UKBRC 2017 Annual Meeting.

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Published on: May 4, 2017

It was again a great pleasure to attend the Annual Meeting of the UK Brassica Research Community (UKBRC). After the 2016 event in Norwich, this year it moved to the Department of Plant Sciences at the University of Nottingham, hosted by Dr Neil Graham. The meeting was split into two sections, the first of which allowed for short talks updating on (mostly) PhD student and postdoc projects and the latter providing updates on the resources that are being developed for use by the Brassica research community.

Ian Bancroft describes the available community OSR lines.

As in 2016 many talks focussed on research that has used the RIPR Oil Seed Rape (OSR) Diversity Set lines that have been developed in Ian Bancroft’s lab following support from the BBSRC. During the meeting Ian provided clarification as to the relationship between sets of commonly used OSR lines, which was particularly useful for those of us attending from outside of the field!

 


Over the course of a few years it is excellent to see the process of research projects from the early planning stages into the generation of publishable data. Thomas Alcock (University of Nottingham) has used the RIPR lines to search for QTLs that are important in metal tolerance and has found some interesting genes. Similarly Marie Bruser used these lines to look at seed pod development and discovered that genes involves in programmed cell death participate in this process. Both Thomas and Marie took an experimental approach shared by a number of other speakers, including Richard Broughton (Rothamsted Research) who works on seed phytosterol content, namely that they have discovered interesting Brassica QTLs and then moved their research back into Arabidopsis in order to test the function of orthologs. This strategy again highlights the importance of Arabidopsis for underpinning many aspects of UK crop science.

Thomas Alcock describes his work with the RIPR lines.

 


Rumiana Ray (University of Nottingham) and Graham Teakle (University of Warwick) provided updates on the ICAROS and ‘Roots of Decline’ projects respectively. ICAROS looks to develop a sustainable protection strategy for OSR against the effects of Rhizoctonia solani. Little is known about the overall impact of this pathogenic fungus so part of the project will quantify the UK yield loss and the epidemiology of the disease together with potential future management plans.

Rumiana Ray describes the ICAROS project

The Roots of Decline project is part of a set of grants funded under the SARISA (Soil and rhizosphere interactions for sustainable agri-ecosystems) scheme. The overall aim of this research project is to determine the effect of the soil microbiome on the growth of OSR. One part of the experimentation involves growth of plants across three UK sites (Wellesbourne, Rothamsted, Harper Adams) in different rotations with wheat. This will hopefully provide important information on how a differing soil microbiome coincides with changing yields of OSR.

Graham Teakle discusses experimental design of the Roots of Decline project.

After a pleasant lunch kindly funded by the OREGIN grant, Wiktor Jurowski (Earlham Institute) provided an update about the Brassica Information Portal (BIP) and how they are integrating their tools with CyVerse and ElixirUK. They have recently published a pre-print describing the tools available in the BIP and are also planning to hold a Workshop on these tools at the Earlham Institute on June 15th. Please contact Wiktor for details about this meeting.

Lars Ostergaard discusses the BRAVO work packages.

Lars Ostergaard introduced the very exciting BRAVO project, which is a recently funded BBSRC sLOLA. BRAVO will fund research across seven UK academic sites and importantly provides opportunities for collaboration with members of the agricultural industry. Across five work packages the project aims to understand the gene networks that control flowering time and study how these networks affect all developmental stages, from vegetative growth to seed production. The £4.4million of funding will truly move this area of research forward over the next five years….. look out for its outputs soon.


The final presentation was provided by Mathew Nelson who is the Research Leader for Crop Plants at Kew Gardens. He hopes to lead a consortium that will investigate the production of novel bioactive compounds that are produced in Brassicas. This is somewhat inspired by the development of Beneforte broccoli, which has elevated levels of glucoraphanin, a phytonutrient that boosts the levels of antioxidant enzymes in humans.

Earlier in the day Mikhaela Neequaye (Quadram Institute) had given a talk on a similar topic, describing her PhD work that aims to identify broccoli lines that have altered levels of glucosinolates. As part of this study she is using the BRACT facility at the John Innes Centre to generate gene-edited Brassica oleracea mutants.

Mathew Nelson introduces the project idea.

Mathew Nelson is organising a meeting for potential stakeholders in his proposed project at Kew gardens in June or July so please contact him if you have interest in this exciting research area.

Future Fuels for Flights and Freight: £22million available!

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Published on: April 28, 2017

The use of plants as biofuels has great potential for mitigating the effects of future fossil fuel use. However this use cannot be performed at any cost and to date making the process cost-effective has been challenging.

