GARNet Community podcast w Rea Antoniou-Kourounioti

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Published on: February 19, 2020

Rea Antoniou-Kourounioti works with Martin Howard and Caroline Dean at the John Innes Centre and we discuss a recent paper in Genes and Development entitled ‘Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC‘. It’s the latest episode in exciting saga that seeks to explain the regulation of the engimatic FLC gene.

GARNet Research Roundup: February 18th 2020

This weeks GARNet Research Roundup begins with two studies that characterize the role of proteins that are involved in the control of meiotic recombination. The first study is from the Henderson lab at the University of Cambridge and investigates the role of the REC8 protein whilst the second is from John Doonan’s group at Aberystwyth University and investigates the role of the cyclin-dependent kinase CDKG.

The third paper is from the same research group in Aberystwyth and investigates how alternative splicing can impact the function of the FLOWERING LOCUS M gene.

The next papers is a cross-UK collaboration led from Rothamsted Research and the John Innes Centre that identifies an important QTL associated with the generation of high-fibre wheat. The fifth paper is from the JIC and reveals how the immune resistance gene MLO plays a role in a plants association with beneficial microbial symbiotes.

The sixth paper is from the Gibbs lab at the University of Birmingham and further characterizes the function of the VRN2 component of the polycomb repressive complex 2.

Nick Harberd from Oxford is a corresponding author of the next paper, which identifies a new gene that could be used to improve nitrogen-use efficiency in rice.

The eighth paper is a proteomic-based study from the University of Cambridge that identifies novel stress-induced components of the Arabidopsis spliceosome.

The penultimate paper is from Jonathan Jones’ lab at the Sainsbury lab, Norwich in which they characterize a new transgenic line useful for studying the plant immune response.

The final paper includes Liam Dolan from Oxford as a co-author in a study that characterizes a novel ATPase from the algae Chara australis.

Lambing C, Tock AJ, Topp SD, Choi K, Kuo PC, Zhao X, Osman K, Higgins J, Franklin FCH, Henderson IR (2020) Interacting genomic landscapes of REC8-cohesin, chromatin and meiotic recombination in Arabidopsis thaliana. Plant Cell. doi: 10.1105/tpc.19.00866
Open Access

This study is led by Chris Lambing from Ian Henderson’s group at the University of Cambridge and includes collaborators from Leicester and Birmingham. They use ChIP-seq to identify the genomic regions associated with the REC8 protein, showing that it interacts with regions with multiple distinct chromatin states. This interaction plays a key role in controlling the formation of double strands breaks and is required to organize meiotic chromosome architecture and interhomolog recombination.

Nibau C, Lloyd AH, Dadarou D, Betekhtin A, Tsilimigka F, Phillips DW, Doonan JH (2020) CDKG1 Is Required for Meiotic and Somatic Recombination Intermediate Processing in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00942 Open Access

Candida Nibau from Aberystwyth University leads this research that reveals a critical role for the cyclin-dependent kinase G1 (CDKG) in the control of recombination, both during meiosis and within somatic cells. The authors discover that this role occurs early in the process through the stabilization of recombination intermediates.

Nibau C, Gallemí M, Dadarou D, Doonan JH, Cavallari N (2020) Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2. Front Plant Sci. doi: 10.3389/fpls.2019.01680 Open Access

Candida Nibau is first author on this collaboration between researchers in the UK (Aberystwyth University) and Vienna, Austria. They assess the factors that control the contribution of two splicing variants of the FLOWERING LOCUS M gene on flowering time across a temperature range. They find that this process is controlled by the activity of the cyclin-dependent kinase G2 (CDKG2) and its cognate cyclin, CYCLIN L1 (CYCL1).

