Meeting Report: Monogram 2019

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Published on: July 31, 2019

by Cara Wheeldon, University of Leeds working in the Bennett Lab.


This April I attended Monogram 2019, my first conference, and I have to say that I had a great time. I didn’t know what to expect, but I was very pleased to discover how friendly and welcoming the UK cereal research community is. In addition to academic researchers, representatives from plant breeding companies were present.


The conference talks were grouped into sessions each with a different focus. I was fascinated to learn about all the exciting developments in cereal research from across the UK, and how varied these areas are. From grain size to root morphology to nutritional gain, the field is vast and brimming with new discoveries and technological developments.

I was especially interested in the work being carried out at NIAB, as presented by Alison Bentley. As my research is focussed on how plants respond to physical aspects of the rhizosphere such as soil volume and the presence of neighbouring plants, I found Vera Hecht’s work on field sowing density to be of particular interest. As highlighted by Vera, space is a valuable commodity in farming and over sowing can have costly, negative effects on plant growth. Research into this subject area has highly valuable applications to crop production.

Alison Bentley presenting her research. Photo @StephanieSwarbr

On the second day, there was an open discussion about the current and future requirements needed to facilitate advances in cereal research. Issues raised included the need for improvements in database access and use, in order to aid the exchange of knowledge amongst the research community.


On the first day I had the opportunity to present my poster titled ‘’Root density sensing allows pro-active modulation of shoot growth to avoid future resource limitation’’. During the poster session, and indeed during the following few days, I was able to have incredibly interesting and thought-provoking discussions with many of the delegates about both my own and their research. I certainly found this opportunity to discuss ideas with people from different areas of crop research highly valuable for project progression and forming new connections.

Cara presenting her poster. Photo @CaraWheeldon

Despite being a Masters by Research student, I achieved highly commended for my poster in the PhD category, several months before embarking on my PhD. I found this to be a brilliant validation of my hard work and dedication to this area of research and I am incredibly grateful for the recognition.

I would like to thank GARNet for providing me with a travel grant to attend this year’s conference and I hope to see you all next year!



GARNet Research Roundup: July 26th 2019

This summer-time-reading bumper edition of the GARNet Research Roundup begins with two papers from the University of Sheffield that each use advanced imaging techniques. Firstly Andrew Fleming’s group leads a study on the link between stomatal function and mesophyll space morphology. Second is a study from Matthew Johnson’s group that looks at the dynamic arrangement of thylakoid stacks.

Next are two papers that include Alison Smith from the JIC as a corresponding author. The first also includes Vasilios Andriotis from the University of Newcastle and looks at the role of the plastidial pentose phosphate pathway during post-germination growth. Second uses a gene-editing strategy to generate potatoes with altered starch morphologies.

The fifth paper also looks at starch; researchers from Cambridge and Norwich are involved in a study that characterises the role of the LIKE SEX4 1 protein in starch degradation.

The sixth paper is from Aberystwyth University and identifies a transcription factor that alters secondary cell wall composition in Brachypodium and maize. Next is research from the University of Bath that looks at the role of a protein S-acyl transferase during seed germination.

The eighth and ninth papers are led by Spanish research groups and include contributions from UK-based co-authors in Cambridge and Nottingham, working on photoperiod perception or phosphate signaling respectively.

The tenth paper features work from Cardiff University and looks at the role of heterologous expression of the Arabidopsis WEE1 protein. The Bancroft lab from the University of York leads the next paper that investigates glucosinolate signaling in Brassica napus.

The final three manuscripts are methods papers. The first from Edinburgh introduces a new NanoLUC reporter whilst the other two include techniques involved in the investigation of light-regulated growth processes.


Lundgren MR, Mathers A, Baillie AL, Dunn J, Wilson MJ, Hunt L, Pajor R, Fradera-Soler M, Rolfe S, Osborne CP, Sturrock CJ, Gray JE, Mooney SJ, Fleming AJ (2019) Mesophyll porosity is modulated by the presence of functional stomata. Nat Commun. doi: 10.1038/s41467-019-10826-5

Open Access

This UK-wide study is led from Andrew Fleming’s lab in Sheffield and includes Marjorie Lundgren as first author (now working in Lancaster). They use microCT imaging alongside more traditional measurements linked to analysis of gas exchange to show that mesophyll airspace formation is linked to stomatal function in both Arabidopsis and wheat. This allows the authors to propose that coordination of stomata and mesophyll airspace pattern underpins water use efficiency in crops.