The development of second generation biofuels, such as switchgrass or coppice willow, has arguably shown the greatest potential for production of biofuels yet over recent years. However it is clear that exploration of novel germplasm in isolation is not the only solution to this challenging problem.

The BBSRC funded Lignocellulosic Biorefinery Network (LBNet) has began to bring together plant scientists with microbiologists and industrial planners in order to develop an overall approach to dealing with plant biomass for biofuel production. This leads from growing plants, harvesting, transport of biomass, degradation and saccharification, maximising the extraction of various fractions and distribution of final products into existing and novel pipelines. Last year GARNet reported from the inaugural meeting of the LBNet network.

Along these lines, on April 27th the Department of Transport together with Ricardo launched the ‘Future Fuels for Flights and Freight Competition (F4C)‘ that encourage applications that promote the development of the advanced low carbon fuels industry within the UK, including supplier capabilities and skills in relevant technologies, while maximising value for money for the taxpayer.

The key objectives of this competition are:

  • To increase domestic production of advanced low carbon fuels capable of tackling emissions from the hard-to-decarbonise aviation and HGV sectors in pursuit of long-term UK decarbonisation targets.
  • To stimulate investment and create jobs through the development of a prosperous domestic industry.

Although plant scientists might sit at the very start of this process it might be worth planning an application given the funding available……F4C will provide up to £20 million in capital grant funding over 3 years (2018-21) for major demonstration projects providing transformative and innovative solutions.

The F4C will also provide up to £2 million of Project Development Funding in 2017-18 to support the development of proposals. The F4C will  operate in two stages; Stage One (Project Development) and Stage Two (Capital Funding). Further details are be found here.

Stage One is open to applications between 27 April and 30 June 2017. The funding pipeline is below:

More information and FAQ can be found here:

http://ee.ricardo.com/en/transport/case-studies/f4c

 

Arabidopsis Research Roundup: April 20th

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Published on: April 20, 2017

This Easter basket of papers again features a selection across many topics of research involving Arabidopsis work. Firstly is a paper led from Dundee that introduces a novel Arabidopsis transcript assembly that takes into account alternatively spliced transcripts. Secondly is a paper that identifies a role for an auxin influx carrier in nodule formation in Medicago. Thirdly is a novel characterization of two enzymes involved in SA biosynthesis whilst the fourth paper identifies a novel signaling component that acts during innate immunity to nematodes. Finally is a study that demonstrates a use for microfluidics in the generation of in vitro plant membrane bilayers.

Zhang R, Calixto CP, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W,, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JW (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. https://doi.org/10.1093/nar/gkx267

Open Access

This work is led by John Brown (James Hutton Institute, University of Dundee) in collaboration with colleagues from Glasgow, Vienna and Paris and Toronto. They have looked at the wide array of transcript isoforms that are produced in the Arabidopsis transcriptome. For analysis of these isoforms these researchers have generated a novel pipeline that effectively discriminates between isoforms and results in a Reference Transcript Dataset for Arabidopsis (AtRTD2) that contains over 80K non-redundant transcripts from approximately 35K genes. The testing of AtRTD2 showed that it can outperform other transcriptomes in RNAseq analysis. In addition to their specific Arabidopsis work they provide a methodology for the design of similar workflows for use in other species. The AtRTD2 is currently being integrated with the new Araport11 genome assembly.

The differences between the RTD2 and Araport11 assemblies are presented in the GARNish Vol25 newsletter


Roy S, Robson FC, Lilley JL, Liu C, Cheng X, Wen J, Bone C, Walker S, Sun J, Cousins D, Bennett MJ, Downie JA, Swarup R, Oldroyd GE, Murray JD (2017) MtLAX2, a functional homologue of the auxin importer AtAUX1, is required for nodule organogenesis. Plant Physiology

http:/​/​dx.​doi.​org/10.1104/pp.16.01473 Open Access

Researchers from the JIC and Nottingham lead this study that looks at the role of the auxin influx carrier LAX2 in nodule organogenesis in Medicago. In Arabidopsis there are no reported specific roles for LAX2 but in Medicago they show that MtLAX2 is necessary for nodule formation alongside other auxin-mediated root growth responses. This provides insights into a developmental-specific role for this protein during plant evolution.


Macaulay KM, Heath GA, Ciulli A, Murphy AM, Abell C, Carr JP, Smith AG (2017) The biochemical properties of the two Arabidopsis thaliana isochorismate synthases. Biochem J. http:/​/​dx.​doi.​org/10.1042/BCJ20161069 Open Access

Alison Smith (Cambridge) is the lead author of this study that characterises two isochorismate synthase (ICS) enzymes that are involved in salicylic acid biosynthesis. Expression of AtICS1 is induced by pathogens whilst AtICS2 is constitutive expressed, mostly in vascular tissues. This work shows that both proteins are enzymatically active yet have a narrow window of activity.