Lovegrove A, Wingen LU, Plummer A, Wood A, Passmore D, Kosik O, Freeman J, Mitchell RAC, Hassall K, Ulker M, Tremmel-Bede K, Rakszegi M, Bedő Z, Perretant MR, Charmet G, Pont C, Salse J, Waite ML, Orford S, Burridge A, Pellny TK, Shewry PR, Griffiths S (2020) Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour. PLoS One. doi: 10.1371/journal.pone.0227826
Open Access

Alison Lovegrove at Rothamsted Research is the first author on this cross-UK research that has gained significant interest from the main–stream media. Through analysis of a Chinese wheat variety with high dietary fibre due to the high amounts of cell wall polysaccharide arabinoxylan the authors identified a QTL that is responsible for this phenotype. Understanding this QTL will allow use of both marker-assisted breeding and new breeding technologies to aid in the generation of high yield, high fibre varieties.

Jacott CN, Charpentier M, Murray JD, Ridout CJ (2020) Mildew Locus O facilitates colonization by arbuscular mycorrhizal fungi in angiosperms. New Phytol. doi: 10.1111/nph.16465

Catherine Jacott is first author on this study from the JIC that investigates the role of the known barley resistance gene Mildew Resistance Locus O (MLO) during arbuscular mycorrhizal interactions in wheat, barley and Medicago. They show that MLO is important for this beneficial symbiotic association and that the role of MLO has been appropriated during infection with pathogenic powdery mildew.

Labandera AM, Tedds HM, Bailey M, Sprigg C, Etherington RD, Akintewe O, Kalleechurn G, Holdsworth MJ, Gibbs DJ (2020) The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development. New Phytol. doi: 10.1111/nph.16477

Anne-Marie Labandera is first author on this work from Dan Gibbs’ lab in Birmingham. They show that ubiquitin-mediated proteolysis of the VERNALIZATION2 (VRN2) protein via the oxygen-dependent PRT6 N-degron pathway is important for many areas of plant development. This regulation of VRN2 has different developmental outcomes depending on whether it occurs in or out of meristematic tissues.

Wu K, Wang S, Song W, Zhang J, Wang Y, Liu Q, Yu J, Ye Y, Li S, Chen J, Zhao Y, Wang J, Wu X, Wang M, Zhang Y, Liu B, Wu Y, Harberd NP, Fu X (2020) Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice. Science. doi: 10.1126/science.aaz2046

Kun Wu is first author on this Chinese-led investigation that also includes Nick Harberd from Oxford University as a corresponding author. Working in rice they link genomic-wide chromatin changes with expression of the NGR5 (NITROGEN-MEDIATED TILLER GROWTH RESPONSE 5) transcription factor during nitrogen-induced growth. Overexpression of NGR5 can uncouple nitrogen-sensing from tiller production and therefore provide a novel tool to possibly enhance agricultural production in low nitrogen conditions.

Marondedze C, Thomas L, Lilley KS, Gehring C (2020) Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components. Front Mol Biosci. doi: 10.3389/fmolb.2019.00163 Open Access

Claudius Marondedze is the first author on this collaboration between the University of Cambridge and KAUST in Saudi Arabia. They perform label-free mRNA interactome-capture to identify RNA interacting proteins that are induced after drought stress. This reveals over 40 novel spliceosome-interacting proteins but also 32 proteins that associate with stress granules, which are indicative of transcriptional arrest. This provides new insights into how plant stress responses might be altered by the activity of spliceosome components.

Ngou BPM, Ahn HK, Ding P, Redkar A, Brown H, Ma Y, Youles M, Tomlinson L, Jones JDG (2020) Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity. J Exp Bot. doi: 10.1093/jxb/erz571

This research from Jonathan Jones’ group at the Sainsbury Lab, Norwich is led by Bruno Pok Man Ngou. They have developed a transgenic line that enables the transient in planta expression of AvrRps4, which is a potent bacterial immune effector. This stimulates the RRS1/RPS4-dependent immune response and provides insights into certain mechanisms of this pathway without exposing the plants to pathogens.