https://www.nature.com/articles/s41467-019-10826-5

Wood WH, Barnett SFH, Flannery S, Hunter CN, Johnson MP (2019) Dynamic thylakoid stacking is regulated by LHCII phosphorylation but not its interaction with photosystem I. Plant Physiol. doi: 10.1104/pp.19.00503

Open Access

William Wood is the first author on this study from the University of Sheffield that uses 3D structured illumination microscopy (3D-SIM) to look at the dynamics of thylakoid stacking in both Arabidopsis and spinach. They show that the processes they observe are dependent on light harvesting complex II phosphorylation.

http://www.plantphysiol.org/content/early/2019/06/11/pp.19.00503.long

Andriotis VME, Smith AM (2019) The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1908556116

Open Access

Vasilios Andriotis (now at the University of Newcastle) is the lead author of this work performed in Alison Smith’s lab at the JIC. They look at the role of the plastidial oxidative pentose phosphate pathway (OPPP) during embryo development. This involved demonstrating that production of ribose-5-phosphate (R5P), which in turn leads to synthesis of purine nucleotides, is a critical function of the OPPP.


Tuncel A, Corbin KR, Ahn-Jarvis J, Harris S, Hawkins E, Smedley MA, Harwood W, Warren FJ, Patron NJ, Smith AM (2019) Cas9-mediated mutagenesis of potato starch-branching enzymes generates a range of tuber starch phenotypes. Plant Biotechnol J. doi: 10.1111/pbi.13137

Open Access

Alison Smith and Nicola Patron who work in Norwich Research Park are corresponding authors of this study that includes Aytug Tuncel as first author. They have used Cas9-mediated gene editing to generate potato plants that have a range of different tuber starch structures. This shows that gene-editing techniques allows the transgene-free alteration to generate potentially healthier crops.


Schreier TB, Umhang M, Lee SK, Lue WL, Shen Z, Silver D, Graf A, Müller A, Eicke S, Stadler M, Seung D, Bischof S, Briggs SP, Kötting O, Moorhead GB, Chen J, Zeeman SC (2019) LIKE SEX4 1 acts as a β-amylase-binding scaffold on starch granules during starch degradation. Plant Cell. doi: 10.1105/tpc.19.00089

Open Access

Tina Schreier from the University of Cambridge is the first author on this international study led from Switzerland that also includes Alexander Graf and David Seung from the JIC as co-authors. This study defines a precise role for the LIKE SEX FOUR 1 (LSF1) protein that binds starch and is required for normal starch degradation. Through a variety of experiments they show that the glucan binding, rather than phosphatase activity, is required for LSF1 function during starch degradation.


Bhatia R, Dalton S, Roberts LA, Moron-Garcia OM, Iacono R, Kosik O, Gallagher JA, Bosch M (2019) Modified expression of ZmMYB167 in Brachypodium distachyon and Zea mays leads to increased cell wall lignin and phenolic content. Sci Rep. doi: 10.1038/s41598-019-45225-9

Open Access

Rakesh Bhatia is the first author on this work from the lab of Maurice Bosch at Aberystwyth University. They overexpress the maize MYB transcription factor ZmMYB167 in both Brachypodium and maize. Both species show increased lignin content with Brachypodium but not maize showing a biomass deficit. This indicates that ZmMYB167 could be a useful molecular tool for the alteration of secondary cell wall biosynthesis.

https://www.nature.com/articles/s41598-019-45225-9

Li Y, Xu J, Li G, Wan S, Batistic O, Sun M, Zhang Y, Scott R, Qi B (2019) Protein S-acyl Transferase 15 is Involved in Seed Triacylglycerol Catabolism during Early Seedling Growth in Arabidopsis (2019) J Exp Bot. doi: 10.1093/jxb/erz282

First author on this UK-Chinese collaboration is Yaxiao Li who works with Baoxiu Qi at the University of Bath. The authors characterise the function of Arabidopsis Protein Acyl Transferase 15, AtPAT15. This protein is involved in essential β-oxidation of triacylglycerols during post-germination growth.


Ramos-Sánchez JM, Triozzi PM, Alique D, Geng F, Gao M, Jaeger KE, Wigge PA, Allona I, Perales M (2019) LHY2 Integrates Night-Length Information to Determine Timing of Poplar Photoperiodic Growth. Curr Biol. doi: 10.1016/j.cub.2019.06.003

Open Access

This Spanish-led study includes co-authors from the Sainsbury Laboratory in Cambridge and attempts to define the factors that control photoperiod perception in trees, using poplar as a model system. FLOWERING LOCUS T2 (FT2) has been previously shown to be involved in this process and this study builds on that work to show that night-length information is transmitted by the clock gene LATE ELONGATED HYPOCOTYL 2 (LHY2) and is able to control FT2 expression.

https://www.cell.com/current-biology/fulltext/S0960-9822(19)30696-7?