Mendy B, Wang’ombe MW, Radakovic ZS, Holbein J, Ilyas M, Chopra D, Holton N, Zipfel C, Grundler FM, Siddique S (2017) Arabidopsis leucine-rich repeat receptor-like kinase NILR1 is required for induction of innate immunity to parasitic nematodes. PLoS Pathog.

http:/​/​dx.​doi.​org/10.1371/journal.ppat.1006284 Open Access

Cyril Zipfel (Sainsbury lab, Norwich) is a co-author on this study that investigates the role of the leucine-rich repeat receptor-like kinase NILR1 in the innate immune response. The novelty of this work comes in the fact that this is the first characterised immune receptor that responds to parasitic nematodes and therefore might provide a new target for pathogen control strategies in crop plants.


Barlow NE, Smpokou E, Friddin MS, Macey R, Gould IR, Turnbull C1, Flemming AJ, Brooks NJ, Ces O, Barter LM (2017) Engineering plant membranes using droplet interface bilayers. Biomicrofluidics. http:/​/​dx.​doi.​org/10.1063/1.4979045 Open Access

This fascinating study from resarchers at Imperial College describes the use of a microfluidic system to generate in vitro plant membrane bilayers. Droplet interface bilayers (DIBs) from Arabidopsis, tobacco and oat have been replicated by varying the amount of membrane components. In future this system could be used in experiments that study membrane translocation or in novel chemical biology screens.

Arabidopsis Research Roundup: March 31st.

This bumper edition of the Arabidopsis Research Roundup includes a wide range of research topics. Firstly Mike Roberts leads a study that adds another layer of complexity to our understanding of the factors that control seed dormancy. Secondly a paper from Ottoline Leyser’s lab at SLCU provides more details regarding the role of BRC1 during shoot branching. Next is a paper that continues David Salt’s collaborative work that aims to understand how the root endodermal barrier influences nutrient uptake. Fourthly is work from Bristol that looks at the interaction between viral infection, the structure of the leaf surface and the polarization of reflected light. The fifth paper features a wide collaboration from the Sainsbury lab in Norwich and aims to more fully understand the factors that lead to non-host infection by Phytophthora infestans. The penultimate paper looks at the interaction of aldolase enzymes with the plant actin cytoskeleton and the final paper brings us full circle back to seed dormancy where researchers from University of Warwick investigate the link between this complex growth response and the circadian clock.

Singh P, Dave A, Vaistij FE, Worrall D, Holroyd GH, Wells JG, Kaminski F, Graham IA, Roberts MR (2017) Jasmonic acid-dependent regulation of seed dormancy following maternal herbivory in Arabidopsis. New Phytol http:/​/​dx.​doi.​org/10.1111/nph.14525

Taken from: http://www.snakesandspiders.com/wp-content/uploads/2013/05/red-spider-mite-control.jpg

Open Access

Mike Roberts (University of Lancaster) kindly provides an audio description of this paper on the GARNet YouTube channel, explaining that, in collaboration with Ian Graham at the University of York, they have identified a new control mechanism that links jasmonic acid, herbivory and seed dormancy. ABA and GA are known to be important hormones in the control of seed dormancy but this study adds complexity to this story by showing that following herbivory (or leaf wounding), the level of JA increases within Arabidopsis seeds. Perhaps counter-intuitively, in the following generation this leads to a reduction in dormancy, causing seed to germinate sooner than those from non-predated parents. The authors show that this is due to an increase in JA within seeds that importantly also alters sensitivity to ABA. Unlike transgenerational defence priming that acts through a epigenetic mechanism and persists for multiple generations , this study shows that the JA effect on seeds is a more direct response. Ultimately the mechanism in which parents prepare their offspring for subsequent generations is a complex trade off between multiple sources of predation and pathogenesis, environmental factors as well as through the effect of interacting hormone signaling pathways.


Seale M, Bennett T, Leyser O (2017) BRC1 expression regulates bud activation potential, but is not necessary or sufficient for bud growth inhibition in Arabidopsis. Development http:/​/​dx.​doi.​org/10.1242/dev.145649 Open Access

This is the latest contribution from Ottoline Leyser’s lab that looks into the hormonal control of shoot branching. A key determinant of this process is the transcription factor, BRANCHED1 (BRC1) yet this study shows that under certain conditions, in this case with varied amount of strigolactone, the controlling effect of BRC1 expression levels can be mitigated. The authors provide evidence for a mechanism for branching control that involves the coordinated activity of BRC1 and an auxin-transport mechanism, both of which are influenced by a separate strigolactone-mediated signaling pathway.