Zhang S, Habets M, Breuninger H, Dolan L, Offringa R, van Duijn B (2020) Evolutionary and Functional Analysis of a Chara Plasma Membrane H(+)-ATPase. Front Plant Sci. doi: 10.3389/fpls.2019.01707 Open Access

Liam Dolan from the University of Oxford is a co-author on this Dutch-led research that includes Sutun Zhang as first author. They characterize a plasma membrane localised ATPase from the algae Chara australis and perform complementation studies in both yeast and Arabidopsis. These studies allow the authors to propose that the mode of regulation of this algal ATPase is likely different from that of known yeast and land plant PM H+-ATPases.

Introducing Auxin2020

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Published on: February 14, 2020

The four-yearly Auxin Workshop (#Auxin2020) will take place in Cavtat, Croatia between October 4th-8th 2020.

This workshop brings together established group leaders and early career researchers to discuss the latest developments in research that is linked to the ubiquitous phytohormone auxin.

Workshop highlights:

– Seven plenary sessions featuring twenty-eight invited speakers

– Twenty-eight places for plenary talks selected from submitted abstracts

– Two evening poster sessions with introductory short talks

– Afternoon boat trip along the Dalmatian Coast

The workshop takes place at the Hotel Croatia, Cavtat for which delegates will have preferential booking rates. This location is just 10minutes from Dubrovnik airport.

Key #Auxin2020 dates:

Feb 1st- March 31st: Early Bird Registration is open (£275/£425 + fee)

April 1st- May 31st: Regular Registration is open (£375/£525 + fee)

June 6th- August 31st: Late Registration is open (£475/£625 + fee)

April 30th: Deadline for submitting abstracts to be considered for oral presentations

July 31st: Deadline for submitting abstracts to be considered for poster presentations

If you have any questions about this exciting workshop then please contact

Please download this flyer to distribute amongst your network.

Report from PhenomUk Annual Meeting

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Published on: February 13, 2020

The PhenomUK network is into its second year of operating supported by the UKRI Technology Touching Life scheme. PhenomUK focuses on how technological developments in plant phenotyping can impact agricultural productivity for the benefit of UK and global food production.

Despite being early in its four-year funding cycle PhenomUK has a growing mailing list, social media following and welcomed around 60 attendees to this annual meeting at the National Physical Laboratory (NPL). For those not familiar; the NPL is situated in west London and employs 600 people who research and support the science of measurement, Metrology. Around 50% of NPL funding comes direct from UK government with the remainder from competitive grants and private partnerships. The core activities of the NPL are in calibration services that are linked to the maintenance of SI base units such as the kilogram, second, ampere or metre. However as part of their data science program, researchers at NPL are applying their technical expertise to agricultural challenges.

NPL scientist Andrew Thompson presented some of his groups early data in which they first used 3D imaging to visualize wheat fields and then applied density calculations to isolate individual wheat-ears. There will be plenty to come from this research program and they are happy to discuss collaborations with anyone who wants to tap into their expertise.

Andrew Thompson shows his 3D imaging of wheat

The keynote talks were provided by Hanno Scharr from Forschungszentrum Jülich and Mark Aarts from Wageningen University & Research (WUR). Jülich has an outstanding selection of across-scale technologies to support phenotyping, from automated seed picking through to satellite-enabled field imaging whilst WUR are collaborating with the University of Utrecht to develop the Netherlands Plant Eco-phenotyping Centre (NPEC). Both facilities cost in excess of €20M and highlight the infrastructural support required to develop a national capability. It remains to be seen whether this will be possible across the more fragmented UK plant science community.

UKRI/BBSRC understand the importance of plant phenotyping technologies and are supportive of the community….however a £10M+ investment might be a little way off! It was excellent to hear Professor Aarts provide an perspective of where the NEPC will sit within the European and International phenotyping communities.

Mark Aarts explains where NPEC fits into the International communitty.