Silva-Navas J, Conesa CM, Saez A, Navarro-Neila S, Garcia-Mina JM, Zamarreño AM, Baigorri R, Swarup R, Del Pozo JC (2019) Role of cis-zeatin in root responses to phosphate starvation. New Phytol. doi: 10.1111/nph.16020

Ranjan Swarup from the University of Nottingham is a co-author on this Spanish-led study that has Javier Silva-Navas as first author. Through analysis of dark-grown seedlings they have identified a set of new genes involved in root phosphate signaling. In addition they provide evidence of a links between cytokinin and phosphate signaling through modulation of the cell cycle.


Siciliano I, Lentz Grønlund A, Ševčíková H, Spadafora ND, Rafiei G, Francis D, Herbert RJ, Bitonti MB, Rogers HJ, Lipavská H (2019) Expression of Arabidopsis WEE1 in tobacco induces unexpected morphological and developmental changes. Sci Rep. 2019 Jun 18;9(1):8695. doi: 10.1038/s41598-019-45015-3

Open Access

Ilario Siciliano leads this work that includes colleagues from Hilary Rogers’ lab at Cardiff University. The WEE1 protein regulates the cell cycle across eukaryote lineages. In this work they show that overexpression of AtWEE1 in tobacco causes precocious flowering and increased shoot morphogenesis of stem explants whilst in cell culture this WEE1 OX causes smaller cell sizes.


Kittipol V, He Z, Wang L, Doheny-Adams T, Langer S, Bancroft I (2019) Genetic architecture of glucosinolate variation in Brassica napus. J Plant Physiol. doi: 10.1016/j.jplph.2019.06.001

Open Access

This study from the Bancroft lab at the University of York is led by Varanya Kittipol. Through use of Associative Transcriptomics (AT) across a diversity panel of 288 Brassica napus genotypes they are able to identify a set of genes involved in synthesis of glucosinate hydrolysis products.


Urquiza-García U, Millar AJ (2019). Expanding the bioluminescent reporter toolkit for plant science with NanoLUC. Plant Methods. doi: 10.1186/s13007-019-0454-4

Open Access

This study from the University of Edinburgh introduces NanoLUC, a new more stable luciferase-based reporter for use by the plant community.

The final two papers are methods papers that focus on different aspects of light-regulated growth. These are from the University of Southampton and University of York.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0454-4

Terry MJ, Kacprzak SM (2019) A Simple Method for Quantification of Protochlorophyllide in Etiolated Arabidopsis Seedlings. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_14

Oakenfull RJ, Ronald J, Davis SJ (2019) Measuring Phytochrome-Dependent Light Input to the Plant Circadian Clock. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_15

Meeting Report from Monogram 2019

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Published on: July 25, 2019

By Laura Taylor, University of Cambridge

In April this year I attended the Monogram meeting hosted by the University of Nottingham. This was my second time attending the meeting and I was looking forward to hearing about the new research conducted by the UK small grain community. 


Keith Edwards, from the University of Bristol, kicked off the meeting with a fantastic plenary talk focusing on genetic variation in hexaploid wheat. I had never previously considered the consequences of mixed cultivation of tetraploid and hexaploid wheat before and certainly would never have thought that mixed cultivation was still occurring in some areas of the world today. I felt that Keith Edwards put in perspective the opportunities that high levels of genetic diversity in wheat present for both academia and industry and set an upbeat tone for the rest of the meeting.

Keith Edwards kicks off the meeting. Photo @GuilleMendiondo

In the next session, entitled ‘Below and above ground processes’, Tom Bennett from the University of Leeds presented work completed by his group on hormone signalling in wheat roots (Biorxiv link to this research). He presented data which demonstrated that plants can sense root density and alter shoot growth accordingly via root-to-shoot hormonal signalling.

Looking back to my own work, I have in the past noticed that plants accumulate less biomass when grown in small pots or not potted up quickly enough. This talk highlighted to me the importance of considering factors such as root restriction when growing plants in pots in controlled environment conditions. Moving into the field, Tom Bennett also clearly framed his work in the context of agricultural practice and crop breeding through a discussion on nutrient use efficiency.

Tom Bennett explains how root sensing impact shoot biomass. Photo @AlisonRBentley

Simon Orford, based at the John Innes Centre Germplasm Resource Unit (GRU), spoke in the ‘Phenotyping’ session. He gave an insight into the work completed in the unit and described the methods used to maximise seed viability. Having used the GRU myself during my PhD work and communicated with Simon over e-mail many times before, it was nice to finally hear him speak in person.

