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.

NIAB Wheat-Rice Transformation Resource: Open for Applications

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Published on: April 30, 2019

THE COMMUNITY RESOURCE FOR WHEAT AND RICE TRANSFORMATION is a resource for UK plant scientists to apply for their genes to be transformed into wheat or rice free of charge, funded by the BBSRC’s Biological and Bioinformatic Resources fund (BBR).

THE CURRENT ROUND OF THE APPLICATION PROCESS IS OPEN UNTIL 24TH JUNE 2019, for transformation slots in the autumn. There is an online application form via the following link:

http://www.niab.com/transgenic

Further details are available on the website, and enquiries should be directed to croptransformation@niab.com in the first instance.

One hundred novel genes will be tested during the course of this five year project, selected with help from an external project advisory group comprised of researchers, industry members and stakeholders.

We anticipate that half of the project capacity will be used by scientists working with model species such as Arabidopsis thaliana or
Brachypodium distachyon, in order to find new sources of genes and to encourage and support the scientists to test them in wheat and rice.

The project also provides capacity to characterise 50 regulatory elements in wheat and rice. Promoter and terminator sequences will be included for their expression in a wide range of tissue types.

Researchers can either nominate promoters to be included in this project. Further details are again available on the website.

DR. EMMA WALLINGTON CROP TRANSFORMATION PROGRAMME LEADER

NIAB, HUNTINGDON ROAD, CAMBRIDGE CB3 0LE
Tel (direct) +44 (0)1223 345001

EMAIL EMMA.WALLINGTON@NIAB.COM

John Christie talks to GARNet

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Published on: April 29, 2019

John Christie discusses a recent paper just published in Plant Physiology entitled ‘De-etiolation Enhances Phototropism by Modulating NON-PHOTOTROPIC HYPOCOTYL 3 Phosphorylation Status‘.

GARNet Research Roundup: April 29th 2019

This edition of the GARNet research roundup features fundamental plant science research conducted in a range of experimental organisms. Firstly Liam Dolan’s lab in Oxford looks at the function of bHLHs proteins in cell differentiation across land plant evolution. Secondly Anthony Hall’s group at the Earlham Institute have identified a novel RecQ helicase involved in work exclusively conducted in wheat. Thirdly researchers from Nottingham work with Arabidopsis to characterise an EXPANSIN protein essential for lateral root development.

The fourth paper is the first of two that look at germination and uses a new model, Aethionema arabicum, to study the role of light in seed dormancy. This work includes research from Royal Holloway. The second ‘dormancy’ paper is from Peter Eastmond’s lab at Rothamsted and further characterises the DOG1 gene in Arabidopsis. The penultimate paper includes co-authors from Warwick and Leeds and introduces a novel chemical inhibitor of auxin transport. The final paper from researchers in Birmingham introduces the 3DCellAtlas Meristem, a powerful tool for cellular annotation of the shoot apical meristem.


Bonnot C, Hetherington AJ, Champion C, Breuninger H, Kelly S, Dolan L (2019) Neofunctionalisation of basic helix loop helix proteins occurred when embryophytes colonised the land. New Phytol. doi: 10.1111/nph.15829 https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15829

Clemence Bonnot is lead author on this study from Liam Dolan’s lab at the University of Oxford in which the authors assess the role of ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes during evolution of plant development. They look at the function of a member of this bHLH transcription factor family called CbbHLHVIII identified in the charophyceaen alga Chara braunii. This gene is expressed at specific morphologically important regions in the algae and cannot rescue the function of related RSL genes in Marchantia or Arabidopsis. This suggests that the function of RSL proteins in cell differentiation has evolved by neofunctionalisation through land plant lineages.


Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A (2019) Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol. 20(1):69. doi: 10.1186/s13059-019-1675-6 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1675-6

Open Access

Laura Gardiner and Anthony Hall lead this work that was conducted at the Earlham Institute and uses a bespoke set of bioinformatic tools that allow fundamental questions to be asked in hexaploid wheat. They looked at crossover and gene conversion frequencies in 13 recombinant inbred mapping populations and were able to identity an important QTL and confirm functionality for a novel RecQ helicase gene. This gene does not exist in Arabidopsis and therefore this discovery-motivated research needed to be conducted in wheat. They hope that this identification will provide future opportunities to tackle the challenge of linkage drag when attempting to develop new crops varieties.


