Monogram 2019 by Laure Forquet

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Published on: May 29, 2019

Monogram 2019 was my first conference attended as part of my master degree final year internship at NIAB. As it was my first conference, I was very excited to meet the UK cereal research community.

Being very new to wheat research and having focused mainly on model plants like ​Arabidopsis thaliana so far, I really enjoyed having such a complete overview of wheat research in the UK and abroad.
The talks were organized in clear sessions making the whole conference a lot easier to follow and connect between the talks.


The wide diversity of subjects covered was eye-opening. I was very interested in the bioinformatics session which opened the conference on the first morning as it relates to my project in quantitative genetic. It introduced me to the brilliant tools that are available for wheat genetic research such as the resources from the Designing Future Wheat program.

The plenary talk from Keith J. Edwards from the University of Bristol was a very nice introduction to the conference and was a good reminder of wheat hybridization history. He offered some new insight into the origin of the genetic variation in bread wheat resulting from the unaware side-by-side cultivation of the newly hybridized hexaploid wheat with the tetraploid wheat.

Opening keynote from Keith Edwards. Photo: @GuilleMendiondo

I also really enjoyed discovering about other subjects further away from my domain such as the quality and nutrition session. I especially liked the talk from Alison Lovegrove from Rothamsted Research. She presented insights on the way to improve the quality of cereals to increase the health benefits, with a focus on white versus brown rice. Brown rice has a higher quality for health but is not very popular with consumers who prefer the taste of white rice. Increasing the nutrient and fiber content and lowering the glycemic index of white rice, without altering the taste, would help improve global health, notably by reducing the risk of type 2 diabetes.


I was given the opportunity to present a poster on my project at NIAB on flowering time in wheat during the poster session. I enjoyed discussing the subject with other researcher and receiving outside perspective, advice and feedback. It was also a great occasion to have one-to-one conversation with the other people presenting their posters.

At the end of the second day there was a very interesting panel discussion covering the challenges that the breeding community. The panel discussed their points of view between and took questions from the audience.

Panel discussion. Photo @HuwJonesLabour

The conference was overall pretty intense so I really appreciated the opportunity to interact and meet professional researchers and students during the tea breaks, lunches and the formal conference diner.

I am very grateful to GARNet for offering me a travel grant to attend this exciting event and I hope I will be able to return next year to have updates on all these inspiring projects and meet the community again. I would recommend any students or early career researchers interested in cereals to go to the annual Monogram meeting!

GARNet Research Roundup: May 27th 2019

This bumper edition of the GARNet research roundup begins with a set of papers from the John Innes Centre. Anne Osbourn’s group is involved with two papers; firstly they discover how altering metabolic networks in the Arabidopsis root can cause changes in the associated microbiota. Second they characterise the role of a light-induced transcription factor in Artemisia. Next Caroline Dean’s group leads a global consortium that investigates the role of liquid-liquid phase separation in the formation of nuclear bodies. The final paper from the JIC is from Philippa Borrill and Cristobal Uauy, in which they identify novel transcription factors in wheat.

The fourth paper is led by Peter Etchells at Durham and characterises receptor kinase activity involved in vascular patterning in Arabidopsis.

The next two papers focus on stomatal patterning; firstly Julie Gray’s group at Sheffield looks at the stomatal responses to long-term pathogen infections. The second paper is from Glasgow and describes improvements in the OnGuard2 software, which models the factors controlling stomatal density.

Jose Gutierrez-Marcos is a co-author on a paper that uses FACS/ATAC-seq to define chromatin changes within cells of the shoot apical meristem. Richard Harrison leads the next paper that is also method-focused; describing use of CRISPR-Cas9 gene editing in Strawberry.

Andrew Miller at the University of Edinburgh is the corresponding author of the penultimate paper, which presents a whole-life-cycle, multi-model Framework that links many aspects of the Arabidopsis life cycle. The final paper is Seth Davies’s group at York and investigates the role of sucrose in the control of the circadian clock.


Huang AC, Jiang T, Liu YX, Bai YC, Reed J, Qu B, Goossens A, Nützmann HW, Bai Y, Osbourn A (2019) A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science. doi: 10.1126/science.aau6389

Ancheng Huang and Ting Jiang are first authors on this UK, Chinese and Belgian collaboration led by Anne Osbourn at the John Innes Centre. They reconstitute three biosynthesic pathways in the Arabidopsis roots and show how this affects the associated microbiota.