At the meeting a variety of other resources and tools were presented; Knetminer, CerealsDB, International Plant phenotyping network (IPPN), The Wheat Expression Browser plus more were discussed. Laura-Jayne Gardiner from IBM Research UK gave a highly interesting talk on uses of Artificial Intelligence (AI) in life sciences and agriculture. As a circadian biologist, I enjoyed hearing about the work she had completed in using AI to predict genes which show rhythmic expression patterns.


Finally, I would like to thank GARNet for awarding me the travel bursary to attend the Monogram meeting this year. I had a fantastic time and I am already looking forward to next year (meeting to be held at the James Hutton Institute)!

XV Cell Wall Meeting 2019

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Published on: July 23, 2019

By Christian Donohoe (@donohoho), University of Edinburgh

For my first conference since starting this PhD I attended the triennial XV Cell Wall Meeting, which in its latest iteration was at the University of Cambridge, with Professor Paul Dupree as the chair of the local organising committee. Along with my lab the Edinburgh Cell Wall Group and my supervisor Professor Stephen C. Fry, we came down for the week to present posters on our work and for Stephen to give a talk.

Stephen C. Fry showing Thuryya Al Hinai’s work studying  the enzymes behind fruit ripening

The meeting covers all disciplines related to plant cell wall research so there was a diverse mix of expertise in attendance, ranging from physicists studying secondary cell wall structure in poplar wood using atomic force microscopy, to geneticists over-expressing or supressing genes to uncover the effect of certain enzymes on cell wall structure. Even though I come from a mainly chemistry background this was of no hindrance as the 15-minute talks were all well designed and approachable for anyone with a scientific background.


Posters were hung and left standing all week to allow for casual browsing/lurking during lunches and coffee breaks. This relaxed ambiance carried across into the poster presentations, allowing for easy introductions and bustling halls of conversation throughout each session. I managed to engage with many posters and their presenters, mainly focusing on cell wall structure but the posters themselves were again were well written, so even the mass spec analysis posters that spared no detail were understandable when guided by the author.

Christian proudly presents his poster @donohoho

Throughout the years the meeting has been running there have been certain themes as the field has progressed, and currently it is said to be the ‘practical age’ of plant cell wall research – taking the tools and discoveries from the past 40 years and applying them in fields such as modifying cotton cell walls for physical improvements of the collected fibres, or the genetic optimisation of crop development for biofuel production. A particular highlight was from PhD student James Cowley from the University of Adelaide, looking the utilisation of seed mucilage of the plantago for better gluten-free bread.


Another highlight for me was the focus on personal workplace responsibility, equalities, and ethics that were discussed in busy well-attended sessions. Starting with Dame Professor Athene Donald and keeping pace from there, the talks covered a wide range of important issues that are usually only quietly acknowledged, and it was good to see open challenges to the biases of today people face, with clear instructions for how to help those around you. #just1action4WIS

From a early postgrad perspective, the diversity at the senior levels of research does not reflect the broad range of PhD students currently studying or graduating – by discussing these issues, putting in the time to listen, and vigilant self – criticism we can all work to improve this.

Edinburgh Cell Wall Group
Back: Marie Rapin, Ninni Nuorti, Stephen C. Fry
Front: Christian Donohoe, Thuryya Al Hinai, Lenka Frankova, Rifat Ara Bergum
Photo @donohoho

In all, it was a pleasure and a privilege to attend such a meeting, special thanks to the GARNet travel grant for helping me afford to attend the meeting. For the next meeting I am greatly looking forward to presenting my entire PhD work in 2022, when the meeting will be held in beautiful Malaga, Spain.   

John Innes Centre Gene Editing Workshop.

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Published on: July 22, 2019

Professor Wendy Harwood leads a team of researchers and technicians at the John Innes Centre who have expertise in tissue-culture based plant transformation techniques (BRACT- Biotechnology Resources for Arable Crop Transformation).

            Transformation is often considered a dark-art of plant science, as history informs that it requires an established set of protocols that have been well-tested for local experimental conditions. It takes significant time and expertise to set up an effective and reliable transformation pipeline, which is why few places around the UK undertake this type of work. These challenges can provide a significant bottleneck in the establishment of high-throughout transformation platforms.

            The BRACT expertise in transformation was aligned with gene editing technology to successfully gain UKRI-BBSRC Bioinformatics and Biological Resources Funding (BBR) funding in 2016 with a grant entitled ‘Targeted gene knockouts in crops using RNA-guided Cas9 nucleases’. Professor Harwood shares Co-I status on this grant with Dr Nicola Patron who is an expert on synthetic biology and genome editing based at the Earlham Institute.