On that note the EMPHASIS project is now reaching the end of its exploratory phase and will thereafter hopefully provide a constant presence for plant phenotyping within the European funding landscape. The meeting included a promising discussion that suggested that the EMPHASIS legal entity sits outside of the Horizon program (and its successor) so the UK should be able to remain a full participant. Fingers crossed!

The remainder of the meeting was taken with an update from PhenomUK PI Tony Pridmore who outlined the aims of the network and the available funding schemes:

1. Networking Visit Funding. PhenomUK can fund travel, accommodation and subsistence bursaries to support short fact-finding and networking visits between UK institutions and between UK and international centres. This is an open call yet no-one has taken advantage of this scheme. Please consider applying for it!

2. Pilot Project Funding. This is the main funding instrument through which PhenomUK supports plant-phenotyping applications on behalf of UKRI-BBSRC. Network members can request £25K for these pilot projects and in the first round 4 projects were funded from 13 applications. Professor Pridmore was very clear to emphasise that proposals are only eligible if the project contains a technology-development component. Proposals that ‘simply’ support a scientific experiment will not be considered. The second round of applications will open over the coming weeks. These grants represent significant finance support for a nascent project so please consider how you might take advantage of this opportunity.

Tony Pridmore presents the next pilot project scheme

 Representatives from the four successful pilot projects outlined their plans, which are at different levels of complexity and progress. Dr Bo Li from UWE outlined his team’s early attempts to use microwaves to image fruit damage and root development whilst Dr Ji Zhou from NIAB demonstrated their plans for large-scale field phenotyping using drones. The full list of pilot projects can be found here

Ji Zhou presents his lab’s field phenomics research through Designing Future Wheat

 The PhenomUK community is characterised by excellent multidisciplinary relationships between plant scientists, computer scientists, data scientists, engineers and imaging technologists. The increasingly complex technical capabilities and development of advanced image processing is moving this field forward at a rapid rate. The major challenge will come in ensuring that there is access to these technologies across a wider set of academics, members of industry and even farmers. Hopefully PhenomUK will facilitate this process

Some work needs to be done with the gender diversity within this community as this meeting didn’t include any female contributors. This will hopefully change over the life of the project.

Claire Hayes is the project coordinator and would be delighted to hear from anyone who wants to get involved with PhenomUK!

GenSoc Arabidopsis Meeting: Free Rice Transformation Workshop

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Published on: February 12, 2020

After a 10 year hiatus, the Genetics Society Arabidopsis Meeting is back with a two-day meeting on the 21st and 22nd of April, 2020 at the department of Biosciences at Durham University

On April 20th we have have added a FREE GARNet-supported hands-on workshop on rice transformation.

The lab-based workshop, led by rice transformation expert Dr Cunjin Zhang, will provide hands-on experience of aseptic technique, plant tissue culture, tissue sampling, explant preparation, and the generation of somatic embryogenic callus. Attendees will have the opportunity to practice (1) seed sterilisation (2) callus subculturing and (3) see a demonstration of culture inoculation and proper handling of Agrobacterium .

Programme Monday April 20th:
    1.00 – 1.15 pm : Welcome from Prof Ari Sadanandom
    1.15 – 2.00 pm : Introduction to transformation by Dr Cunjin Zhang
    2.00 – 2.30 pm : Tour of facilities
    2.30 – 3.00 pm : Coffee break
    3.00 – 4.30 pm : Practical session
    4.30 – 5.30 pm : Pizza
    5.30 – 6.00 pm : Q&A

The main GenSoc meeting runs from on April 21st-22nd and includes the following Scientific sessions include:
– Development
– Abiotic Interactions
– Teaching Plant Biology
– Natural Variation
– Biotic Interactions
– Computational Biology

Invited Speakers include:
Christian Hardtke (University of Lausanne)
Veronica Grieneisen (Cardiff University)
Steven Spoel (University of Edinburgh)
Vardis Ntoukakis (University of Warwick)
Mary Williams (ASPB & University of Glasgow)
Henrik Jönsson (SLCU, Cambridge)
Celia Knight (University of Leeds)
Ian Henderson (University of Cambridge)
Yoselin Benitez-Alfonso (University of Leeds)
Uli Bechtold (University of Essex)
Heather Knight (Durham University)
Dan Gibbs (University of Birmingham)
Sarah Robinson (SLCU, Cambridge).

