GARNet Research Roundup: September 24th 2019

Due to a significant delay this GARNet Research Roundup is a bumper overview of recent(ish) publications across discovery-led plant science, which have at least one contributor from a UK institution.

These can be (very) loosely separated into the following categories:

Circadian Clock: Greenwood et al, PloS Biology. Belbin et al, Nature Communications.

Environmental responses: Rodríguez-Celma et al, PNAS. Walker and Bennett, Nature Plants. Conn et al, PLoS Comput Biology. de Jong et al,PLoS Genetics. Molina-Contreras et al,The Plant Cell.

Defence signaling: Van de Weyer et al, Cell.Hurst et al, Scientific Reports. Xiao et al, Nature. Wong et al, PNAS.

Cell Biology: Miller et al, The Plant Cell. Coudert et al, Current Biology. Burgess et al,The Plant Cell. Harrington et al, BMC Plant Biology.

Metabolism: Jia et al, J Biol Chem. Perdomo et al, Biochem J. Gurrieri et al, Frontiers in Plant Science. Mucha et al, The Plant Cell. Atkinson et al, JXBot.

Cell Wall Composition: Wightman et al, Micron. Milhinhos et al, PNAS.

Signaling: Hartman et al, Nature Communications. Dittrich et al, Nature Plants. Villaécija-Aguilar et al, PLoS Genetics


Greenwood M, Domijan M, Gould PD, Hall AJW, Locke JCW (2019) Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana. PLoS Biol. 17(8):e3000407. doi: 10.1371/journal.pbio.300040 Open Access

Lead author is Mark Greenwood. UK contribution from The Sainsbury lab University of Cambridge, University of Liverpool and Earlham Institute. Using a mixture of experimental and modeling this paper shows that individual organs have circadian clocks that runs at different speeds.


Belbin FE, Hall GJ, Jackson AB, Schanschieff FE, Archibald G, Formstone C, Dodd AN (2019) Plant circadian rhythms regulate the effectiveness of a glyphosate-based herbicide. Nat Commun. 2019 Aug 16;10(1):3704. doi: 10.1038/s41467-019-11709-5 Open Access

Lead author is Fiona Belbin. UK contribution from University of Bristol and Syngenta Jealott’s Hill. Activity of the circadian clock determines that the plant response to the herbicide glyphosate is lessened at dusk, promoting the idea of agricultural chronotherapy. Fiona discusses this paper on the GARNet Community Podcast.


Rodríguez-Celma J, Connorton JM, Kruse I, Green RT, Franceschetti M, Chen YT, Cui Y, Ling HQ, Yeh KC, Balk J (2019) Arabidopsis BRUTUS-LIKE E3 ligases negatively regulate iron uptake by targeting transcription factor FIT for recycling. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1907971116 Open Access

Lead author is Jorge Rodríguez-Celma. UK contribution from John Innes Centre, University of East Anglia.The Arabidopsis E3 ubiquitin ligases, BRUTUS-LIKE1 (BTSL1) and BTSL2 target the FIT transcription factor for degradation, altering the plant response to harmful level of iron.


Walker CH, Bennett T (2019) A distributive ‘50% rule’ determines floral initiation rates in the Brassicaceae. Nat Plants. doi: 10.1038/s41477-019-0503-z
Lead author Catriona Walker. UK contribution from the University of Leeds. The authors introduce the 50%-rule that defines the relationshop between the total number of flowers the number of secondary inflorescences


Conn A, Chandrasekhar A, Rongen MV, Leyser O, Chory J, Navlakha S (2019) Network trade-offs and homeostasis in Arabidopsis shoot architectures. PLoS Comput Biol. doi: 10.1371/journal.pcbi.100732 Open Access

Lead author is Adam Conn. UK contribution from Sainsbury Laboratory, University of Cambridge. This study performed 3D scanning of 152 Arabidopsis shoot architectures to investigate how plants make trade-offs between competing objectives.


de Jong M, Tavares H, Pasam RK, Butler R, Ward S, George G, Melnyk CW, Challis R, Kover PX, Leyser O (2019) Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness. PLoS Genet. doi: 10.1371/journal.pgen.1008366 Open Access

Lead author is Maaike de Jong. UK contribution from the Sainsbury Laboratory, University of Cambridge, the University of York and the University of Bath. This study looks at phenotypic plasticity of shoot branching in Arabidopsis diversity panels grown until different nitrate concentrations.


Molina-Contreras MJ, Paulišić S, Then C, Moreno-Romero J, Pastor-Andreu P, Morelli L, Roig-Villanova I, Jenkins H, Hallab A, Gan X, Gómez-Cadenas A, Tsiantis M, Rodriguez-Concepcion M, Martinez-Garcia JF (2019) Photoreceptor Activity Contributes to Contrasting Responses to Shade in Cardamine and Arabidopsis Seedlings. Plant Cell. doi: 10.1105/tpc.19.00275 Open Access

Lead author is Maria Jose Molina-Contreras. UK contribution from the University of Oxford. The authors looks at the response to different light conditions and how they contribute to phenotypic determination in Cardamine and Arabidopsis seedlings.


Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F (2019) A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell. doi: 10.1016/j.cell.2019.07.038 Open Access

Lead author is Anna-Lena Van de Weyer. UK contribution from The Sainsbury Laboratory, Norwich. Using sequence enrichment and long-read sequencing the authors present the pan-NLRome constructed from 40 Arabidopsis accessions.