Li B, Kamiya T, Kalmbach L, Yamagami M, Yamaguchi K, Shigenobu S, Sawa S, Danku JM, Salt DE, Geldner N, Fujiwara T (2017) Role of LOTR1 in Nutrient Transport through Organization of Spatial Distribution of Root Endodermal Barriers. Current Biology

http:/​/​dx.​doi.​org/10.1016/j.cub.2017.01.030

Former GARNet chairman David Salt is a co-author on this paper that is lead by Japanese and Swiss colleagues and continues his work on the development of the casparian strip. These rings of lignin polymers are deposited within root endodermal cells and play a key role in the movement of water and nutrients into the vascular tissue. Suberin lamellae have a similar function and surround endodermal cells, likely acting as a barrier to apoplastic movement. This paper documents the identification of the Tolkienesquely-named LOTR1, which is essential for casparian strip formation. Lotr1 mutants show disrupted casparian strips, ectopic suberization and reduced calcium accumulation in the shoot. Further analysis demonstrates that it is this suberized layer substitutes for the CS in regions of lateral root emergence. Utliamtely they show that the relationship between suberization of the endodermal layer is a key determinant of calcium movement into the root and then around the rest of the plant.


Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD (2017) The effects of surface structure mutations in Arabidopsis thaliana on the polarization of reflections from virus-infected leaves. PLoS One

http:/​/​dx.​doi.​org/10.1371/journal.pone.0174014.g003 Open Access

Gary Foster (University of Bristol) leads this study that continues his labs work on the effect that viral infection has on light polarization when reflected off leaves. This attribute is important to attract insect predators, which in turn increase the possibility of successful viral transmission. Light polarization is affected by structures on the leaf surface such as trichomes or the makeup of the waxy cuticle. Here the authors show that the cer5 wax synthesis mutant alters the polarization of light following infection with Turnip vein clearing virus (TVCV) but not following infection with Cucumber mosaic virus (CMV). The paper provides no mechanism for this difference but the authors do show that leaf viral titre is equivalent in these mutants and therefore speculate that these changes might influence transmission of each virus by a different insect carrier that in turn responses to different patterns of polarized light.


Prince DC, Rallapalli G, Xu D, Schoonbeek HJ, Çevik V,, Asai S,, Kemen E,, Cruz-Mireles N, Kemen A,, Belhaj K, Schornack S,, Kamoun S, Holub EB, Halkier BA, Jones JD (2017) Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. BMC Biol. 

http:/​/​dx.​doi.​org/10.1186/s12915-017-0360-z  Open Access

This paper is a wide collaboration that features many colleagues from the Sainsbury lab in Norwich. Wildtype Arabidopsis plants are suspectible to Phytophthora infestans only after earlier infection with Albugo laibachii yet the molecular explanation of this complex interaction between plant and microbes remained opaque. This study demonstrates that Albugo infection alters the levels of a set of tryptophan-derived antimicrobial compounds, which were then found to be relevant for infection with P.infestans. This shows that these antimicrobial compounds might be key for the general maintenance of non-host resistance and might provide important information to aid future strategies to improve food security by reducing biomass loss due to plant pathogens.


Garagounis C, Kostaki KI, Hawkins TJ, Cummins I, Fricker MD, Hussey PJ, Hetherington AM2, Sweetlove LJ (2017) Microcompartmentation of cytosolic aldolase by interaction with the actin cytoskeleton in Arabidopsis. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx015

This collaboration between the Universities of Oxford, Bristol and Durham looks into the functional role that molecular microcompartments play in the workings of a cell. Animal models have shown that certain aldolase enzymes are able to function as actin-bundling proteins and so this study focuses on a major plant cytosolic aldolase, FBA8, which is predicted to have two actin binding sites. Although the authors could not detect co-localisation of FBA8-RFP with the actin cytoskeleton they provide in vitro evidence that FBA8 can functionally interact with F-actin. In addition in fba8 mutants there is altered arrangement of actin filaments in guard cells that concomitantly results in a reduced rate of stomatal closure. Therefore these findings leads the authors to propose that FBA8 is able to subtly interact with actin in vivo, evidenced by some FRET-FLIM experiments, and that this may modulate actin dependent cell responses.