Professor Harwood introduces the workshop. Photo @SadiyeHayta

Expanding UK capability in gene editing of crops

            This BBR funding is absolutely community-facing and included the provision for 50 genes, selected from open applications, to be targeted by CRISPR-Cas9 gene editing. Initially successful applicants would benefit from BRACT expertise in guide RNA (gRNA) design after which the optimised gRNAs and Cas9 would then be introduced into either barley or Brassica oleracea. However, the success of the BRACT service meant that over 60 genes were ultimately selected for targeted knock-out and in the second round of applications the available crops were expanded to include wheat, Brassica napus and tomato.

            This grant allowed users throughout the UK to take advantage of expertise in gene editing and transformation, which is beyond the capabilities of most individual research departments. The grant also included a requirement to provide training for new users and a training event was successfully delivered between July 10-12th at the JIC. On days 1 and 3, 12 successful applicants worked with the BRACT team to learn how to design CRISPR guides, assemble constructs, screen edited plants and perform the basics of plant transformation. In between these two days was a day of scientific talks that included talks from successful community applicants as well as updates on the latest technical developments at BRACT. The day 2 workshop was attended by 62 participants from across the UK.  The demand for training was significantly higher than the number of spaces available, with the course being 3x oversubscribed. Hopefully this may encourage the course organisers to consider running similar training events again.   


Demonstrating a clear community need.

During the two rounds of applications, researchers from 43 UK research groups across 26 institutions applied to have one or more genes of interest targeted by this resource. Due to high demand ultimately 61 genes were selected for targeting from a total of 126 requested genes. Multiple guide RNAs were designed and primary transformation conducted at BRACT before transgenic and potentially edited plants were sent out to users. The users then screen these plants for Non-homologous end joining (NHEJ)-editing events and, if needed, identified transgene-free germplasm. BRACT provided help with screening and growing on the selected plants as required.

Success Stories

            Mikhaela Neequaye presented the most complete study of those that have used the BRACT facility through this BBR funding. She works with Richard Mithen, formally from the Quadram Institute and Lars Ostergaard at the JIC on the Brassica oleracea MYB28 transcription factor, which is involved in glucosinolate biosynthesis. In collaboration with BRACT she has identified plants with edited MYB28 that show altered glucosinate levels and has even successfully gone through the onerous process of applying to DEFRA to conduct a field trial with these edited plants. An impressive output from a PhD project!

            Kate Henbest is a PhD student who works with Lorraine Williams at the University of Southampton on the challenge of developing plants with altered capacity to transport zinc. She targeting two loci encoding bZIP transcription factors in barley and had successfully identified the predicted double ‘CRISPR mutants’. In addition she also found a surprising triple mutant that also contained a mutation in a related bZIP family member. These multi-mutants were identified from a relatively small number of edited lines, which so far is a very satisfying result.

            However the appearance of the triple mutant highlights that we have an incomplete understanding of the editing events that will occur after NHEJ and demonstrate the importance of users feeding back this information to BRACT. This will allow them to build a valuable database about the particular editing events observed by users. The handful of users who presented their research at the workshop documented both small deletions as well as single nucleotide substitutions and deletions.


Growing plants can be surprisingly challenging!

            Early user feedback indicates that obtaining full-value from this BBR grant might rely on the extent of post-editing support that the BRACT team is able to provide (and how this might be financially supported). Some applicants had previously only worked with Arabidopsis, so after a successful application they will be confronted with the challenge of growing much larger (transgenic) plants that will require more space and different growth conditions. This might seem like a trivial problem but in order for the BRACT team to show that their project has been successful (in terms of follow-on publications or future grants) then this relies on end-users being able to correctly grow plants in order to obtain useful data. The BRACT team has been able to provide some advice on these issues without impinging on the time they must devote to other projects, but as is often the case, these additional requirements are often hidden time constraints that aren’t always factored into grant funding.

            Somewhat related to these issues was a talk from Gustaf Degen from Lancaster University who had received Brassica oleracea plants with edits within a gene involved in photosynthesis. His progress in this project has been delayed as all of the edited plants died during a particularly (surprisingly) hot summer in Lancaster! Fortunately, the plants were saved by returning to the original tissue-culture and although this was a fluke event, it does rather highlight that users need to be able to grow the plants that they intend to work with!

Penny Hundleby overseeing the Brassica transformation practical Photo @MarkSmedley15

Overcoming the challenges of HDR.