Registration and Conference Fees:

Genetics Society Members: £45
(Membership number required (see www.genetics. to join)

Non-members: £65

Contact Peter Etchells for more information

Matthew Parker, Kasia Knop and Anya Sherwood talk to the GARNet community podcast

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Published on: February 12, 2020

This research team from the Simpson lab at the James Hutton Institute, University of Dundee discuss a recent paper published in elife entitled ‘Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.

Apologies for the poor sound quality of the transmission coming down the line from Dundee!

GARNet Research Roundup: February 7th 2020

This latest edition of the GARNet Research Roundup begins with two studies that look at different aspects of lateral root formation and include members of Malcolm Bennett’s lab in Nottingham. The first investigates a critical role for hydropatterning in the control of lateral root initiation whilst the second looks at how cell death in overlying tissue layers plays an active role in the control of lateral root emergence.

The third paper is from the John Innes Centre and investigates the mechanism through which a small number of noncoding SNPs can alter chromatin dynamics at the FLC locus. The fourth paper is from Glasgow and assesses a link between auxin signaling and proteins involved in membrane trafficking.

The next paper is from Rothamsted Research and looks at how aerial differences in wheat cultivars can affect the root-associated microbiome. The sixth paper is from the James Hutton Institute and investigates the relationship between phosphate and zinc signaling during the growth of Brassica oleracea.

The final three papers focus on some aspect of plant mechanical strength. The first paper is from Aberystwyth and looks at the how mechanical stress impacts growth of Brachypodium. The next two papers are led from the US and Sweden respectively and include UK co-authors from Leeds, the JIC and York. The first looks at how lignin modifications illicits defence responses whilst the second begins to demonstrate how xyloglucan modifications alter secondary cell wall growth.

von Wangenheim D, Banda J, Schmitz A, Boland J, Bishopp A, Maizel A, Stelzer EHK, Bennett M (2020) Early developmental plasticity of lateral roots in response to asymmetric water availability. Nat Plants. doi: 10.1038/s41477-019-0580-z Open Access with link.

This brief communication is led by Daniel von Wangenheim, who worked with Malcolm Bennett and colleagues at the University of Nottingham. They use light sheet fluorescence microscopy to investigate how the local water environment controls the initiation of lateral root primordia. They show that this response is extremely plastic and that the initiation of pericycle cell files is linked to the external hydrological landscape. This study reveals a potential adaptive advantage when roots forage under heterogeneous soil conditions, which of course exists in all ‘real-world’ situations.

BotanyOne has written a nice blog about this paper and Daniel von Wangenheim has produced a superb explanatory video.

Escamez S, André D, Sztojka B, Bollhöner B, Hall H, Berthet B, Voß U, Lers A, Maizel A, Andersson M, Bennett M, Tuominen H (2020) Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2019.11.078 Open Access

Ute Voss and Malcolm Bennett from Nottingham are co-authors on this Finnish-led study in which Sacha Escamez is first author. They show that cell death occuring in advance of emerging lateral roots is an active developmental process rather than a passive effect of lateral root initiation. Plants with a cell-death-deficiency show delayed lateral root development, which is rescued through physical or genetic removal of outer cell files.

Qüesta JI, Antoniou-Kourounioti RL, Rosa S, Li P, Duncan S, Whittaker C, Howard M, Dean C (2020) Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC. Genes Dev. doi: 10.1101/gad.333245.119 Open Access

This research from the John Innes Centre is led by Julia Qüesta and Rea Antoniou-Kourounioti. They show that four noncoding SNPs in the Lov-1 Arabidopsis accession are responsible for the reactivation of FLC after only a short cold treatment. They combine experimentation and modelling to also propose that the control of FLC reactivation is linked to the extent of DNA replication during the cold period.

