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.
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.
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!
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.
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.
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.
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.
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
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.
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].
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.
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.
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.
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!
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.
Over the past thirty years the Multinational Arabidopsis Steering Committee (MASC) has represented the global Arabidopsis community through its collaborative oversight of the annual International Conference on Arabidopsis Research (ICAR), production of a MASC annual report and preparation of the series of decadal Roadmaps that have helped coordinate the future activities of the community. In[…]
https://meetings.embo.org/event/20-plant-systems This EMBO Workshop on international Plant Systems Biology (iPSB) is the central gathering of plant systems biology researchers from across the world. Climate change poses unique challenges for how to feed and power humanity without further degrading the environment. Plant science therefore is a key discipline in meeting the challenge of adapting food and[…]
The spring season of #UKPlantSciPresents begins on January 12th and we have a strong schedule set until the end of April! Each webinar is at Tuesday afternoon at 3pm GMT (or BST)! Registration is free and webinars will be made freely available soon after the event. Although closed captioning/subtitles are not available for live webinars,[…]
The previously awesome #GARNetPresents webinar series is morphing into the #UKPlantSciPresents webinar series. This series has the aim of promoting plant science excellence across the UK! UK plant science research uses many different experimental organisms such as Arabidopsis, Wheat, Brassicas, Brachypodium, Marchantia, Physomitrella and many others. This webinar series is supported by both GARNet and[…]
Contents: – Society Updates– Introducing Quantitative Plant Biology– Congratulations to Ottoline Leyser– Conference Updates– Bacterial Plant Diseases Programme– Introducing CHAP– Twenty Years of GARNet– GARNet Research Roundup– MASC Publication Update– Plant RNA Interactome Capture– Update on new BBSRC Projects– Spotlight on University of Nottingham Download here: https://www.garnetcommunity.org.uk/sites/default/files/newsltr/GARNish33_Online_Final_0.pdf
Marcel Bach-Pages works with Gail Preston at the University of Oxford and we discuss a new protocol to identify the RNA-Binding Proteome from Arabidopsis leaves. This community-focused work includes full instructions for use of the protocol and they provide an accessible list of proteins that they have identified. This research is published in Biomolecules and[…]
This edition of GARNet Research Roundup begins with a remarkable four papers that include work from Caroline Dean’s lab at the John Innes Centre. The first two papers are collaborations with members of Martin Howard’s lab and look at the molecular mechanisms that control long-term cold sensing or the antisense regulation of FLC respectively. The[…]
Christos Velanis works at the University of Edinburgh and discusses work published in PloS Genetics entitled ‘The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)‘. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/07/Velanis_edit-13072020-09.32.mp3Pumi Perera is co-first author on this work from the Goodrich lab that[…]
This has been a challenging time for both conference organisers and conference venues. Most 2020 plant science conferences have cancelled, postponed or majorly changed their events. Below is a non-exhaustive list of the changes that have been made to different conferences. Up to date as July 6th 2020. (download)
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