Hurst CH, Wright KM, Turnbull D, Leslie K, Jones S, Hemsley PA (2019) Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function. Sci Rep. doi: 10.1038/s41598-019-49302-x Open Access

Lead author is Charlotte Hurst. UK contribution from the James Hutton Institute and the University of Dundee. They look at the functional role of post-translational modification S-acylation with a focus on the plant pathogen perceiving receptor-like kinase FLS2.


Xiao Y, Stegmann M, Han Z, DeFalco TA, Parys K, Xu L, Belkhadir Y, Zipfel C, Chai J (2019) Mechanisms of RALF peptide perception by a heterotypic receptor complex. Nature. doi: 10.1038/s41586-019-1409-7
Lead author is Yu Xiao. UK contribution from The Sainsbury Laboratory, Norwich. This study investigates how RAPID ALKALINIZATION FACTOR (RALF) peptides induce receptor complex formation to regulate immune signaling.


Wong JEMM, Nadzieja M, Madsen LH, Bücherl CA, Dam S, Sandal NN, Couto D, Derbyshire P, Uldum-Berentsen M, Schroeder S, Schwämmle V, Nogueira FCS, Asmussen MH, Thirup S, Radutoiu S, Blaise M, Andersen KR, Menke FLH, Zipfel C, Stougaard J (2019). A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1815425116
Open Access

Lead author is Jaslyn Wong. UK contribution from The Sainsbury Laboratory, University of East Anglia. This work was conducted in the legume Lotus and after a proteomic screen, the authors identified NFR5-interacting cytoplasmic kinase 4 that is involved in control of Nod factor perception.


Miller C, Wells R, McKenzie N, Trick M, Ball J, Fatihi A, Dubreucq B, Chardot T, Lepiniec L, Bevan MW (2019) Variation in expression of the HECT E3 ligase UPL3 modulates LEC2 levels, seed size and crop yield in Brassica napus. Plant Cell. doi: 10.1105/tpc.18.00577
Open Access

Lead author in Charlotte Miller. UK contribution from the John Innes Centre. Activity of the Brassica napus HECT E3 ligase gene BnaUPL3 controls seed weight per pod through degradation of LEC2, a master transcriptional regulator of seed maturation and reveals a potential target for crop improvement


Coudert Y, Novák O, Harrison CJ (2019) A KNOX-Cytokinin Regulatory Module Predates the Origin of Indeterminate Vascular Plants. Curr Biol. 2019 Aug 19;29(16):2743-2750.e5. doi: 10.1016/j.cub.2019.06.083

Lead author is Yoan Coudert. UK contribution from the University of Cambridge and University of Bristol. Class I KNOX gene activity is shown to be necessary for axis extension from an intercalary region of determinate moss shoots, in part through promotion of cytokinin biosynthesis.


Burgess SJ, Reyna-Llorens I, Stevenson SR, Singh P, Jaeger K, Hibberd JM (2019) Genome-wide transcription factor binding in leaves from C3 and C4 grasses Plant Cell.  doi: 10.1105/tpc.19.00078 Open Access

Lead author is Steven Burgess. UK contribution from University of Cambridge, The Sainsbury lab University of Cambridge, University of Leeds The authors use DNaseI-SEQ to assess the similarities and differences in transcription factor binding sites in the leaves across a set of four C3 and C4 grasses.


Harrington SA, Overend LE, Cobo N, Borrill P, Uauy C (2019) Conserved residues in the wheat (Triticum aestivum) NAM-A1 NAC domain are required for protein binding and when mutated lead to delayed peduncle and flag leaf senescence. BMC Plant Biol. doi: 10.1186/s12870-019-2022-
Lead author is Sophie Harrington. UK contributions from the John Innes Centre and University of Birmingham. The authors used a wheat TILLING resource to investigate mutrant allele with the NAC domain of the NAM-A1 transcription factor and their contribution to phenotypes in lab and field.


Jia Y, Burbidge CA, Sweetman C, Schutz E, Soole K, Jenkins C, Hancock RD, Bruning JB, Ford CM (2019) An aldo-keto reductase with 2-keto- L-gulonate reductase activity functions in L-tartaric acid biosynthesis from vitamin C in Vitis vinifera. J Biol Chem. doi: 10.1074/jbc.RA119.010196 Open Access

Lead author Yong Jia. UK contribution from the James Hutton Institute. This work conducted in grape reveals the mechanism by which an aldo-keto reductase functions in tartaric acid biosynthesis.


Perdomo JA, Degen GE, Worrall D, Carmo-Silva E (2019) Rubisco activation by wheat Rubisco activase isoform 2β is insensitive to inhibition by ADP. Biochem J. doi: 10.1042/BCJ2019011 Open Access

Lead author is Juan Alejandro Perdomo. UK contribution from Lancaster University. They show through analysis of site-directed mutations across three isoforms of wheat Rubisco activase that these isoforms have different sensitivities to ADP.


Gurrieri L, Distefano L, Pirone C, Horrer D, Seung D, Zaffagnini M, Rouhier N, Trost P, Santelia D, Sparla F (2019) The Thioredoxin-Regulated α-Amylase 3 of Arabidopsis thaliana Is a Target of S-Glutathionylation. Front Plant Sci. doi: 10.3389/fpls.2019.00993 Open Access

Lead author is Libero Gurrieri. UK contribution from John Innes Centre. The chloroplastic α-Amylases, AtAMY3 is post-translationally modified by S-glutathionylation in response to oxidative stress.