Hao X, Zhong Y, Nützmann HW, Fu X, Yan T, Shen Q, Chen M, Ma Y, Zhao J, Osbourn A, Li L, Tang K (2019) Light-induced artemisinin biosynthesis is regulated by the bZIP transcription factor AaHY5 in Artemisia annua. Plant Cell Physiol. doi: 10.1093/pcp/pcz084

Anne Osbourn is a co-author on this Chinese-led study that has identified that the basic leucine zipper transcription factor (TF) AaHY5 regulated of light-induced biosynthesis of artemisinin in Artemisia annua.


Fang X, Wang L, Ishikawa R, Li Y, Fiedler M, Liu F, Calder G, Rowan B, Weigel D, Li P, Dean C (2019) Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes. Nature. doi: 10.1038/s41586-019-1165-8

Xiaofeng Fang, Liang Wang and Ryo Ishikawa are first authors of this UK, German and Chinese collaboration led by Caroline Dean’s lab at the John Innes Centre. They characterise the molecular factors that are required for the formation of nuclear bodies through liquid-liquid phase separation (PDF). These proteins are the Arabidopsis RNA-binding protein FCA and the coiled-coil protein FLL2.

From https://www.nature.com/articles/s41586-019-1165-8

Borrill P, Harrington SA, Simmonds J, Uauy C (2019) Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling. Plant Physiol. doi: 10.1104/pp.19.00380

Open Access

Philippa Borrill, now a faculty member at the University of Birmingham, conducted this work with Cristobal Uauy at the John Innes Centre. They have developed a range of research tools for use in wheat and this paper describes the identification of novel transcription factors involved in senescence.


Wang N, Bagdassarian KS, Doherty RE, Kroon JT, Connor KA, Wang XY, Wang W, Jermyn IH, Turner SR, Etchells JP (2019) Organ-specific genetic interactions between paralogues of the PXY and ER receptor kinases enforce radial patterning in Arabidopsis vascular tissue. Development. doi: 10.1242/dev.177105

Ning Wang works with Peter Etchells at Durham University where they have characterised the interactions between the receptor kinase gene families that regulate radial patterning in the development of vascular tissue.


Dutton C, Hõrak H, Hepworth C, Mitchell A, Ton J, Hunt L, Gray JE (2019) Bacterial infection systemically suppresses stomatal density. Plant Cell Environ. doi: 10.1111/pce.13570

Christian Dutton leads this work conducted at the University of Sheffield. They have investigated the longer-term systemic response to the presence of pathogens that involves reducing stomatal density. This process is mediated via salicylic acid signaling and slows disease progression.

From https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13570

Jezek M, Hills A, Blatt MR, Lew VL (2019) A constraint-relaxation-recovery mechanism for stomatal dynamics. Plant Cell Environ. doi: 10.1111/pce.13568

Mareike Jezek leads this work from the University of Glasgow in which they have updated the OnGuard2 modelling software that has demonstrated substantial predictive power to describe stomatal dynamics. Their improvements allow for the development of models that are more similar to in vivo observations.


Frerichs A, Engelhorn J, Altmüller J, Gutierrez-Marcos J, Werr W (2019) Specific chromatin changes mark lateral organ founder cells in the Arabidopsis thaliana inflorescence meristem. J Exp Bot. doi: 10.1093/jxb/erz181

Jose Gutierrez-Marcos from the University of Warwick is a co-author on this German study led by Anneke Frerichs in which they analysed the chromatin state of lateral organ founder cells (LOFCs) in the peripheral zone of the Arabidopsis inflorescence meristem in wildtype and apetala1-1 cauliflower-1 double mutants. Importantly they showed that the combined application of FACS/ATAC-seq is able to detect chromatin changes in a cell-type specific manner.


Wilson FM, Harrison K, Armitage AD, Simkin AJ, Harrison RJ (2019) CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry. Plant Methods. doi: 10.1186/s13007-019-0428-6. eCollection 2019

Open Access

This paper is lead by Fiona Wilson at NIAB-EMR in which they present their methods to undertake gene editing in the challenging experimental system of diploid and octoploid strawberries.