Footitt S, Ölcer-Footitt H, Hambidge AJ, Finch-Savage WE (2017) A laboratory simulation of Arabidopsis seed dormancy cycling provides new insight into its regulation by clock genes and the dormancy-related genes DOG1, MFT, CIPK23 and PHYA. Plant Cell Environ http:/​/​dx.​doi.​org/10.1111/pce.12940

William Savage-Finch (University of Warwick) is the corresponding author on this paper that investigates mechanisms that control seed dormancy, which has been built from the analysis of a variety of genetic and environmental factors. They test their predictions by testing a range of mutants in both known dormancy related genes and in the function of the circadian clock. This provides a link between the circadian cycle and the daily variation in the level of seed dormancy in Arabidopsis.

Stockbridge Technology Centre

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Published on: March 22, 2017

Following the conclusion of the CyVerseUK workshop at the University of York I was delighted to take a brief visit to StockBridge Technology Centre (STC) to have a look at their facilities.

STC are involved in a range of research projects that involve different aspects of plant growth across many conditions and species. As well as initiating independent research projects they are equally at home working with a broad cross section of collaborators and as such sit in an excellent position to make linkages between interest groups who can be challenging to bring together.

STC has received significant public interest for the work they do, with a number of high profile appearances in the mainstream media, most recently in early March on BBC Countryfile (see from 24minutes onward). At their site in the Vale of York they have a large number of highly adaptable greenhouses that sit in alongside 70 hectares appropriate for field trials. In addition they are involved with more technology-facing projects such as the LED4Crops that is run by Dr Phillip Davis at STC.
This project is highly relevant at a time when there are concerns about UK food security and our reliance of imported produce. Use of LED technology is proving extremely useful in improving our understanding of the light regimes that are required in order to both maximise biomass production and improve different traits. This is particularly relevant as there is a growing need to work on a constant 12-month rotation.

Researchers at the LED4Crops facility work with both ornamental and food crops and they are hoping to soon gain funding to greatly expand their operation. If the potential of Stacked Urban Farming is to be realised then the type of research undertaken at STC will be critical for understanding the light conditions needed to maximise production in those sunlight-less environments.

For academic researchers STC sits at an advantageous position of being able to bridge the gap between basic research, industry and farmers and are therefore happy to interact with any potential partners. Although researchers at STC are unable to indepedently apply for RCUK funding they are partners on many grants and work on plenty of EU-funded projects.

Please take a look at the STC website and I’m sure they’d be delighted to host anyone who is interested in visiting their facilities.

Phill Davis will be writing a longer piece for the next issue on the GARNish newsletter so please look out for that!

Arabidopsis Research Roundup: March 17th

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Published on: March 17, 2017

This weeks UK Arabidopsis Research Roundup includes three papers featuring researchers from the University of Nottingham as well as manuscripts from Leeds, Lancaster, QMUL and The Sainsburys Lab in Norwich

Firstly Stefan Kepinski (Leeds) leads a study that investigates how Gravitropic Set Point Angle (GSA) is controlled in response to different growth factors. Secondly are two Methods papers featuring researchers from CPIB in Nottingham, the first of which is in collaboration with Lancaster University and introduces the Microphentron, which is an automated phenotyping platform that can be used for chemical biology screens. The second paper describes a non-destructive method for imaging floral tissues using CT scanning.

Ranjan Swarup is also a member of CPIB and in the next paper he has collaborated with French colleagues to investigate the role of SHR on root development in rice.

The fourth paper includes Cyril Zipfel as a co-author and investigates the role of damage-associated molecular patterns (DAMPs) in the response to pathogen attack whereas this weeks final paper is from the lab of Alexander Ruban (QMUL) and discovers the phenotypic consequences of persistent damage to PSII by photoinhibition.


Suruchi Roychoudhry, Martin Kieffer, Marta Del Bianco, Che-Yang Liao, Dolf Weijers Stefan Kepinski (2017) The developmental and environmental regulation of gravitropic setpoint angle in Arabidopsis and bean Scientific Reports http://dx.doi.org/10.1038/srep42664

Open Access

Stefan Kepinski (University of Leeds) leads this study that involves a collaboration with Dolf Weijers from Wageningen University. They investigate the role of both auxin and environmental factors in determining gravitropic set point angle (GSA), which is a measure of the growth of lateral organs away from primary shoots and roots. They show that nitrogen and phosphorous deficiency causes opposing effects on lateral root GSA, each of which are auxin-dependent. This contrasts with previous findings from work using bean adventitious roots. They find that these differences are maintained when Arabidopsis and bean roots are treated with different auxin concentrations. Latterly they also look at the effect of different light conditions on shoot GSA and put these findings into the context of potentially altering crop growth.

Stefan takes some time to discuss this paper for the GARNet YouTube Channel.