Rea discusses this paper on the GARNet Community podcast. Look out for it on February 19th.

Xia L, Marquès-Bueno MM, Karnik RA (2020) Trafficking SNARE SYP132 Partakes in Auxin-associated Root Growth. Plant Physiol. doi: 10.1104/pp.19.01301 Open Access

This short communication is led by Lingfeng Xia in the Karnik lab at the University of Glasgow and looks at the role of auxin in the control of expression of the SNARE protein SYP132 during root growth and the gravitropic response. This linkage is indicative of an important role for membrane trafficking during the auxin response.

Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo IS, Hirsch PR, Mendes R, Mauchline TH (2020) Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep. doi: 10.1038/s41598-020-58402-y
Open Access

Vanessa Kavamura is first author on this study led from Rothamsted Research that looks at how the aerial phenotypes of different wheat cultivars impacts root traits and the soil microbiome. Interestingly they show that taller wheat varieties are predicted to have a more connected bacterial network, which might lead to a more favourably rhizosphere for plant growth.

Pongrac P, Fischer S, Thompson JA, Wright G, White PJ (2020) Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply. Front Plant Sci. doi: 10.3389/fpls.2019.01645 Open Access

Paula Pongrac is the first author on this study led from the James Hutton Institute in which they investigate how plants respond to their access to environmental phosphate and zinc. They assess gene expression of Brassica oleracea plants grown under different mineral conditions and reveal important relationships between the response to phosphorous and zinc that will inform future nutrient supply strategies and identification of novel germplasm.

Gladala-Kostarz A, Doonan JH, Bosch M (2020) Mechanical stimulation in Brachypodium distachyon: implications for fitness, productivity and cell wall properties. Plant Cell Environ. doi: 10.1111/pce.13724.

Agnieszka Gladala‐Kostarz who works with Maurice Bosch at Aberystwyth University is the first author on this research that looked at the effect of both wind- and mechanical- treatments on growth of two accessions of Brachypodium distachyon. They catalogue the physical changes that occur in this important base-line study that tracks the relevance of these environmental factors on the multiple growth traits.

Gallego-Giraldo L, Liu C, Pose-Albacete S, Pattathil S, Peralta AG, Young J, Westpheling J, Hahn MG, Rao X, Knox JP, De Meester B, Boerjan W, Dixon RA (2020) ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1914422117 Open Access

Lina Gallego-Giraldo is the first author on the US-led paper that includes Paul Knox and Sara Pose-Albacete from the University of Leeds. In this work they look at the link between lignin modifications and the inappropriate initiation of plant defence responses. They show that cell wall pectin remodeling mediated by the ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) protein releases defence elicitors and as such provides important information on the link between these processes.

Kushwah S, Banasiak A, Nishikubo N, Derba-Maceluch M, Majda M, Endo S, Kumar V, Gomez L, Gorzsás A, McQueen-Mason S, Braam J, Sundberg B, Mellerowicz EJ (2020) Arabidopsis XTH4 and XTH9 contribute to wood cell expansion and secondary wall formation. Plant Physiol. doi: 10.1104/pp.19.01529 Open Access

Sunita Kushwah leads this Swedish-study that has co-authors from the JIC and York. They investigate a novel role for the XTH4 and XTH9 xyloglucan endo-transglycosylase/ hydrolases during secondary growth in Arabidopsis. The activity of these enzymes has a significant effect on cell wall composition and in the control of wood formation

Zaigham Shahzad on the GARNet Community podcast

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Published on: February 5, 2020

Zaigham Shahzad who works with Anna Amtmann at the University of Glasgow chats to GARNet about a paper published in Nature Communications entitled ‘Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed‘.

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