From https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0428-6

Zardilis A, Hume A, Millar AJ (2019) A multi-model framework for the Arabidopsis life cycle. J Exp Bot. doi: 10.1093/jxb/ery394

Open Access

Argyris Zardilis conducted this modeling-focussed research at University of Edinburgh. The authors present a whole-life-cycle, multi-model Framework that links vegetative, inflorescence as fruit growth as well as seed dormancy in Arabidopsis. This Framework allows the authors to simulate at the population level in various genotype × environment scenarios.

From https://academic.oup.com/jxb/article/70/9/2463/5336616

Philippou K, Ronald J, Sánchez-Villarreal A, Davis AM, Davis SJ (2019) Physiological and Genetic Dissection of Sucrose Inputs to the Arabidopsis thaliana Circadian System. Genes (Basel). doi: 10.3390/genes10050334

Open Access

Koumis Philippou from Seth Davis’ research group the University of York leads this work that investigates the role of sucrose into the function of the circadian clock.

Monogram 2019 by Emily Marr

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Published on: May 22, 2019

Emily Marr, NIAB and the University of Cambridge, ecm53@cam.ac.uk

After hearing scientists at NIAB (Cambridge) wax lyrical about Monogram year on year, I finally attended the conference this April, in the third year of my PhD. Monogram is an annual meeting for the small-grain cereal and grass research community, bringing together academics, commercial scientists and plant breeders. This year, it seemed that there were more presenters from Universities than previously; it is encouraging to see the University community becoming more engaged in the food system at a time when Food Security is a growing issue.


Monogram 2019 was held on the Jubilee Campus of the University of Nottingham, which – aside from the unexpected shattering of a glass window in the café (it couldn’t contain its excitement about Monogram) – proved to be a fantastic venue with excellent green credentials boosted by on-site lakes used for heating and cooling systems, solar panels and green roofs.

The meeting kicked off with a Bioinformatics session, an area that plays a significant role in the development of the agricultural sector. We received an overview of the genetic resources available for cereals online and a reminder that although new resources are constantly emerging, we must not forget the old resources, which can be just as useful.

The meeting continued with eight sessions: Below and Above Ground Processes, Phenotyping, Abiotic and Biotic Stress, Reproduction and Grain Development, Genomics and Technologies for Crop Improvement, Future Plant Sciences, Quality & Nutrition, Rice and Other Grasses.


The first day ended with a poster session, accompanied by wine and a BBQ. With a total of 76 posters, there was a lot to talk about. Topics ranged from molecular-scale research to large-scale phenotyping.

Poster session in full flow. Photo from @BazRaubach

From a personal point of view, the poster session catalysed a meeting with someone whose previous PhD student had worked with the same wheat mapping population as me, investigating a similar phenotype as the one I am focusing on. It was a fantastic to have the opportunity to compare results.


As a root researcher, I was particularly tuned into the talks on roots which featured heavily in the session entitled “Below and Above Ground Processes”. Root system architecture, the spatial configuration of roots in the soil, has often been overlooked in crop breeding due to the challenge of phenotyping organs below ground. However, it is becoming more of a hot topic as roots represent a target for improving the ability of crops to maintain high yield in spite of increasing exposure to drought. We heard from Vera Hecht about the impact of sowing density on root traits in barley from a phenotypic point of view. Linking in to this, Tom Bennett talked about the root density-sensing system in wheat as a means to regulate root and shoot growth. Silvio Salvi talked us through the role of mutant screens and bulk segregant analysis in providing information about position and effect of QTLs affecting root genetic variation.

Silvio Salvi on roots. Photo from @GuilleMendiondo

Richard Whalley focussed on the interaction of soil architecture and deep rooting while Alek Ligeza turned his attention to the relationship between roots and nitrogen uptake.

Overall it was a highly engaging conference that I highly recommend to anyone working with cereals. [Next year’s meeting will be at the James Hutton Institute- Ed].

TRAINING EVENT: TARGETED GENE KNOCK-OUTS IN CROPS USING RNA-GUIDED CAS9

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Published on: May 14, 2019

10 – 12TH JULY 2019 AT THE JOHN INNES CENTRE

The course will run from 09.00 on Wednesday 10th July to 15.00 on Friday 12th July 2019.

Accommodation will be provided for participants for 3 nights from 9th July to 11th July inclusive.

Meals during the course will be provided but participants will be responsible for their own travel costs and evening meals.

In the event of the course being over-subscribed, the project steering committee will select participants based on the statements submitted.