Ramakrishna P, Ruiz Duarte P, Rance GA, Schubert M, Vordermaier V, Vu LD, Murphy E, Vilches Barro A, Swarup K, Moirangthem K, Jørgensen B, van de Cotte B, Goh T, Lin Z, Voβ U, Beeckman T, Bennett MJ, Gevaert K, Maizel A, De Smet I (2019) EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. Proc Natl Acad Sci U S A. 2019 Apr 3. pii: 201820882. doi: 10.1073/pnas.1820882116 https://www.pnas.org/content/early/2019/04/02/1820882116.long

Open Access

This pan-European study is led by Priya Ramakrishna at the University of Nottingham and includes co-authors from the UK, Belgium, Germany and Denmark. The authors look at the lateral root development and characterise the function of the EXPANSIN A1 protein. This protein influences the physical changes in the cell wall that are needed to enable the asymmetry cell divisions that define the location of a new lateral root. Plants lacking EXPA1 function do not properly form lateral roots and are unable to correctly respond to an inductive auxin signal. This clearly demonstrates an important requirement for the activity of genes that transmit cell signals into the physical relationships that exist between cells.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Mérai Z, Graeber K, Wilhelmsson P, Ullrich KK, Arshad W, Grosche C, Tarkowská D, Turečková V, Strnad M, Rensing SA, Leubner-Metzger G, Scheid OM (2019) Aethionema arabicum: a novel model plant to study the light control of seed germination. J Exp Bot. pii: erz146. doi: 10.1093/jxb/erz146

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Open Access

This paper includes authors from the UK, Germany, Austria and the Czech Republic including Kai Graeber and Gerhard Leubner-Metzger at Royal Holloway. They introduce the Brassica Aethionema arabicum as a new model to investigate the mechanism of germination inhibition by light as they have identified accessions that are either light-sensitive or light-neutral. In contrast germination in Arabidopsis is stimulated by light. Transcriptome analysis of Aethionema arabicum accessions reveal expression changes in key hormone-regulated genes. Overall they show that largely the same module of molecular components are involved in control of of seed dormancy irrespective of the effect of light on germination. Therefore any phenotypic changes likely result from changes in the activity organisms-specific of these genes.

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Bryant FM, Hughes D, Hassani-Pak K, Eastmond PJ (2019) Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. Plant Cell. pii: tpc.00892.2018. doi: 10.1105/tpc.18.00892 http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Open Access

http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Fiona Bryant is lead author on this research from Rothamsted Research that investigates the factors that control expression of the DOG1 gene, which is a key regulator of seed dormancy. They show that LEUCINE ZIPPER TRANSCRIPTION FACTOR67 (bZIP67) regulates DOG1 expression and have uncovered a mechanism that describes the temperature-dependent regulation of DOG1 expression. Finally they identity a molecular change that explains known allelic difference in DOG1 function, which informs different levels of dormancy in different accessions.


Oochi A, Hajny J, Fukui K, Nakao Y, Gallei M, Quareshy M, Takahashi K, Kinoshita T, Harborough SR, Kepinski S, Kasahara H, Napier RM, Friml J, Hayashi KI (2019) Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiol. 2019 Apr 1. pii: pp.00201.2019. doi: 10.1104/pp.19.00201 http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

Open Access

http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

This Japanese-led study includes co-authors from the Universities of Warwick and Leeds and describes the identification of a novel positive chemical modulator of auxin cellular efflux. This aptly named PInStatic Acid (PISA) prevents PIN protein internalization yet does not impact the SCFTIR1/AFB signaling cascade. Therefore the authors hope that PISA will be a useful tool for unpicking the cellular mechanisms that control auxin transport.


Montenegro-Johnson T, Strauss S, Jackson MDB, Walker L, Smith RS, Bassel GW. (2019) 3D Cell Atlas Meristem: a tool for the global cellular annotation of shoot apical meristems. Plant Methods. 15:33. doi: 10.1186/s13007-019-0413-0

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Open Access

Thomas Montenegro-Johnson, Soeren Strauss, Matthew Jackson and Liam Walker lead this methods paper that was prepared following research that took place at the University of Birmingham and the Max Planck Institute for Plant Breeding Research in Cologne. They describe the 3DCellAtlas Meristem, a tool allows the complete cellular annotation of cells within a shoot apical meristem (SAM), which they have successfully tested in both Arabidopsis and tomato. The authors state that ‘this provides a rapid and robust means to perform comprehensive cellular annotation of SAMs and digital single cell analyses, including cell geometry and gene expression’.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0
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