Genome Biology

This is a collaboration between Wendy Harwood, Cristobal Uauy, Nicola Patron and Lars Ostargaard from the John Innes Centre and the Sainsbury Lab in Norwich. Over the past few years, CRISPR-Cas technology has been presented as important technology to be used in the future generation of gene edited crops. However only a few studies have been published to date where this technology has been effectively used. This paper describes the use of CRISPR-Cas to generate specific mutations in both barley and Brassica oleracea. Across both species they identified targeted mutations in 10%-25% of the first generation plants although interestingly they were also able to identify B.oleracea mutants in the T0 generation. They also observed off-target activity in both species even though the designed guide RNAs contains mismatches with the incorrectly edited sequences.
This is important work demonstrating that this type of gene editing can be used to rapidly generate stable mutants in crop species. The creation of mutants in off-target genes is a potential concern from a regulatory perspective although can be viewed as a positive factor for targeting multigene families that do not have appropriate identical target sequences.

Arabidopsis Research Roundup: December 18th

The final Arabidopsis Research Roundup of 2015 contains a bumper crop of papers that again highlights the diversity of research occuring in UK plant science. Justin Goodrich from the University of Edinburgh kindly provides an audio description of work that identifies a novel role for a member of a transposon gene family. Elsewhere are studies about a specific aspect of the biochemistry of crytochromes as well as confirmation of a role for DNA gyrases in Arabidopsis. Paul Dupree (Cambridge) leads a study into the mechanism of ascorbic acid production while Heather Knight is the UK representative in a study about cell wall composition. We also present an investigation into the mechanism and subsequent expression changes that occur following infection with different isolates of the Turnip Mosaic Potyvirus. Finally are two short studies from Ive de Smet (Nottingham) and Matt Jones (Essex).

Liang SC, Hartwig B, Perera P, Mora-García S, de Leau E, Thornton H, de Alves FL, Rapsilber J, Yang S, James GV, Schneeberger K, Finnegan EJ, Turck F, Goodrich J (2015) Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2. PLoS Genet. 11 e1005660. Open Access

Justin Goodrich (Edinburgh) is the lead of this collaborative study between UK, German and Australian researchers that investigates the role of the evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) genes during plant development. These homeotic genes influence gene expression by causing epigenetic chromatin changes, usually in the form of histone methylation. Previously the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene was found to act as a genetic suppressor the Arabidopsis PcG gene, LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In this study ALP1 is shown to genetically interact with members of these two gene families and its activity is necessary for the activation of several floral homeotic genes. Surprisingly the ALP1 gene is shown to encode for a transposase of the PIF/Harbinger class, which is conserved throughout land plants. The authors suspect that the transposase activity has been lost in the angiosperm lineage, where the gene obtained a novel function. Interestingly ALP1 can interact with the core PrC complex, which most notably participates in H3K27me3 methylation and therefore appears to act, along with other proteins such as EMBRYONIC FLOWER 1 (EMF1), as a plant-specific accessory component that controls histone modification. The authors speculate that this novel function might have arisen as a “means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity”. Over the coming years it will be interesting to discover if other transposon-encoded genes share novel functions and this study represents an important lesson for researchers not to ignore transposon sequences as ‘junk’ DNA that they might feel can clutter up their analysis!

Justin Goodrich kindly provides an audio summary of this paper:

van Wilderen LJ, Silkstone G, Mason M, van Thor JJ, Wilson MT (2015) Kinetic studies on the oxidation of semiquinone and hydroquinone forms of Arabidopsis cryptochrome by molecular oxygen FEBS Open Bio. 5:885-892 Open Access

This study is a collaborative effort between researchers from Imperial College and the University of Essex, led by emeritus biochemistry Professor Michael Wilson and is an in vitro analysis of the oxidation of the Arabidopsis cryptochrome (CRY) photoreceptor in the presence and absence of an external electron donor. They show that a more complex model than previously thought is required to explain the mechanism by which the CRY-associated flavin molecule is oxidised. The authors propose that the final steps in this reaction require cooperative interaction between partners in a CRY homodimer or between separate CRY molecules.

Evans-Roberts KM, Mitchenall LA, Wall MK, Leroux J, Mylne JS, Maxwell A (2015) DNA Gyrase is the Target for the Quinolone Drug Ciprofloxacin in Arabidopsis thaliana. J Biol Chem. Open Access

Antony Maxwell from the Biological Chemistry department from the John Innes Centre is the UK academic lead on this UK-Australian study. This group has previously shown that Arabidopsis contains three proteins thought to function as DNA Gyrases (AtGYRA, ATGYRB1, ATGYRB2) although they could not provide direct evidence that are were involved in DNA supercoiling. This study moves the work on by identifying mutant plants that are resistant to the drug ciprofloxacin and contain a point mutation in AtGYRA. Furthermore ATGYRA heterologously expressed in insect cells has supercoiling activity. Therefore the authors unequivocally show that plants encode an organellar-targeted DNA gyrase that, like bacterial gyrases, is a  target for ciprofloxacin. This work has important consequences for our understanding of plant physiology and in the future development of novel herbicides.