Please contact wendy.harwood@jic.ac.uk should you require further details.

https://www.jic.ac.uk/genomic-enabled-technologies/

Annual meeting of the UK Rice Research Consortium

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Published on: May 8, 2019

University of Nottingham: May 2nd-3rd 2019.

As you can read elsewhere on the GARNet blog, the Monogram Network consists of UK based researchers with an active interest in small grain cereals and grasses. Although this encompasses a range of different plant species, over recent years the Monogram annual meeting has focused on world-leading UK research in barley and wheat. In addition each meeting usually include at least a half-day session focused on UK research on other plants such as rice or brachypodium.

However a small group of researchers is actively looking to build the UK Rice Research community. Over the past two years the BBSRC has supported a two-day meeting aimed at community-building and exploring the potential for resource development in the UK within this research area.


This years UK Rice Research Consortium meeting was held at the end of Monogram2019 at the University of Nottingham. This arrangement was successful in persuading the group of PIs to stay on and contribute to this community-building exercise.  The meeting was led by Ari Sadanandom  from Durham University and Erik Murchie at the host institution.

When you do some research it is clear that there is a surprising high amount of rice-focused research already happening in the UK. This ranges from the large groupings in (perhaps surprisingly) Aberdeen, Sheffield and NIAB (PDF) through to smaller individuals pockets around the country . The UK Rice Research Consortium website (http://ukrrc.org/) is managed by Andy Jones at the University of Liverpool and is becoming a growing repository of information about UK-focused activities.

Arguably the biggest road-block to building this community is that rice cannot be grown in the field in the UK (at least not before significant climate change :/) and is therefore not a significant contributor to UK agriculture. However throughout the meeting it was clear that all attendees considered that the main internationally recognised strength of UK Rice research is in answering fundamental questions in plant biology. This strength will be key in the development of new varieties in collaboration with overseas institutions who have the capacity to undertake large field trials.


The meeting was split into two main phases: Firstly a set of speakers gave a global perspective on the current status of rice research. Rod Wing from the University of Arizona outlined his collaborations that have recently sequenced 3010 diverse accession of rice. This highlights that the diploid Oryza sativa genome (430Mb) is a more manageable size when compared to bread wheat (14.5Gb)! However even with the enormous amount of genome information the impression that came across from the meeting was that there currently a lack of joined-up thinking when it comes to the provision of genomic resources that will bring together this vast amount of information.

To show what can be possible in this regard, Cristobal Uauy from the John Innes Centre presented the remarkable progress that the global wheat community has made in the generation of resources and in acceptance of a genomic assemblies and annotations. With some planning the UK rice research community should be able to take an international leadership role in the development of equivalent rice resources.

Cristobal updates the progress of the wheat commuity.

Usha Vijayraghavan (Indian Institute of Science, Bangalore) and Xinguang Zhu (Chinese Academy of Sciences) provided an introduction to their fundamental research in rice that has looked at floral development or in making improvements in photosynthesis respectively. Usha has taken knowledge from the genes identified in Arabidopsis to understand how they function during the development of branched inflorescence meristems in rice (JXBot paper). Xinguang and his colleagues in the RIPE and eRice projects have targeted a range of strategies to enhance photosynthesis, which have resulted in remarkable improvements of up to 15% in field trials.

Ajay Kohli on the myriad challenges to rice production

The final international talk was from Ajay Kohli at the International Rice Research Institute (IRRI) who highlighted that ‘everyone wants rice’ and the importance of including social considerations in any global strategies to advance the sustainability of more efficient rice varieties that can be used by small holders across Asia. Kohli proposed that the UK community can link with IRRI by contributing both upstream (by developing fundamental knowledge) and downstream (by providing mechanistic understanding for newly bred varieties) discoveries.

Ajay Kohli reports that everyone wants rice!

In the second phase of the meeting, Sadanandom and Murchie led a series of group discussions that had the aim of developing a roadmap for UK rice research. Overall the strengths of UK rice research are in fundamental areas of discovery, in the excellence of genomic resources, within a collaborative outlook to research and in community-facing transformation resources. The challenges include the actual growth of the plant and therefore in persuading funders of the importance of supporting something that is not currently a large portion of the UK research portfolio.

However the UK Rice Industry is significant, according to both The Rice Association and more anecdotally from the public enjoyment of curry! Clearly there is potential for interactions between local and international agri-tech companies and the UK research community; both in the support of studentships or in providing space for downstream field trials.