Mucha S, Heinzlmeir S, Kriechbaumer V, Strickland B, Kirchhelle C, Choudhary M, Kowalski N, Eichmann R, Hueckelhoven R, Grill E, Kuster B, Glawischnig E (2019) The formation of a camalexin-biosynthetic metabolon. Plant Cell. doi: 10.1105/tpc.19.00403 Open Access

Lead author is Stefanie Mucha. UK contribution from Oxford Brookes University and University of Warwick. The authors performed two independent untargeted co-immunoprecipitations to identify components involved in biosynthesis of the antifungal phytoalexin camalexin.


Atkinson N, Velanis CN, Wunder T, Clarke DJ, Mueller-Cajar O, McCormick AJ (2019) The pyrenoidal linker protein EPYC1 phase separates with hybrid Arabidopsis-Chlamydomonas Rubisco through interactions with the algal Rubisco small subunit. J Exp Bot. doi: 10.1093/jxb/erz275
Open Access

Lead author is Nicky Atkinson. UK contribution from the University of Edinburgh. This study uses Arabidopsis-Chlamydomonas to investigate the protein-protein interaction between Rubisco and essential pyrenoid component 1 (EPYC1).


Wightman R, Busse-Wicher M, Dupree P (2019) Correlative FLIM-confocal-Raman mapping applied to plant lignin composition and autofluorescence. Micron. doi: 10.1016/j.micron.2019.102733
Lead author Raymond Wightman. UK contribution from the Sainsbury Laboratory, University of Cambridge and the University of Cambridge. This study uses applies a novelmethod of correlative FLIM-confocal-Raman imaging to analyse lignin composition in Arabidopsis stems.


Milhinhos A, Vera-Sirera F, Blanco-Touriñán N, Mari-Carmona C, Carrió-Seguí À, Forment J, Champion C, Thamm A, Urbez C, Prescott H, Agustí J (2019) SOBIR1/EVR prevents precocious initiation of fiber differentiation during wood development through a mechanism involving BP and ERECTA. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1807863116
Lead author is Ana Milhinho. UK contribution from the University of Oxford. The authors used GWAS in Arabidopsis to identify the SOBIR1/EVR as an important regulator of the control of secondary growth in xylem fibers.


Hartman S, Liu Z, van Veen H, Vicente J, Reinen E, Martopawiro S, Zhang H, van Dongen N, Bosman F, Bassel GW, Visser EJW, Bailey-Serres J, Theodoulou FL, Hebelstrup KH, Gibbs DJ, Holdsworth MJ, Sasidharan R, Voesenek LACJ (2019) Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress. Nat Commun. doi: 10.1038/s41467-019-12045-4 Open Access

Lead author is Sjon Hartman. UK contribution from the University of Nottingham, Rothamsted Research and the University of Birmingham. This multinational collaboration looks into the relationship of how ethylene mediated nitric-oxide signaling responds to environmental signals.


Dittrich M, Mueller HM, Bauer H, Peirats-Llobet M, Rodriguez PL, Geilfus CM, Carpentier SC, Al Rasheid KAS, Kollist H, Merilo E, Herrmann J, Müller T, Ache P, Hetherington AM, Hedrich R (2019) The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration. Nat Plants. doi: 10.1038/s41477-019-0490-0
Lead author Marcus Dittrich. UK contribution from the University of Bristol. This work looks at the role of ABA signaling in stomatal responses and that the multiple ABA receptors can be modulated differentially in a stimulus-specific manner.


Villaécija-Aguilar JA, Hamon-Josse M, Carbonnel S, Kretschmar A, Schmid C, Dawid C, Bennett T, Gutjahr C (2019). SMAX1/SMXL2 regulate root and root hair development downstream of KAI2-mediated signalling in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1008327 Open Access

Lead author Jose Antonio Villaécija-Aguilar. UK contribution from the University of Leeds and The Sainsbury lab, University of Cambridge. This demonstrates that KAI2 signalling through SMAX1/SMXL2 , is an important new regulator of root hair and root development in Arabidopsis.

GARNet Research Roundup: August 16th 2019

This holiday-time edition of the GARNet research roundup begins with two papers that include the late Ian Moore from the University of Oxford as a co-author. The first looks at the role of RAB-A5c in the control of cellular growth anisotropy whilst the second characterises the Transport Protein Particle II (TRAPPII) complex.

The third paper is a UK-wide collaboration that assesses the role of UVA signaling on stomatal development. Next is a paper from Cambridge and the JIC that has identified the TAF4b protein as a novel regulator of meiotic crossovers.

The fifth paper is from the University of York and characterizes a role for cis-12-oxo-phytodienoic acid (OPDA) during seed germination.

The next three papers feature scientists from the University of Leeds in research that investigates 1, a peroxisomal ABC transporter; 2, the role of LRR-RLKs in plasmodesmata development and 3, the cell wall characteristics of banana and mango fruit.

The ninth paper is from the University of Edinburgh and investigates the role of S-nitrosylation in the control of SUMO conjugation.

The next two papers include Steve Penfield at the JIC as a corresponding author; the first looks at the role of endosperm-expressed transcriptional factors during seed dormancy and the second, in collaboration with researchers at the University of Warwick, identifies novel QTLs involved in seed dormancy.