            Tufan Oz had recently joined the Patron lab at the Earlham Institute but gave a talk about his previous research conducted in Florida. He worked with sugarcane and had successfully targeted the acetolactate synthase (ALS) gene using homology-directed repair (HDR). He explained that sugarcane provides an excellent model for HDR as the tissue-culture transformation frequency is very high.

            One of the BRACT CRISPR-experts is Tom Lawrenson and he gave an informative update about his work aiming to undertake HDR in barley. HDR uses a ‘conventional’ gRNA/CRISPR system along with an additional DNA template with homology arms to a specific pre-selected region within the genome. Although HDR results in the insertion of a ‘foreign’ gene unlike conventional GMOs that rely on random insertion, HDR allows targeted insertion to a chosen place in the genome.

            A particular challenge of using HDR is ensuring that there is a sufficiently high quantity of the DNA template in the vicinity of the Cas9 cut site. Poor transformation frequencies will also be an impediment to this work as with fewer transformations there is less chance of obtaining a line with sufficient high levels of the template. Tom reported that overall this means that successful HDR occurs 10-100x times less efficiently than NHEJ.

            A major strength of this BBR grant is that it complements other funded work [wh(1] aiming to troubleshoot challenging protocols (such as HDR) precluding the need for replicated efforts in labs around the country. In these HDR experiments Tom is attempting to directly knock-in a N-terminal mCherry fusion and his primary advice is to ensure that you use very efficient gRNAs. Due to the low efficiency of HDR in order to obtain a correctly edited plant a researcher has the choice to either a) look at more primary transformants, b) to use a viral vector to improve expression or c) to screen a lower number of transformants over multiple generations. Tom has experimented with viral-derived components but found that this wasn’t necessary for successful HDR. As with NHEJ, the requirements for efficient HDR will vary on a plant-to-plant basis but the BRACT team are working out the basics so that the entire community will benefit from using this powerful technique in the future.


Future technologies

            The latter stages of the workshop focused on future technologies that could be of use to the community. The BRACT team discussed their recent work on:

1. Use of Cpf as an alternative to Cas9 (it doesn’t work as well in their hands)

2. On their testing of base-editing and epigenome editing techniques (work in progress)

3. Strategies to obtain multiple knock-outs from a single transformation (use different promotors to ensure even expression of all gRNAs in a single construct).

            Workshop participants were invited to suggest what they needed to improve their research using CRISPR-based technologies. The consensus amongst those few people I talked to was that more hands-on training would be very useful and that nothing is too simple to be taught. This type of training requires a significant commitment in time and space so there needs to be a community discussion around the mechanisms that could be used to enable these opportunities. CRISPR-based gene editing techniques are clearly game-changing technologies but, as with anything, without correct use they can take a lot of time for little reward.

            During discussions Professor Harwood gave a comment on the ‘Freedom To Operate’ study that they have commissioned as part of this BBR grant. This suggests that they will have no difficulty using CRISPR-based technology for projects working with academic applicants. Interestingly it was positive to learn that whereas there may be complications when they work with for-profit companies, it should be possible for those companies to use the CRISPR technology without having to pay a prohibitive licensing fee. However as the legal battles over the CRISPR-patent have not yet been resolved any opinion given in this area might be liable to change.

Relaxing after the meeting. Photo @SadiyeHayta

            The day of presentations ended in traditional John Innes Centre fashion with some locally brewed beer and wine on the terrace in the summer sun! The three-day workshop / training course then concluded for the trainees with the third day allowing hands-on experience of tissue-culture transformation techniques. Hopefully the training course participants will take this knowledge back to their home institutions in order to allow more researchers to master one of the dark-arts of plant science!

European Plant Science Retreat 2019:

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Published on: July 15, 2019

University of Nottingham, July 8th-10th 2019

By Sophie Mogg, University of Manchester. @Mini_Moggy

The European Plant Science Retreat is an annual event hosted by PhD students for PhD students.

The fact that this event was orchestrated by my own peers was simply amazing and a feat not to be sniffed at.  As any PhD student knows, sometimes walking into those big society-led conferences can be daunting and even more so when you want to approach those in your field.

However, at the EPSR, it was a level playing field allowing for a more easy-going approach to networking – especially as those we were talking to could be potential collaborators in the near future.

The Organising Team!

The three days of proudly presented research was arranged in a series of talks and poster sessions to open the floor to like-minded students. Somewhat unusually only a few hours over the whole conference was dedicated to more experienced keynote speakers. This for me is what made the conference. Both new and more experienced PhD students were able to interact, share ideas and advice and feel free to ask questions that otherwise might not have been asked in a more ‘serious’ setting.