Overall this second UK Rice Consortium meeting was an extremely positive experience and there is significant motivation to grow the community. Importantly UK researchers already have major overseas collaborators that support their research and the production of a ‘Rice Roadmap’ will define the future direction of the community.

The UKRRC group. Photo from @HuwJonesLabour

Watch out for updates on the Consortium website and on social media at #UKRiceResearch and @ukrrc.  The 2020 meeting will be hosted at Rothamsted Research.

Monogram 2019

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Published on: May 8, 2019

By Sophie Harrington at the John Innes Centre

This year I attended the UK Monogram conference for the third and final time in my PhD. It was a pleasure to have another opportunity to engage with the UK small grains community, both with the academics and the breeding companies that attend.

The conference opened with a brilliant plenary talk by Professor Keith Edwards from the University of Bristol, sharing his thoughts on the origin of variation within Triticum aestivum, hexaploid bread wheat. His talk highlighted the continuation of hybridisation between hexaploid wheat and its tetraploid parents as a result of mixed cultivation. The impacts of this hybridisation can still be seen in the genomes of hexaploid wheat varieties today.

Sophie giving her MECEA award talk. From @malcolmacaulay

This theme of natural genetic variation continued to thread throughout the conference, with the importance of tapping into the diversity present in landraces and wild wheats highlighted during a panel discussion session on the second day. A particularly intriguing example of variation in the grasses was discussed by Dr. Luke Dunning, when he spoke about the evidence for lateral gene transfer in the grasses. This was quite a different method for obtaining variation in grasses compared to what had previously been discussed in the conference and naturally the resounding question in the audience following his talk was how exactly such lateral gene transfer could occur! I’m sure many people are looking forward to hearing what comes out of this story in the future.

Monogram this year also had a substantial focus on methods and platforms that we can use to increase the quality and utility of our data. From the very first session, exploring the bioinformatics tools available for the cereals, it was clear that within the past few years a substantial leap in the quality and quantity of informatics tools available for wheat and barley has occurred. It was thrilling to hear of the large new datasets available for the public, from the wheat transcriptome through to the so-called barley “variome.” Moving beyond bioinformatics, we were also exposed to the potential of using machine learning in our research, as Dr. Laura-Jayne Gardiner from IBM Research highlighted the many biological and agricultural projects in which IBM has successfully applied machine learning technology. This seems to be an area that has substantial potential to tap into the hidden value of the large datasets being developed particularly in cereal genomics.

Of course, without studying the plants themselves it can be difficult (if not impossible) to turn genomic data into biologically relevant information. To that end, the discussion of new phenotyping platforms and consortiums, such as the EU-funded EMPHASIS project, highlighted new ways to increase the throughput and fidelity of phenotyping data.

The importance of establishing a framework for data labelling and curation was also highlighted.

Overall, the 2019 Monogram conference was an excellent opportunity to hear about the cutting-edge research in cereals taking place in the UK and abroad. I was thrilled to have the opportunity to attend with a GARNet travel bursary, and to receive the Monogram Early Career Award for a PhD researcher. I’m already looking forward to next year!

Plant responses to environmental stimuli: differences, similarities and crosstalk

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Published on: May 3, 2019

4th – 6th September, 2019, Glasgow, Scotland, UK

From Maria Papanatsiou (University of Glasgow)

This conference offers a holistic view on how plants respond to the environment and provides delegates with an opportunity to appreciate the wider context of their research. Marking the 40th anniversary of Plant, Cell & Environment the symposium will be a celebration of plant physiology. We offer delegates an impressive line-up of speakers and tutors who will share with you their research and expertise at the forefront of modern plant physiology.

The aim is not only to introduce a new generation of plant scientists to the breadth and importance of modern plant physiology but also to motivate scientists with a more molecular focus to embrace plant physiological techniques and embed their findings into a physiological context.

Several workshops will allow participants to explore essential physiological techniques (gas exchange measurements) as well as software for phenotyping (root system architecture) and modelling (guard cell models). Our tutors are experts in their fields and will be able to discuss your specific needs.

The training aspect of this symposium is further enhanced by science writing workshops. These small-group sessions led by experienced editors will allow the participants to discuss how to best organise and present their research in a paper and improve writing skills.

To foster communications the delegate number will be limited to 100. Early registration is therefore recommended.

https://www.wileypcesymposium.com/

Organisers:

Anna Amtmann & Mike Blatt, Glasgow, UK

Supported by Wiley.

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