The penultimate study is from Lancaster and presents a surprising outcome resulting from the overexpression of the wheat CA1Pase gene. The final paper includes Alison Tidy and Zoe Wilson from University of Nottingham as co-authors on a study that looks at male fertility in Arabidopsis.


Kirchhelle C, Garcia-Gonzalez D, Irani NG, Jérusalem A, Moore I (2019) Two mechanisms regulate directional cell growth in Arabidopsis lateral roots. Elife. pii: e47988. doi: 10.7554/eLife.47988

Open Access

Charlotte Kirchhelle leads this work that was conducted in the lab of the late Ian Moore at the University of Oxford. She investigates the role of the plant-specific small GTPase RAB-A5c during growth anisotropy in lateral roots, which involves coordinated orientations of cellulose microfibrils (CMFs) and by cortical microtubules (CMTs). They identify RAB-A5c dependent and independent mechanisms to control cellular growth anisotropy in this growing tissue.

From https://elifesciences.org/articles/47988

Kalde M, Elliott L, Ravikumar R, Rybak K, Altmann M, Klaeger S, Wiese C, Abele M, Al B, Kalbfuß N, Qi X, Steiner A, Meng C, Zheng H, Kuster B, Falter-Braun P, Ludwig C, Moore I, Assaad FF (2019) Interactions between Transport Protein Particle (TRAPP) complexes and Rab GTPases in Arabidopsis. Plant J. doi: 10.1111/tpj.14442

This German-led study includes Monika Kalde from the University of Oxford as first author as well Ian Moore as co-author. They characterize the components and function of the Transport Protein Particle II (TRAPPII) complex. TRAPPII plays multiple roles in intra-cellular transport and this study identified 13 subunits, including several that were previously uncharacterised.


Isner JC, Olteanu VA, Hetherington AJ, Coupel-Ledru A, Sun P, Pridgeon AJ, Jones GS, Oates M, Williams TA, Maathuis FJM, Kift R, Webb AR, Gough J, Franklin KA, Hetherington AM (2019). Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase. Curr Biol.29(15):2580-2585.e4. doi: 10.1016/j.cub.2019.06.071

Open Access

Jean-Charles Isner is the first author on this collaboration between labs in Bristol, York, Oxford and Cambridge. They show that UVA radiation (which represents 95% of the UV radiation reaching earth) inhibits stomatal opening through a process that involves a reduction in the cytosolic level of cGMP. The AtCN-PDE1 gene (a cGMP-activated phosphodiesterase) is needed to decrease cGMP levels in Arabidopsis. This response is present across the tree of life except in metazoans. They show AtCN-PDE1 is needed for the UVA response and that prolonged UVA exposure causes increased growth yet reduced water use efficiency.


Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR (2019) Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Curr Biol. pii: S0960-9822(19)30844-9. doi: 10.1016/j.cub.2019.06.084

Open Access

This work from Ian Henderson’s lab in Cambridge and Xiaoqi Feng’s lab at the JIC is led by Emma Lawrence and isolates a novel modifier of meiotic crossover frequency, TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. They show TAF4b expression is enriched in meiocytes, compared to the more general expression of its paralog TAF4. Ultimately they reveal TAF4b drives a novel mode of meiotic recombination control through its activity as a general transcription factor.


Barros-Galvão T, Dave A, Cole A, Harvey D, Langer S, Larson TR, Vaistij FE, Graham IA (2019) cis-12-oxo-phytodienoic acid represses Arabidopsis thaliana seed germination in shade light conditions. J Exp Bot. pii: erz337. doi: 10.1093/jxb/erz337

Open Access

Thiago Barros-Galvão is first author on this study from Ian Graham’s lab at the University of York. They investigate how the jasmonic acid pre-cursor cis-12-oxo-phytodienoic acid (OPDA) contributes to control of seed germination, particularly under shade conditions. OPDA acts through the activity of the transcription factor MOTHER-OF-FT-AND-TFL1 (MFT).

From https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz337/5536641

Carrier DJ, van Roermund CWT, Schaedler TA, Rong HL, IJlst L, Wanders RJA, Baldwin SA, Waterham HR, Theodoulou FL, Baker A (2019) Mutagenesis separates ATPase and thioesterase activities of the peroxisomal ABC transporter, Comatose. Sci Rep. 9(1):10502. doi: 10.1038/s41598-019-46685-9

Open Access

Alison Baker at the University of Leeds is the corresponding author of this UK, Dutch collaboration that includes David Carrier as first author. They characterise the peroxisomal ABC transporter, Comatose (CTS) through mutagenesis of key residues responsible for the proteins intrinsic acyl-CoA thioesterase (ACOT) activity. Ultimately they show that ACOT activity depends of endogenous ATPase activity but that these activities could be functional separated by mutagenesis of key residues.


Grison M, Kirk P, Brault M, Wu XN, Schulze WX, Benitez-Alfonso Y, Immel F, Bayer EMF (2019). Plasma membrane-associated receptor like kinases relocalize to plasmodesmata in response to osmotic stress. Plant Physiol. pii: pp.00473.2019. doi: 10.1104/pp.19.00473

Open Access

GARNet advisory committee member Yoselin Benitez-Alfonso and members of her research group are co-authors on the next two studies. This work is led by Magali Grison in Emmanuelle Bayer’s lab in Bordeaux. They show that the PM-localised Leucine-Rich-Repeat Receptor-Like-Kinases (LRR-RLKs), QSK1 and IMK2 relocate and cluster to the plasmodesmata under osmotic stress conditions. Through a variety of assays that focuses on QSK1 the authors show that reorganisation of RLKs can be important for the regulation of callose deposition at plasmodesmata and under osmotic stress this can have a functional effect on lateral root development.