Sawake S, Tajima N, Mortimer JC, Lao J, Ishikawa T, Yu X, Yamanashi Y, Yoshimi Y, Kawai-Yamada M, Dupree P, Tsumuraya Y, Kotake T (2015) KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis The Plant Cell

Paul Dupree (Cambridge) is the British lead on the UK-Japanese collaboration that investigates the role of the GDP-mannose pyrophosphorylase (GMPP), VITAMIN C DEFECTIVE1 (VTC1) enzyme in catalysis of the rate-limiting step in the production of ascorbic acid (AsA). They identify two novel pyrophosphorylase-like proteins, KONJAC1 (KJC1) and KJC2 that stimulate VTC1. Mutant analysis showed that these proteins are necessary for normal growth that coincides with control of AsA production via stimulating GMPP activity. Yeast 2 Hybrid  analysis is indicative of a direct interactin between KJC and VTC1 proteins. In future, it will be interesting to investigate the role of these proteins in plants that are more relevant to human consumption of AsA.

Sorek N, Szemenyei H, Sorek H, Landers A, Knight H, Bauer S, Wemmer DE, Somerville CR (2015) Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor MONGOOSE1. PNAS

Heather Knight (Durham) is the sole UK representative on this manuscript that is led by the lab of Chris Somerville from the University of California. In this work the authors identified suppressors of the Arabidopsis cobra mutant, which have defects in cellulose formation. The appropriately named mongoose (mon1) mutant partially restored cellulose levels and also restored the esterification ratio of pectin to wild-type levels. MON1 was cloned to the MEDIATOR16 (MED16)/ SENSITIVE TO FREEZING6 (SFR6) locus and single mon1 mutants are resistant to cellulose biosynthesis inhibitors. Concomitantly, transcriptome analysis demonstrated that a set of ‘cell wall’ genes are misregulated in mon1/med16/sfr6, including two encoding pectin methylesterase inhibitors. Overall the authors suggest that cellulose biosynthesis is closely linked to esterification levels of pectin and offer a number of possible explanations for this functional relationship.

Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, López-González S, Jenner C, González-Melendi P, Elena SF, Walsh J, Ponz F (2015) Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns Mol Plant Microbe Interact.

The UK contributor to this Spanish-led study is Carol Jenner, who at the time was a research fellow at the University of Warwick. This study highlights the morphological changes that occur in Arabidopsis plants infected by different isolates of Turnip mosaic virus (TuMW). The UK1 and JPN1 versions of TuMW were shown to have highest levels of sequence divergence in the P3 cistron and following the generation and use of viral chimeras, it is this region that was identified as the major viral determinant of plant developmental changes. However when the P3 gene was constitutively expressed in Arabidopsis it did not cause any development effects, which highlights the importance of performing infection studies in a whole-plant context. Latterly the authors performed transcriptomic and interactomic analysis, showing that infection with the most severe UK1 strain primarily causes changes, perhaps unsurprisingly, in genes involved in transport and in the stress response.

Czyzewicz N, De Smet I (2015) The Arabidopsis thaliana CLAVATA3/EMBRYO-SURROUNDING REGION 26 (CLE26) peptide is able to alter root architecture of Solanum lycopersicum and Brassica napus. Plant Signal Behav

This work was performed in the lab of Ive De Smet, who is a BBSRC research fellow at the University of Nottingham. In this short communication they show that overexpression of the Arabidopsis AtCLE26 peptide is able to induce architectural change in the agriculturally important crops, Brassica napus and Solanum lycopersicum. Having previously shown that AtCLE26 is similarly active in Arabidopsis, Brachypodium and Triticum, these experiments further demonstrate that small peptide signaling plays an important role in root development across plant lineages.

Litthauer S1, Battle MW1, Jones MA (2015) Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signal Behav.

Matt Jones (Essex) leads this accompanying study to the more substantial project previously published in Plant Journal. This manuscript reports that phototropin photoreceptors are not involved in the nuclear accumulation of evening-phased circadian transcripts. In addition they show that even in phototropin mutants, the rhythms of nuclear clock transcript accumulation are maintained under fluctuating light regimes.

Great British Success in ERA-CAPS

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:
Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

Effector-triggered defence: A new concept in plant pathogen defence

In June, a team of Brassica researchers from the University of Hertfordshire proposed a new classification for a type of plant defence mechanism: effector-triggered defence (ETD).