The keynote speakers themselves made quite the contribution, sharing with us their journey from being PhD students to their current revered positions! It was important for us to learn that each journey was DIFFERENT. What stuck with me was that there was no necessity to jump ship to another country, or even publish a single paper, in order to gain a post doc position.

Therefore as long as you persevere, remained passionate and show your worth, many doors will remain open for your future! It was great to hear their love for science in their voices as they told their tales.


Speaking with others at the conference, my experience wasn’t unique and I didn’t hear a single negative comment, no doubt owing to the great organisation and planning done by the EPSR2019 team.

Sadly, this was my first and only European Plant Science Retreat, but I hope that the tradition continues for many years, allowing students from across Europe to practice their networking skills, present their research and have a all round great experience at a conference designed especially for them.

Jason and Marty, part of the EPSR2019 team, offered words of wisdom for the 2020 organising team. They highlighted that although it may seem like a giant undertaking, especially in terms of sourcing funding from sponsors, that the entire team had improved their organisation and team-work skill sets, giving them invaluable experience that they will undoubtedly make use of in the future.

Finally they advised to keep it light and enjoy it! Because how often do you get to organise a conference?

Meeting attendees in the University of Nottingham Millennium Garden

Meeting Report from ICAR2019

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Published on: July 11, 2019

Gina Garzón Martínez, Aberystwyth University

Four days full of knowledge, innovative research, interesting culture this is what summarizes my time at the ICAR2019, Wuhan, China.

Thanks to the Gatsby foundation and GARNet, I had the opportunity to attend the ICAR2019 conference in Wuhan, China. The meeting was hosted by the Huazhong Agricultural University-a partnership University which I also managed to visit during my stay in Wuhan.

Mornings at ICAR2019 started with a plenary sessions leading by scientists from Asia, Australia, USA and Europe who delighted us with their latest work in Arabidopsis. In particular, I found interesting a plenary session called “From Models to Crops”, where Barry Pogson from Australia showed us the importance of translational genetics. As an example, he showed us drought stress regulators discovered in Arabidopsis that also play a role in a range of crop plants such as wheat.

Barry Pogson gave a fantastic talk!

Every afternoon, there were concurrent sessions and more interesting talks given by PI researchers and early career scientists from all around the world. Of particular interest to me were the talks on the use of Arabidopsis to elucidate biotic and abiotic interactions. As an example, Lin Li from Fudan University gave a good talk about how the transcription factor PHY7 is involved in shade avoidance response when plants compete with their neighbours. Also, Ling Li from Mississippi State University shared with us her work in a starch gene with great potential to improve protein and disease resistance in other crops such as rice, soybean and corn, using innovative strategies.

Poster Session

At the end of the day, there was a poster session and a range of different workshops. I really enjoyed the workshop called “Communicating your science to the broader community” organized by Isabel Mendoza (Global Plant Council) and including Geraint Parry (GARNet) and Mary Williams (ASPB). This workshop gave me ideas of how I can increase the impact of my work by using social media and how to share my work not only to the scientific community but also to the regular public. Thanks to this workshop I gained more encouragement to be more active in social media, considering the importance of sharing my work with others at this stage of my PhD.

I really encourage all PhD students to not miss this kind of opportunities of networking, learning, sharing your work, along with having a cultural experience and making friends from other parts of the world. Next year, ICAR2020 will be held in the USA, followed by Belfast, UK in 2021, so I already recommend you to book some time off in your calendar and prepare for another productive and exciting week of science!

Gina with her poster

GARNet Research Roundup: July 5th 2019

This edition of the GARNet research roundup begins with a study from the University Leicester that investigates the rate of selection of genes expressed in Arabidopsis pollen.

The second and third papers focus on the function of members of the AP2 family of transcription factors. Sarah McKim’s lab in Dundee characterizes the role of APETALA2 during barley stem elongation whilst the other paper investigates the function of the Arabidopsis PUCHI gene and includes co-authors from the University of Nottingham.

The fourth paper is from Lars Ostergaard’s lab at the John Innes Centre and demonstrates the benefit of using models to understand developmental processes in crop plants. The next paper from the University of Glasgow investigates the plant response to low fluence rates of UV-B light.

The penultimate paper features authors from Oxford Brookes University and characterizes a novel LINC-KASH protein in maize whilst the final paper is from the University of Cambridge and investigates the novel function of two members of DUF579 family in methylation of glucuronic acid residues.