Rongkaumpan G, Amsbury S, Andablo-Reyes E, Linford H, Connell S, Knox JP, Sarkar A, Benitez-Alfonso Y, Orfila C (2019) Cell Wall Polymer Composition and Spatial Distribution in Ripe Banana and Mango Fruit: Implications for Cell Adhesion and Texture Perception. Front Plant Sci. 10:858. doi: 10.3389/fpls.2019.00858

Open Access

Ganittha Rongkaumpan is first author on this interdisciplinary collaborative research from multiple departments at the University of Leeds. They characterise the composition of the cell wall in two fruits, banana and mango, which soften during ripening. The authors compared structural information, obtained using Atomic Force Microscopy and biochemical analysis, with data from rheology and tribology assays to understand why these fruits feel different in the mouth during ingestion.


Skelly MJ, Malik SI, Le Bihan T, Bo Y, Jiang J, Spoel SH, Loake GJ (2019) A role for S-nitrosylation of the SUMO-conjugating enzyme SCE1 in plant immunity Proc Natl Acad Sci U S A. pii: 201900052. doi: 10.1073/pnas.1900052116

Michael Skelly from the University of Edinburgh is the lead author of this study from the labs of Gary Loake and GARNet chairman Steven Spoel. They investigate the mechanism through which nitric oxide signaling after pathogen recognition stimulates inhibitory S-nitrosylation of the Arabidopsis SUMO E2 enzyme, SCE1. S-nitrosylation occurs on the evolutionary conserved Cys139 of SCE1 and they investigate the wider significant of this residue in the control of immune responses across eukaryotes.


MacGregor DR, Zhang N, Iwasaki M, Chen M, Dave A, Lopez-Molina L, Penfield S (2019) ICE1 and ZOU determine the depth of primary seed dormancy in Arabidopsis independently of their role in endosperm development. Plant J. 98(2):277-290. doi: 10.1111/tpj.14211

Open Access

Dana MacGregor (now at Rothamsted Research) leads this work from the lab of Steve Penfield at the JIC that investigates the extent of control on depth of primary dormancy that is mediated by the endosperm-expressed transcription factors ZHOUPI (ZOU) and INDUCER OF CBF EXPRESSION1 (ICE1). These effects are additive and independent of their role in endosperm development since the dormancy defect in ice1 and zou mutants can be ameliorated without altering seed morphology. They show that ICE1 acts primarily through control of ABA INSENSITIVE 3 (ABI3).


Footitt S, Walley PG, Lynn JR, Hambidge AJ, Penfield S, Finch-Savage WE (2019) Trait analysis reveals DOG1 determines initial depth of seed dormancy, but not changes during dormancy cycling that result in seedling emergence timing. New Phytol. doi: 10.1111/nph.16081

This research is a collaboration between the John Innes Centre and the Universities Liverpool and Warwick, from which Steven Footitt is first author. They used two Arabidopsis ecotypes that have differences in the timing of seedling emergence to identify new QTLs involved in depth of seed dormancy and Seedling Emergence Timing (SET). They revealed that DOG1 is important for determining depth of dormancy. In addition they identified three new SET QTLs, which are each physically close to DOG1, that play a role in the control of SET in the field.


Lobo AKM, Orr D, Gutierrez MO, Andralojc J, Sparks C, Parry MAJ, Carmo-Silva E (2019) Overexpression of ca1pase decreases Rubisco abundance and grain yield in wheat. Plant Physiol. pii: pp.00693.2019. doi: 10.1104/pp.19.00693

Open Access

This research from Lancaster Environmental Centre and their Brazilian collaborators is led by Ana Karla Lobo and demonstrates that overexpression of 2-carboxy-D-arabinitol-1-phosphate phosphatase (CA1Pase) in wheat causes a reduction in above ground biomass and compromises wheat grain yields. As CA1Pase is involved in removing inhibitors of Rubisco activity this result is contrary to the anticipated outcome. This suggests that Rubisco inhibitors might actually protect enzyme activity, thus maintaining the number of active sites that the enzyme is able to support.


Zhao SQ, Li WC, Zhang Y, Tidy AC, Wilson ZA (2019) Knockdown of Arabidopsis ROOT UVB SENSITIVE4 Disrupts Anther Dehiscence by Suppressing Secondary Thickening in the Endothecium. Plant Cell Physiol. doi: 10.1093/pcp/pcz127

Shu-Qing Zhao is the lead author on this China-UK collaboration that includes Alison Tidy and Zoe Wilson from the University of Nottingham. They show that using an artificial microRNA to reduce levels of the RUS4 gene in Arabidopsis causes a decline in male fertility. They perform a detailed analysis of the RUS4 expression module and how it impacts fertility.

GARNet Research Roundup: July 26th 2019

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

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

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

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

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

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

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


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

Open Access

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

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

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

Open Access

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

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

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

Open Access

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


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

Open Access

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


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

Open Access

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


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

Open Access

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

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

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

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


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

Open Access

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

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

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

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


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

Open Access

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


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

Open Access

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


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

Open Access

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

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

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

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

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

John Innes Centre Gene Editing Workshop.

