NIAB Wheat Transformation Resource and BotanyLive

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Published on: May 19, 2017

On May 18th (global Fascination of Plants Day btw) I had the pleasure of attending the wrap-up meeting for the first phase of the NIAB Community Resource for Wheat Transformation Facility (CRWT) at the NIAB Innovation farm site just outside Cambridge.

The CRWT is a BBSRC resource that has provided the opportunity for plant scientists without expertise in wheat transformation (aka most people) to apply to have their gene of interest introduced into hexaploid wheat. Over the course of the grant almost 120 applications have been made to this resource and 50 genes have been pushed through the CRWT pipeline. This generates plantlets that are then sent back to the applicants for further analysis. There will be a full report from this meeting in the upcoming GARNish newsletter but suffice to say it was exciting to learn about successful applications of this technology, in particular those that have directly led into future BBSRC grants from the labs of Julie Gray (Sheffield) and Matthew Paul (Rothamsted).

As part of the #BotanyLive celebration we also put together a short video to advertise NIAB and the CRWT resource. This features Alison Bentley (NIAB), Sinead Drea (University of Leicester), Ben Sibbett (University of Southampton) and Keith Edwards (University of Bristol). You can see the full video through the Periscope website:

https://www.pscp.tv/GARNetweets/1nAKEBqpYolGL?t=3s (will open in the Periscope URL)

Arabidopsis Research Roundup: May 17th

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Published on: May 17, 2017

This weeks Arabidopsis research roundup begins with a paper led by CPIB at the University of Nottingham that discovers a somewhat surprisingly mechanism controling Arabidopsis root hydrotropism. Next are two papers from the University of Leeds that firstly investigate how the JAGGED LATERAL ORGANS gene influences the auxin response and secondly looks at the role of redox regulation in the control of the cell cycle and seed development. Finally are two papers that look at different aspects of the plant pathogen interactions. Jonathan Jones from the John Innes Centre is a co-author on a paper that dissects the multiple gene expression networks that control plant immunity whilst Charles Melnyk at the Sainsbury lab in Cambridge is involved with work that investigates the hormonal control mechanisms that influence the invasion of parasitic plants.


Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM,, Owen MR,, Band LR,, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ,, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ (2017) Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature Plants

http:/​/​dx.​doi.​org/10.1038/nplants.2017.57

Open Access via access link: http://rdcu.be/rSsk

Malcolm Bennett (University of Nottingham) leads a broad international collaboration that looks at the response of Arabidopsis roots to water. Surprisingly they show that this response occurs not in the root meristem but in the elongation zone and is controlled by a ABA signaling mechanism. They show that hydrotropism is dependent on cell elongation in the cortex but not in any other cell file. This is different to the gravitropic response and demonstrates that these tropisms are controlled by distinct tissue-specific mechanisms. To provide for information about this paper, lead author Daniela Dietrich joins Professor Bennett to discuss this paper on the GARNet YouTube channel and speculate on the function of different root cell layers in water uptake.


Rast-Somssich MI, Žádníková P, Schmid S, Kieffer M, Kepinski S, Simon R (2017) The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx131 Open Access

This German-led study includes Stefan Kepinski (University of Leeds) as a co-author. They investigate the role of the JAGGED LATERAL ORGANS (JLO) transcription factor in the establishment of the stem cell niche in the root meristem. JLO interacts with auxin signaling pathway by influencing the degradation of the key regulator BODENLOS (BDL) via the TIR1-mediated degradation pathway. In jlo mutants BDL remains present in the meristem, which does not correctly develop. They discover a novel regulatory mechanism wherein the dosage of the TIR1 and AFB1 auxin receptors is reduced, which in turn prevents BDL degradation. This shows that the JLO transcription factor is a key upstream regulator of meristem formation by playing a significant role in the fine control of the auxin response.


De Simone A, Hubbard R, Vinegra de la Torre N, Velappan Y, Wilson M, Considine MJ, Soppe W, Foyer CH (2017) Redox changes during the cell cycle in the embryonic root meristem of Arabidopsis thaliana. Antioxid Redox Signal. http:/​/​dx.​doi.​org/10.1089/ars.2016.6959

Open Access

Christine Foyer (University of Leeds) collaborates with Australian and German researchers to unpick the role that redox regulation plays in the control of the plant cell cycle. They use an in vivo redox reporter (roGFP2) to show that a cycle of reduction and oxidation occurs throughout the cell cycle. Their experimental system is Arabidopsis seed germination and they show that vitamin c defective mutants with low redox buffering capacity have altered germination rates that coincide with a changed dry seed transcriptome. Overall this paper demonstrates that the cell cycle and embryo size are linked to redox regulation.