Burrell T, Fozard S, Holroyd GH, French AP, Pound MP, Bigley CJ, James Taylor C, Forde BG (2017) The Microphenotron: a robotic miniaturized plant phenotyping platform with diverse applications in chemical biology. Plant Methods

http://dx.doi.org/10.1186/s13007-017-0158-6 Open Access

This methods paper is a collaboration between the Universities of Lancaster and Nottingham led by Brian Forde that describes the Microphenotron. This device has been developed to facilitate chemical biology screens on in vivo plant tissues. This allows for the automated screening of either dicot or monocot roots or aerial tissues that have been grown on media infused with whichever chemical is relevant for the intended expriments. In situ GUS screening is also possible allowing for researchers to integrate information about growth and gene expression. The use of ‘Phytostrips’ in a 96-well format allows for high-throughput screening that is aligned with AutoRoot automated image analysis software to provide a rapid and facile method for undertaking small scale phenotypic screens. The Microphenotron facility is housed at the Lancester University, who are extremely open to collaboration so please get in contact if you are interested in using the facility.


Tracy SR, Gómez JF, Sturrock CJ, Wilson ZA, Ferguson AC (2017) Non-destructive determination of floral staging in cereals using X-ray micro computed tomography (µCT) Plant Methods. http://dx.doi.org/10.1186/s13007-017-0162-x Open Access

Alison Ferguson is the corresponding author on this methods paper that includes GARNet committee member Zoe Wilson and Saoirse Tracy from Dublin. They have developed a technique using X-ray µCT scanning to image developing flowers in Arabidopsis and barley plants, taking advantage of the excellent Hounsfield facility at the University of Nottingham. They show that the technique can be hugely beneficial for plant phenotyping by providing a non-destructive method of analyzing live floral development and how this can response to changes in the growth environment. Members of the Hounsfield facility are happy to discuss any potential collaborative work and future access to these type of facilities will hopefully be improved through the UKs involvement in the pan-european EMPHASIS project.


Henry S, Dievart A, Fanchon D, Pauluzzi G, Meynard D, Swarup R, Wu S, Lee CM, Gallagher K, Périn C (2017) SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice. Dev Biol. http://dx.doi.org/10.1016/j.ydbio.2017.03.001

Ranjan Swarup (CPIB) is a co-author on this study that includes French and US researchers. Previously they had shown that expression of rice SHORTROOT (OsSHR) genes could compliment the Arabidopsis shr mutant. In this study they show that overexpression of OsSHR and AtSHR in rice roots causes growth of wider, shorter roots that have an increased number of cortical cell layers. This demonstrates that the mechanisms that control the differentiation of cortical cell layers is conserved throughout land plants, with SHR being a key determinant in this process.


de Azevedo Souza C, Li S, Lin AZ, Boutrot F, Grossmann G, Zipfel C, Somerville S (2017) Cellulose-derived oligomers act as damage-associated molecular patterns and trigger defense-like responses. Plant Physiol. http://dx.doi.org/10.1104/pp.16.01680

Cyril Zipfel (The Sainsbury Lab) is a co-author on this study from the lab of Shauna Somerville in California that focuses on the concept of damage-associated molecular patterns (DAMPs). These can be defined as cell wall breakdown components and stimulate the same defence responses as more fully characterised pathogen- or microbe-associated molecular patterns (PAMPs). Intuitively this makes sense as during infection many pathogens will cause cell wall breakdown. The authors show that cellulose-derived oligomers trigger a signalling response similar to that caused by oligogalacturonides or chito-oligomers but that lacks an increase in ROS or in callose deposition. These results confirm that cellulose-derived signals feed into the plants mechanism for cell wall scanning and acts synergistically with other signals that result from pathogen attack.


Tian Y, Ungerer P, Zhang H, Ruban AV (2017) Direct impact of the sustained decline in the photosystem II efficiency upon plant productivity at different developmental stages. J Plant Physiol. http://dx.doi.org/110.1016/j.jplph.2016.10.017

Image from http://www.sciencedirect.com/science/article/pii/S0176161717300433

Alexander Ruban (QMUL) leads this Sino-UK collaboration that investigates how the photoinhibiton of photosystem II impacts overall plant growth. In this study they use lincomycin to block chloroplast protein synthesis, which prevents the plant from restoring PSII function after photoinhibitory damage. Treated plants accumulate less starch and showed reduced above-ground biomass. This leads to a decrease in seed yield. Perhaps unsurprisingly this research shows that restoring the full function of PSII after photoinhibition to key to maintaining normally functioning electron transport rate that leads into metabolic production and growth rate.