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Published on: July 22, 2019

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

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

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

Professor Harwood introduces the workshop. Photo @SadiyeHayta

Expanding UK capability in gene editing of crops

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

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


Demonstrating a clear community need.

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

Success Stories

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

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

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


Growing plants can be surprisingly challenging!

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

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

Penny Hundleby overseeing the Brassica transformation practical Photo @MarkSmedley15

Overcoming the challenges of HDR.

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

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

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

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


Future technologies

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

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

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

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

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

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

Relaxing after the meeting. Photo @SadiyeHayta

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

GARNet Research Roundup: July 5th 2019

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

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

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

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


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

Open Access

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


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

Open Access

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

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

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

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


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

Open Access

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


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

Open Access

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


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

Open Access

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

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

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

Open Access

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


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GARNet Research Roundup: June 12th 2019

In another big edition of the GARNet Research Roundup we cover many different areas of research that utilise a varied group of experimental organisms!

The first paper from the Feng lab at the John Innes Centre performs an assessment of the factors influencing heterochromatin activity in sperm companion cells. Second is work from the JIC and Cardiff University that looks at the role of an auxin minima during fruit valve margin differentiation.

The next two papers have authors from Edinburgh. Firstly the McCormick lab has developed a stereo-based 3D imaging system for plants while Steven Spoel is a co-author on a study that looks at the pathogen responsive gene NPR1.

Coming from across the M8 is a paper from the Christie lab in Glasgow that looks into using phototropin genes as potential targets for crop improvement.

The next paper is from Oxford Brookes University where they visualise the movement of protein nanodomain clusters within the plasma membrane. Elsewhere in Oxford is a paper from the van der Hoorn group that characterises the effect of a novel triazine herbicide.

Two papers from the University of Durham also identify and characterise the role of novel herbicides, in this case on the activity of inositol phosphorylceramide synthases.

The final five papers feature research that each use different experimental organisms. Firstly a paper from the Earlham Institute uses delayed fluorescence to investigate the circadian clock in wheat and OSR. Second is a paper from Warwick that assesses the role of nodulation during nitrogen uptake in Medicago. The next paper features the Yant lab at University of Nottingham looks at growth of two species of Arabidopsis in challenging environments.

The penultimate paper includes authors from the University of Oxford and provides a detailed analysis of the factors controlling leaf shape in Cardamine and Arabidopsis thaliana. The final paper uses the imaging facility at the Hounsfield facility in Nottingham to image the roots of date palms.


He S, Vickers M, Zhang J, Feng X (2019) Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife. doi: 10.7554/eLife.42530

Open Access

Lead author on his paper is Shengbo He from Xiaoqi Feng’s lab at the John Innes Centre. This work looks at activation of Transposable elements (TEs) in the sperm companion cell of Arabidopsis. This is catalyzed by the DEMETER-catalyzed DNA demethylation in regions depleted of histone H1, demonstrating a key role for H1 in determining heterochromatin activity.

https://elifesciences.org/articles/42530

Li XR, Vroomans RMA, Fox S, Grieneisen VA, Østergaard L, Marée AFM (2019) Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening. Mol Plant. doi: 10.1016/j.molp.2019.05.003

Open Access

Xin-Ran Li and Renske Vroomans are co-lead authors on this work from the Ostergaard, Grieneisen and Maree labs from the John Innes Centre and (now) Cardiff University.They look at the role of an auxin minima in the control of valve margin differentiation in Arabidopsis fruit. They used a cycle of experimental-modeling to develop a model that predicts the maturation of the auxin minimum to ensure timely fruit opening and seed dispersal.


Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ (2019) A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth. Gigascience. doi: 10.1093/gigascience/giz056

Open Access

Gytis Bernotas from UWE and Livia Scorza from the McCormick lab at the University of Edinburgh lead this work that is the result of a 2+ year collaboration with the Melvyn Smith and others at the Computer Machine Vision (CMV) facility at UWE. The authors have developed hardware and software (including a deep neural network) to automate the 3D imaging and segmentation of rosettes and individual leaves using a photometric stereo approach.

https://academic.oup.com/gigascience/article/8/5/giz056/5498634

Chen J, Mohan R, Zhang Y, Li M, Chen H, Palmer IA, Chang M, Qi G, Spoel SH, Mengiste T, Wang D, Liu F, Fu ZQ (2019) NPR1 promotes its own and target gene expression in plant defense by recruiting CDK8. Plant Physiol. doi: 10.1104/pp.19.00124

GARNet chairman Steven Spoel is a co-author on this US-led study with Jian Chen as lead author. The paper investigates the interacting partners of NPR1 (NONEXPRESSER OF PR GENES 1), which is a master regulator of salicyclic signaling and therefore an important regulation of plant defense response.


Hart JE, Sullivan S, Hermanowicz P, Petersen J, Diaz-Ramos LA, Hoey DJ, Łabuz J, Christie JM (2019) Engineering the phototropin photocycle improves photoreceptor performance and plant biomass production. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1902915116

Open Access

Jaynee Hart is first author on this research from Christie lab at the University of Glasgow in which they target the phototropin blue light receptor as a candidate for crop improvement. They showed plants that engineered to have a slow-photocycling version of PHOT1 or PHOT2 had increased biomass under low light conditions, due to their increased sensitivity to low light.