Hillmer RA, Tsuda K, Rallapalli G, Asai S, Truman W, Papke MD, Sakakibara H, Jones JDG, Myers CL, Katagiri F (2017) The highly buffered Arabidopsis immune signaling network conceals the functions of its components. PLoS Genet. http:/​/​dx.​doi.​org/10.1371/journal.pgen.1006639

Open Access

Jonathan Jones (John Innes Centre) is a co-author on this Japanese-led research that studies the signaling networks invovled in plant immunity. They use a systems biology approach to dissect the network of interactions that occur within the transcriptome when plants are exposed to the immune stimulant flagellin-22. This analysis discovers that there are separated networks that represent pathways controlled by different higher-level signals, such as jasmonate or salicylic acid. This provides the entire network with a degree of buffering that allows a more effective response to pathogen attack. This type of network analysis is able to reveal facets of the defence response that would not be possible when using simple null mutant analysis so adds consideration detail to the already complicated story of plant-pathogen interactions


Spallek T, Melnyk CW, Wakatake T, Zhang J, Sakamoto Y, Kiba T, Yoshida S, Matsunaga S, Sakakibara H, Shirasu K (2017) Interspecies hormonal control of host root morphology by parasitic plants. PNAS

http:/​/​dx.​doi.​org/10.1073/pnas.1619078114

Charles Melnyk (Sainsbury Lab, Cambridge) is an author on this study led by Ken Shirasu at RIKEN and uses Arabidopsis to investigate the relationship between parasitic plants and their hosts, specifically at the level of interspecies transport via a structure called the haustorium. Haustoria are structures through which substances, such as RNA and proteins, reciprocally move between host and parasite. In this paper they look at the interaction between Arabidopsis roots and the hemiparasitic plant Phtheirospermum japonicum, demonstrating that movement of molecules between species occurs via haustoria once a vascular connection is made. Arabidopsis secondary root growth is induced under infection, a response that requires the effect of the hormone cytokinin. They look at the genetics of this interaction and show that cytokinin signaling genes are important in establishing root hypertrophy. Overall this study demonstrates the important of cytokinin during infection with parasitic plants and might be an important target to design strategies to combat these negative interactions in systems.

Arabdopsis Research Roundup: May 11th

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Published on: May 11, 2017

This weeks Arabidopsis Research Roundup is lead by two papers that characterise the relationship between cell size and growth in different Arabidopsis tissues. Firstly the lab of GARNet PI Jim Murray look at how the cell cycle influences cell size progression in the SAM whilst George Bassel’s group from Birmingham investigate cell growth within a developing embryo. Thirdly is a paper from the University of Essex that further defines the role of the CP12 protein in control of photosynthesis. Next is a paper from researchers from the University of Warwick who lead a fascinating piece of rocket science that identifies differences in the vernalisation requirement across Brassica species whilst in the fifth paper, researchers from Lancaster identify environmentally defined QTLs that determine the plant response to glutamate. Finally is a paper that highlights a new software tool that has the self-explanatory title of the ‘UEA small RNA Workbench’ and is applicable for use with plant-derived datasets.

R Jones A, Forero-Vargas M, Withers SP, Smith RS, Traas J, Dewitte W, Murray JAH (2017) Cell-size dependent progression of the cell cycle creates homeostasis and flexibility of plant cell size. Nat Commun http:/​/​dx.​doi.​org/10.1038/ncomms15060

Open Access

This study comes from the lab of current GARNet PI Jim Murray at the Cardiff University. Lead author Angharad Jones kindly provides an audio description of the paper for the GARNet YouTube channel. This  investigation looks at the factors that control the interaction between cell size and cell growth in a developing shoot meristem. They show that the dynamic regulation of this relationship is linked to the activity of two cyclin dependent kinases (CDKs) and that cell size is key in controlling the transition from G1>S and from G2>M phases of the cell cycle. Importantly this work uses precise imaging to track the progression of individual cell lineages and is therefore able to suggest that cell size is an emergent and not a directly determined property.


Souza NM, Topham AT, Bassel GW (2017) Quantitative analysis of the 3D cell shape changes driving soybean germination. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx048

Open Access

George Bassel (University of Birmingham) leads this paper that uses information gained from the study of patterns of cell expansion in Arabidopsis embryos to investigate a similar process in soybean. Indeed as in Arabidopsis they show that there is preferential early cell expansion closest to the soybean radicle and that starting cell size corresponds to different growth rates. In addition they show that the growing hypocotyl has complex regulation and that differential ansiotrophy growth drives forward the process of germination. Ultimately they show that this occurs equivalently in both model and crop species.