Arabidopsis Research Roundup: March 6th.

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Published on: March 6, 2017

This weeks Arabidopsis Research Roundup includes four papers that focus on different aspects of plant cell biology. Firstly Ian Henderson’s research group in Cambridge defines the role of a critical component that determines crossover frequency in plants and other eukaryotes. Secondly Karl Oparka (Edinburgh) leads a broad collaboration that defines the mechanism of unloading of solutes and macromolecules from the root phloem. Thirdly Keith Lindsey (Durham) has developed a model that describes how auxin patterns the Arabidopsis root. Finally Mike Blatt (Glasgow) is part of a group that uses Arabidopsis as a framework for the study of ABA-signaling during stomatal movement in ferns.


Ziolkowski PA, Underwood CJ, Lambing C, Martinez-Garcia M, Lawrence EJ, Ziolkowska L, Griffin C, Choi K, Franklin FC, Martienssen RA, Henderson IR (2017) Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination. Genes Dev

http:/​/​dx.​doi.​org/10.1101/gad.295501.116

Open Access

GARNet committee member Ian Henderson (University of Cambridge) leads this work that features collaborators from the UK, US and Poland. They use an experimental technique that allows facile analysis of recombination rates alongside a study of Arabidopsis natural variation to isolate a QTL that is critical for maintaining the correct number of crossovers during meiosis. This HEI10 gene codes for an E3 ligase (the targets of which are currently unknown) whose copy number is a key component in the control of recombination rate. Hei10 mutants have less crossovers whilst plants with extra copies of HEI10 have an increased number, especially in sub-telomeric regions of the genome. HEI10 is a highly conserved protein, demonstrating its important role to ensure appropriate levels of recombination throughout the evolution of eukaryotes.

Ian kindly takes ten minutes to discuss this paper with GARNet on our YouTube Channel.


Ross-Elliott TJ, Jensen KH, Haaning KS, Wager BM, Knoblauch J, Howell AH, Mullendore DL, Monteith AG, Paultre D, Yan D, Otero-Perez S, Bourdon M, Sager R, Lee JY, Helariutta Y, Knoblauch M, Oparka KJ (2017) Phloem unloading in Arabidopsis roots is convective and regulated by the phloem-pole pericycle. Elife.

http:/​/​dx.​doi.​org/10.7554/eLife.24125

Open Access

Karl Oparka (University of Edinburgh) is the corresponding author of this study that includes researchers from the UK, US and Denmark. Movement of solutes and macromolecules through the plant phloem is key for the correct distribution of nutrients allowing for optimal growth. In this paper they discover that unloading of molecules from the phloem occurs via a set of specialized funnel plasmodesmata that link the phloem to adjacent pericycle cells. Remarkably they find that whereas solutes are constantly unloaded, larger proteins are released through these plasmodesmata in discrete pulses, which they describe as ‘batch unloading’. Overall this study provides evidence of a major role for the phloem-pericycle cells in the process of moving essential nutrients from the phloem into surrounding tissues.


Moore S, Liu J, Zhang X, Lindsey K (2017) A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Sci Rep. http:/​/​dx.​doi.​org/10.1038/srep43004

Open Access

The work comes from the lab of Keith Lindsey (University of Durham) and developes a data-driven model that predicts the role of auxin patterning in the recovery of an Arabidopsis root following a perturbation of polar auxin transport. They demonstrate three main principles that define the role of auxin influx and efflux carriers in this process and also provide experimental validation for their predictions.


Cai S, Chen G, Wang Y, Huang Y, Marchant B, Wang Y, Yang Q, Dai F, Hills A, Franks PJ, Nevo E, Soltis D, Soltis P, Sessa E, Wolf PG, Xue D, Zhang G, Pogson BJ, Blatt MR, Chen ZH (2017)

Evolutionary Conservation of ABA Signaling for Stomatal Closure in Ferns Plant Physiol

http:/​/​dx.​doi.​org/10.1104/pp.16.01848

Open Access

Mike Blatt (University of Glasgow) is a co-author on this global study that looks into the evolution of ABA-signaling in the control of stomatal closure. Although this study is focused on this process in ferns they build their findings on the analysis of transcriptional networks from Arabidopsis. Ultimately they find that the evolution of ABA-controlled guard cells movements are important in the adaptation of ferns to a terrestrial environment.

EMPHASIS on Plant Phenotyping

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Published on: February 28, 2017

Some readers might have heard of the EMPHASIS project but the likelihood is that the majority have not……yet it might be extremely significant for the future of plant science across Europe…. which, yes, even in these uncertain times, should include UK researchers!