McKenna JF, Rolfe DJ, Webb SED, Tolmie AF, Botchway SW, Martin-Fernandez ML, Hawes C, Runions J (2019) The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1819077116

Open Access

Joe McKenna from Oxford Brookes University leads this work that takes advantage of their superb imaging facilities to assess the dynamic regulation of specific protein clusters in the Arabidopsis plasma membrane. They show that the cytoskeleton (both actin and microtubule) and the cell wall play roles in the control of intra-PM moment of the pathogen receptor FLS2 and the auxin transporter PIN3.

https://www.pnas.org/content/early/2019/06/07/1819077116

Morimoto K, Cole KS, Kourelis J, Witt CH, Brown D, Krahn D, Stegmann M, Kaschani F, Kaiser M, Burton J, Mohammed S, Yamaguchi-Shinozaki K, Weerapana E, van der Hoorn RAL (2019) Triazine probes targeting ascorbate peroxidases in plants. Plant Physiol. doi: 10.1104/pp.19.00481

Open Access

Kyoko Morimoto is first author on this UK-German-Japanese collaboration led from the lab of GARNet committee member Renier van der Hoorn. They characterise the herbicidal effect of the small 1,3,5-triazine KSC-3 on ascorbate peroxidases (APXs) across a range of plant species.


Pinneh EC, Stoppel R, Knight H, Knight MR, Steel PG, Denny PW (2019) Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana. PLoS One. doi: 10.1371/journal.pone.0217087

Open Access

Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW (2019) The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Sci Rep. doi: 10.1038/s41598-019-44544-1

Open Access

Elizabeth Pinneh leads these two papers from the Denny lab in Durham. In the first paper they use RNAseq data and analysis of overexpression transgenic lines to define the role of inositol phosphorylceramide synthase (IPCS) during abiotic and biotic stress responses.

Secondly they screened a panel of 11000 compounds for their activity against the AtIPCS2 in a yeast two-hybrid assay. Successful hits from the screen were confirmed with in vitro enzyme assays and in planta against Arabidopsis.


Rees H, Duncan S, Gould P, Wells R, Greenwood M, Brabbs T, Hall A (2019) A high-throughput delayed fluorescence method reveals underlying differences in the control of circadian rhythms in Triticum aestivum and Brassica napus. Plant Methods. doi: 10.1186/s13007-019-0436-6

Open Access

Hannah Rees from Anthony Hall’s lab at the Earlham Institute leads this methods paper that introduces the use of delayed fluorescence to investigate the circadian rhythms in wheat and oil seed rape.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0436-6

Lagunas B, Achom M, Bonyadi-Pour R, Pardal AJ, Richmond BL, Sergaki C, Vázquez S, Schäfer P, Ott S, Hammond J, Gifford ML (2019) Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula. Mol Plant. doi: 10.1016/j.molp.2019.03.014

Open Access

Beatriz Lagunas is lead author on this paper from the University of Warwick that investigates the role of nodulation in actual nitrogen uptake by the roots of Medicago truncatula. They use integrated molecular and phenotypic analysis to determine that the respond to nitrogen flux are processed on a whole plant level through multiple developmental processes.

https://www.cell.com/molecular-plant/fulltext/S1674-2052(19)30127-3?

Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L (2019) Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils Philos Trans R Soc Lond B Biol Sci. doi: 10.1098/rstb.2018.0243

Open Access

Veronica Preite is first author on this UK-German collaboration led by Ute Kraemer and Levi Yant in Nottingham. They performed whole genome resequenced of 64 individuals of two Arabidopsis species that grow on calamine metalliferous sites (which have toxic levels of the zinc and cadmium). They revealed a modest amount of gene and network convergence in plants that have colonised these challenging environments.


Kierzkowski D, Runions A, Vuolo F, Strauss S, Lymbouridou R, Routier-Kierzkowska AL, Wilson-Sánchez D, Jenke H, Galinha C, Mosca G, Zhang Z, Canales C, Dello Ioio R, Huijser P, Smith RS, Tsiantis M (2019) A Growth-Based Framework for Leaf Shape Development and Diversity. doi: 10.1016/j.cell.2019.05.011

Open Access

Claudia Canales and Carla Galinha from Oxford are co-authors on this German-led study from Miltos Tsiantis’ lab that performs a detailed dissection of the growth parameters that control differences in leaf-shape in Cardamine and Arabidopsis. They show critical roles for the SHOOTMERISTEMLESS and REDUCED COMPLEXITY homeobox proteins to define differences in shape determination.


Xiao T, Raygoza AA, Pérez JC, Kirschner G, Deng Y, Atkinson B, Sturrock C, Lube V, Wang JY, Lubineau G, Al-Babili S, Ramírez LAC, Bennett MJ, Blilou I (2019) Emergent Protective Organogenesis in Date Palms: A Morpho-devo-dynamic Adaptive Strategy During Early Development. Plant Cell. doi: 10.1105/tpc.19.00008

Open Access

Members of the Hounsfield CT Imaging Facility 
at the University of Nottingham are co-authors on this paper that is led by Tingting Xiao from KAUST in Saudi Arabia. The paper takes a detailed look at root morphology in Date Palm.

GARNet Research Roundup: March 21st 2019

This edition of the GARNet research roundup begins with a study from the John Innes Centre that investigates the role of auxin in the control of fruit development in Capsella.

Auxin is also a central focus of the next paper that is from SLCU, in which the authors characterise the role of different types of auxin transport during shoot development. The third paper, also from Cambridge, identifies a new function for members of the DUF579 enzyme family. The final paper from Cambridge reports on an outstanding citizen science project that looks at how different temperature and light conditions influence the growth of spring onions.