Elena López-Calcagno P, Omar Abuzaid A, Lawson T, Anne Raines C (2017) Arabidopsis CP12 mutants have reduced levels of phosphoribulokinase and impaired function of the Calvin-Benson cycle. J Exp Bot http:/​/​dx.​doi.​org/10.1093/jxb/erx084 Open Access
This study from the photosynthesis group at the University of Essex is led by Tracey Lawson and GARNet committee member Christine Raines. They investigate the role of the CP12 multigene family that has three members in Arabidopsis. These are redox-sensitive proteins that facilitate the formation of a complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) during the Calvin-Benson cycle. They show that plants with reduced levels of CP12-1 or CP12-2 have lower photosynthetic capacity and subsequently exhibit slower growth. The cell biological explanation for this alteration appears to focus on the PRK protein, which is present at lower levels in plants with reduced CP12-1 or CP12-2. Therefore the authors find that CP12-1 and CP12-2 are the key members of this gene family and they likely show functional redundancy in the tight control of photosynthesis.


Taylor JL, Massiah A, Kennedy S, Hong Y, Jackson SD (2017) FLC expression is down-regulated by cold treatment in Diplotaxis tenuifolia (wild rocket), but flowering time is unaffected. J Plant Physiol.

http:/​/​dx.​doi.​org/10.1016/j.jplph.2017.03.015 Open Access
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Steve Jackson (University of Warwick) leads this work that also features Chinese collaborators and investigates the role of FLOWERING LOCUS C (FLC) in the popular peppery salad plant Rocket (Diplotaxis tenuifolia) that, as a Brassica, is a somewhat closely related to Arabdopsis. The authors studied the vernalisation requirement in this plant so isolated its version of FLC, which was shown to functional compliment an Arabidopsis flc null mutant. However they showed that even though cold treatment reduced levels of DtFLC this did not alter the bolting time of the plant. This somewhat surprising result demonstrates that the link between FLC and flowering time is uncoupled in this species and that other mechanisms may take precedence, a situation different to that observed in Arabidopsis and other Brassicas.


Walch-Liu P, Meyer RC, Altmann T, Forde BG (2017) QTL analysis of the developmental response to L-glutamate in Arabidopsis roots and its genotype-by-environment interactions. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx132 Open Access Researchers from the groups of Brian Forde (Lancaster University) and Thomas Altmann (Leibniz Institute) collaborate in this research that identifies three novel QTLs (GluS1-3) that are involved in the response of Arabdopsis roots to external L-glutamate. When this experiment was extended they discovered that different environmental factors play a significant role in the control of this trait. The GluS1 locus is located on Chr3 yet is epistatically controlled by loci on Chr1 and Chr5 in response to temperatures. Overall this study demonstrates that the response to glutamate is controlled by multiple environmentally sensitive loci that vary between Arabidopsis ecotypes


Mohorianu I, Stocks MB, Applegate CS, Folkes L, Moulton V (2017) The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis. Methods Mol Biol.

http:/​/​dx.​doi.​org/10.1007/978-1-4939-6866-4_14

This manuscript from the University of East Anglia describes a set of software tools for the analysis of small RNAs. They used an Arabidopsis dataset to demonstrate the utility of the UEA small RNA Workbench, which can be found here: http://srna-workbench.cmp.uea.ac.uk/

SEB-GARNet Meeting on Post-Translational Modifications

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Published on: May 5, 2017

The SEB and GARNet are delighted to be hosting a SEB Cell Section Satellite meeting entitled ‘From Proteome to Phenotype: role of post-translational modifications’.

This will take place at the University of Edinburgh between December 11th-13th 2017.

We encourage you to mark this in your diaries and pass this information to anyone you know who might be interested in the meeting.

This meeting features two days of outstanding plenary talks that will present the role of Post-translational Modifications on Plant Growth and Development. In addition the Keynote talks will be provided by speakers outside of the plant community to offer context from their work in other experimental systems.

We greatly encourage attendance from early career researchers and feature 10 opportunities for talks from submitted abstracts as well as hosting three poster sessions. GARNet will be also providing a significant number of £200 travel grants.

The third day of the meeting is a separate hands-on workshop that will look at current techniques and tools used for proteomic analysis. This workshop will be led by Dr Alex Jones.

Please find the program below and look out for annoucements regarding registration and travel grants over the coming months.

It is sure to be a fantastic meeting so I hope you are interested in attending.

Yours,
Steven Spoel, Cyril Zipfel and Geraint Parry

 

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.

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