The European Strategy Forum on Research Infrastructures (ESFRI) supports high quality research infrastructures across all disciplines and includes diverse projects such as ELIXIR, A distributed infrastructure for life-science information  and SKA, the Square Kilometer Array Telescope. The process of receiving support from ESFRI starts with inclusion in their annual Roadmap document that leads onto a series of discussions that aim to set the official agenda for the program. This might then result in the establishment of an official infrastructure project a further 5 years later. Importantly this is a different type of project when compared to Horizon2020 or FPs as the funding does not come from a centralised EU pot but is rather distributed from within the individual participating countries.


Last year was an exciting time for European Plant Phenotyping as through the work of Belgian, German, French and UK researchers, the EMPHASIS project (European Infrastructure for multi-scale Plant Phenomics and Simulation for food security in a changing climate) was included in the ESFRI Roadmap in 2016. Within the UK, it was largely members of the UKPPN (UK Plant Phenotyping Network) who worked with the BBSRC to ensure that UK scientists were represented in the EMPHASIS project that was included in the ESFRI Roadmap.

The genesis of EMPHASIS could be traced back to the FP7-funded EPPN (European Plant Phenotyping Network) which was the starting point of the overall aim to develop complimentary tools for lab, greenhouse and field phenotyping that integrates high-tech automated platforms with computer-aided measurements and data management.


EMPHASIS-PREP takes shape.

The EMPHASIS-PREP project has now been funded by Horizon2020 and over the coming years will document the strengths and weaknesses of European plant phenotyping before producing a final document that will highlight why the entire EMPHASIS project should be supported and how it might be regulated across up-to-30 participating countries. As the money for UK scientists will come directly from RCUK, it is hoped that issues surrounding Brexit will not be as significant an issue for this scheme as it might with other centrally administered EU funding. This will support a UK research infrastructure that integrates with European partners and conforms to certain EMPHASIS-defined access requirements to researchers from across the EU.

The EMPHASIS-PREP project is split into 6 work-packages and the BBSRC have taken the lead with WP5, which tackles the legal frameworks that are needed for the project to succeed with minimal interference.


The group participating in EMPHASIS-PREP is much smaller than the proposed final EMPHASIS project so those members involved at the present time (which will be expanded over the course of the discussions) have signed the ‘EMPHASIS Manifesto’ in which they agree to work for the good of the whole future consortium.

Ultimately the aim of EMPHASIS is to host all the necessary infrastructure for state-of-the-art phenotyping and can be split into five very broad topics:

> Controlled conditions: Phenotyping platforms in (semi-) controlled conditions for high resolution and high throughput phenotyping.

> Intensive field: Smart/ Intensive field experimental sites for high throughput phenotyping

> Lean field: Translational, coordinated network of field experiments with lean, efficient phenotyping close to practical breeding setups

> Modelling: Modelling platforms for testing existing or virtual combinations of alleles in a variety of climatic scenarios and management practices

> e-Infrastructure: establish interconnections between different nodes/ installations.


The final organisation of the project will take a classic European Hub-and-Node organisation. The EMPHASIS Hub will likely reside in Germany whilst each national Node will attempt to lead the organisation of the countries phenotyping infrastructure so that it is open, inclusive and conforms to the overall aims of the EMPHASIS program.

As this is a five-year process it will clearly be extremely complicated to organise and over the coming year EMPHASIS-PREP are holding regional meetings to introduce the aims of the project and to receive feedback from those participating countries. As the project planning gains pace then these meetings may become more frequent and could be organized on an individual national level.

These early EMPHASIS-PREP meetings have three main goals:

> Inform: about the EMPHASIS project

> Document: the status of plant phenotyping in each country

> Discuss: future national plans for plant phenotyping

In the early stages of EMPHASIS-PREP the UK will be represented by the University of Nottingham specifically led by Malcolm Bennett, Darren Wells and Tony Pridmore. They will work closely with the BBSRC to ensure that UK interests are represented at each meeting. The location of each meeting can be found on the EMPHASIS website.


What does it mean for me now?

At the moment not a great deal.

Please keep an eye out for developments and then contribute any thoughts and ideas that you have when the appropriate forums are opened up. GARNet has been a contributing member of the UKPPN and as we are mandated to support community infrastructures so we will endeavor to keep the UK community informed as the project rolls forward.

Hopefully in 2018 there will be a UK-based meeting in which members of our outstanding UK plant phenotyping community will be able to submit their opinions as to the direction of travel of this field (pardon the pun) of research that has enormous significance for the development of new crop varieties to mitigate the effects of climate change and ensure global food and nutritional security.

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