Henrik Stotz is first author of the paper describing ETD, currently In Press in Trends in Plant Science. He explains, “In the same way that humans have developed immune responses against human disease pathogens, crops can be bred for resistance against disease pathogens, but we need to improve our understanding of effective resistance mechanisms within plants. Our research enhances the traditional understanding of the plant defence system and describes a new concept, which is how plants protect themselves against the pathogens that grow in the space outside plant cells (the apoplast) – a new concept called effector-triggered defence or ETD.”

Traditionally, plant pathogen defence is broken into two broad forms: pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is the first action the plant takes against a pathogen and is triggered when the pathogen lands on the plant. The pathogen releases molecules called effectors into the plant cells, which the plant recognises and reacts against. If the effectors are not recognised, the pathogen can spread with little resistance.

The team from Hertfordshire, led by Bruce Fitt, argue that one line of defence, R gene-mediated host resistance against fungal pathogens that grow in the space between cells, is not adequately explained by either mechanism.

Effector-triggered defence (ETD) is mediated by R genes encoding cell surface-bound receptor-like proteins that engage the receptor-like kinase SOBIR1 – an extracellular recognition. The response is host cell death after an extended period of endophytic pathogen growth. This is in contrast to ETI, in which detection of the pathogen occurs within cells and usually triggers fast host cell death.

ETD is described in Stotz et al. (In Press) Trends in Plant Science DOI:

The quotes used in this article are from this BBSRC Press Release. This story was originally posted on the UK Brassica Research Community website.


Recently in the GARNet community…

Comments: No Comments
Published on: January 24, 2014

GARNet news

Lisa and I went to the Brassica Growers Association Conference on Tuesday. I wrote two posts on it over on the UK-BRC website, and Lisa put together a very informative Storify of tweets on the #BGAconference stream.

The UK Plant Sciences Federation has been collecting opinions, facts and data for the past year or so and is now ready to launch a report entitled UK Plant Science: Current Status and Future Challenges. Lisa and I helped out with this report so keep an eye out for it on Tuesday and let us know what you think!

I went to the SEB Synthetic Biology conference last week and have written a short report for the SEB Bulletin about it – I’ll share it when it is published. There was some excellent plant science there. Antonio Scialdone presented the plant-arithmatic work from Martin Howard’s lab – you can read his open access 2013 paper modelling starch degredation over night here (Scialdone et al., eLife 2013;2:e00669). Oliver Ebenhoeh discussed how mathematical models for photosynthesis and plant metabolism can help synthetic biology be done in plants and other photosynthetic organisms.


On the GARNet website

If you missed some January funding deadlines, there are plenty more opportunities to submit your proposal – take a look at the funding round-up on our website for ideas for fellowships, travel, collaborations or straightforward research grants.

Lisa is continuing to write her weekly Arabidopsis research round-up, which you can find on the GARNet news pages. It’s the best way to keep informed of what fellow UK Arabidopsis researchers are up to. This week, papers from GARNet committee members Heather Knight and Cyril Zipfel feature.


Your chance to present your work

PlantSci 2014 is in York on 31 March/1 April, and abstract submission is open until the end of February. There are two £200 cash prizes to be won by early career researchers giving short talks, so make sure you submit an abstract! There won’t be a traditional poster session, but delegates are invited to bring mini-posters to discuss during the networking sessions. Abstracts for the mini-posters will be included in the abstract book.

Further away in September, GARNet 2014 is your second chance to present your work at either a poster session or as a short talk. Registration and abstract submission are both open, and news about special opportunities for students will be coming very soon.

Finally, I’ve been reliably informed that the FSPB/EPSO Plant Biology Conference organisers are looking for proposals for short talks for the Big Data in Plant Science session, so if you’re planning on going and do ‘big data,’ think about submitting an abstract!

UK Brassica Research Community

Categories: Brassica
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Published on: March 7, 2013

Brassica crops, which include oilseed rape, cabbage, and brussels sprouts, are major components of the UK arable agriculture and horticulture industries. The close relationship between Brassica and Arabidopsis provides exciting opportunities to translate fundamental science to impact by using it to understand and manipulate crop traits.

If you are interested in finding out more about Brassica research and the UK Brassica research community, come to the annual meeting of the UK Brassica Research Community at Rothamsted on 9 May 2013.

A successful UK brassica industry requires fundamental and applied scientists, breeders, and farmers to work together. The UKBRC provides a hub for them to do so. Everyone can catch up at the annual meetings, but for the rest of the year check out the UKBRC website and join the UKBRC mailing list to get news and find resources.

You can register for the event here, and see talks from previous meetings on the UKBRC website. If you currently work with Brassicas and would like to share your research at the meeting, contact Pierre Carion ( to find out more.

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