Harrison MC, Mallon EB, Twell D, Hammond RL (2019) Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection. Genome Biol Evol. doi: 10.1093/gbe/evz127

Open Access

This research from Hammond and Twell lab’s at the University of Leicester uses Arabidopsis to investigate the hypothesis that pollen genes evolve faster than sporophytic genes. This study is challenging to perform in Arabidopsis as for the past million years the plant has been self-compatible, which causes reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. This study has two main findings: firstly prior to becoming self-compatible pollen genes evolved faster than sporophytic genes. Secondly, since becoming self-compatible selection has relaxed causing higher polymorphism levels and a higher build-up of deleterious mutations.


Patil V, McDermott HI, McAllister T, Cummins M, Silva JC, Mollison E, Meikle R, Morris J, Hedley PE, Waugh R, Dockter C, Hansson M, McKim SM (2019) APETALA2 control of barley internode elongation. Development. doi: 10.1242/dev.170373

Open Access

Vrushali Patil leads his study from the lab of current GARNet committee member Sarah McKim at the James Hutton Institute in Dundee. They show that the APETALA2 (AP2) transcription factor is necessary for stem elongation in Barley. In addition they demonstrate that AP2 expression is controlled by the activity of the microRNA mi172 as well as jasmonate signaling.

https://dev.biologists.org/content/146/11/dev170373.long

Trinh DC, Lavenus J, Goh T, Boutté Y, Drogue Q, Vaissayre V, Tellier F, Lucas M, Voß U, Gantet P, Faure JD, Dussert S, Fukaki H, Bennett MJ, Laplaze L, Guyomarc’h S (2019) PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1906300116

Julien Lavenus, Ute Voß and Malcolm Bennett from University of Nottingham are co-authors on this French-led study that investigates the mechanism by which the AP2 family transcription factor PUCHI controls lateral root development. By performing a transcriptional analysis of developing lateral root cells they show that genes involved in very long chain fatty acid (VLCFA) biosynthesis enzymes are induced in a PUCHI dependent manner. Concomitantly they show puchi-1 mutant roots have reduced VLCFA content when compared with wildtype roots. They conclude that PUCHI regulates VLCFA biosynthesis as part of a pathway controlling cell proliferation during lateral root formation.


Stephenson P, Stacey N, Brüser M, Pullen N, Ilyas M, O’Neill C, Wells R, Østergaard L (2019) The power of model-to-crop translation illustrated by reducing seed loss from pod shatter in oilseed rape. Plant Reprod. doi: 10.1007/s00497-019-00374-9

Open Access

Pauline Stephenson and Lars Østergaard at the John Innes Centre lead this study in which they demonstrate that lessons learnt from understanding the genes involved in fruit ripening in Arabidopsis lead to an ability to adjust the pod-opening process in oilseed rape. They have combined two mutant alleles, first characterized in Arabidopsis, to develop OSR plants that have significantly increased yield. In addition they present a new software tool for the analysis of pod shatter data in other crops plants.


O’Hara A, Headland LR, Díaz-Ramos LA, Morales LO, Strid Å, Jenkins GI (2019) Regulation of Arabidopsis gene expression by low fluence rate UV-B independently of UVR8 and stress signaling. Photochem Photobiol Sci. doi: 10.1039/c9pp00151d

Open Access

This UK-Swedish collaboration is led by Andrew O’Hara from the Jenkins lab in the University of Glasgow. They continue the lab focus on the UV-B receptor UVR8, in this case performing a transcriptomic analysis of wildtype and uvr8 mutants grown under low UV-B fluence rates. They analyse one differentially expressed gene in more detail, the transcription factor ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 13 (ANAC13), which was induced by UV-B but by the activity of any other photoreceptor.


Gumber HK, McKenna JF, Tolmie AF, Jalovec AM, Kartick AC, Graumann K, Bass HW (2019) MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation Nucleus. doi: 10.1080/19491034.2019.1629795

Open Access

Hardeep Gumber is first author on this US-led study that includes Joe KcKenna, Andrea Tolmie and Katja Graumann from Oxford Brookes as co-authors. They characterise the Maize LINC KASH AtSINE-like2 protein, MLKS2, whose targeting to the nuclear periphery requires its N-terminal armadillo repeats. Mutant mlks2 plants have pleiotropic plant phenotypes and on a nuclear level show defects in chromosome segregation and positioning. These findings support a model in which cytoplasmic actin is linked to chromatin through the LINC-KASH nuclear envelope network.

https://www.tandfonline.com/doi/full/10.1080/19491034.2019.1629795

Temple H, Mortimer JC, Tryfona T, Yu X, Lopez-Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct. doi: 10.1002/pld3.117

Open Access

Henry Temple is first author on this work from the University of Cambridge that characterizes two members of the DUF579 family (AGM1 and AGM2). These proteins are required for 4-O-methylation of glucuronic acid within highly glycosylated arabinogalactan proteins (AGPs).


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