The next paper is from the University of Glasgow and investigates the role of the SNARE protein complex during vesicle transport in Arabidopsis.

The final two papers include authors from the University of Nottingham. Firstly Anthony Bishopp leads research that defines determinants of vascular patterning across plant species. Finally Don Grierson is a co-author on work that has identified novel signaling components involved in the response to hypoxia in Persimmon and Arabidopsis.


Dong Y, Jantzen F, Stacey N, Łangowski Ł, Moubayidin L, Šimura J, Ljung K, Østergaard L (2019) Regulatory Diversification of INDEHISCENT in the Capsella Genus Directs Variation in Fruit Morphology. Curr Biol. doi: 10.1016/j.cub.2019.01.057

Open Access

This research from Lars Ostergaard’s lab in the John Innes Centre is led by Yang Dong. The work is primarily conducted in Capsella and investigates the role of the INDEHISCENT (IND) protein in this plant, which has fruits that are morphologically distinct from those in Arabidopsis. Expression of CrIND controls fruit shape by influencing auxin biosynthesis leading to auxin accumulation in specific maxima that are localised to the fruit valves.

doi: 10.1016/j.cub.2019.01.057

van Rongen M, Bennett T, Ticchiarelli F, Leyser O (2019) Connective auxin transport contributes to strigolactone-mediated shoot branching control independent of the transcription factor BRC1. PLoS Genet. doi: 10.1371/journal.pgen.1008023

Open Access

Martin Van Rongen is the lead author on this research performed under the supervision of Ottoline Leyser at the Sainsbury Lab, Cambridge University. They investigate the hormonal signals that underpin the remarkable plasticity of shoot patterning, focusing on a genetic analysis of connective auxin transport (CAT), which moves the hormone across the stem (in contrast to up-down polar transport). Using multiple pin mutant plants, they show CAT is important in the regulation of strigolactone-mediated shoot branching. However shoot branching controlled by the BRANCHED1 transcription factor is reliant on the ABCB19 auxin export protein and is not significantly influenced by the activity of PIN proteins. Martin van Rongen discusses this paper on the GARNet YouTube channel.


Temple, H, Mortimer, JC, Tryfona, T, et al (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct. https://doi.org/10.1002/pld

Open Access

Henry Temple works with Paul Dupree at the University of Cambridge and leads this study that identifies a novel activity of two DUF579 enzymes in the methylation of glucuronic acid within highly glycosylated arabinogalactan proteins (AGPs). This differs from all other previously characterized DUF579 members that have been previously shown to methylate glucuronic acid within the cell wall component xylan.


Brestovitsky, A, Ezer, D (2019) A mass participatory experiment provides a rich temporal profile of temperature response in spring onions. Plant Direct. 2019; 3: 1– 11. https://doi.org/10.1002/pld3.126

Open Access

This citizen science project led by Anna Brestovitsky and Daphne Ezer was performed in collaboration with the BBC Terrific Scientific program. In this study primary school students from across the UK recorded the growth of spring onions over a two-week period, which was then cross-referenced with detailed hourly meteorological data. This allowed the authors to discern the effect of minute temperature and light changes on plant growth and perhaps more importantly demonstrated that even the youngest researchers, when involved a well-designed citizen science project, can yield very useful data.


Zhang B, Karnik RA, Alvim JC, Donald NA, Blatt MR (2019) Dual Sites for SEC11 on the SNARE SYP121 Implicate a Binding Exchange during Secretory Traffic. Plant Physiol. doi: 10.1104/pp.18.01315

Open Access

Ben Zhang and Rucha Karnik are first authors on this paper that continues Mike Blatt‘s lab’s study of SNARE proteins, which are involved in vesicle trafficking. This study defines a new amino acid motif within SNARE SYP121 that is needed for the binding of the SEC11 protein but is not involved in binding plasma membrane K+ channels. This motif is essential for assembly of the entire SNARE complex yet does not influence the interaction of SYP121 with the uptake of K+ ions.


Mellor N, Vaughan-Hirsch J, Kümpers BMC, Help-Rinta-Rahko H, Miyashima S, Mähönen AP, Campilho A, King JR, Bishopp A (2019) A core mechanism for specifying root vascular patterning can replicate the anatomical variation seen in diverse plant species. Development. doi: 10.1242/dev.172411

Open Access

Nathan Mellor is first author on this work led by the lab of Anthony Bishopp at the University of Nottingham. The primary accomplishment of this work is in the development of a mathematical model that is able to predict the role of auxin in the specification of vascular patterning during embryonic development. This model has been tested through experimental interrogation of both transgenic Arabidopsis plants and in a range of other species with different vascular development patterns. Importantly they show that a heterologous auxin input might not be as critical in vascular development when compared to growth patterns that arise from spatial constraints. The authors show that this model has broad relevance to define early vascular patterning across plant species.


Zhu QG, Gong Z, Huang J, Grierson D, Chen KS, Yin XR (2019) High-CO2/hypoxia-responsive transcription factors DkERF24 and DkWRKY1 interact and activate DkPDC2 promoter. Plant Physiol. doi: 10.1104/pp.18.01552

Open Access

Don Greirson is a co-author on this Chinese-led study that identifies a set of transcription factors from Persimmon ((Diospyros kaki). These TFs are involved in responses to high CO2 and the authors show that their Arabidopsis orthologs play a similar role. The authors introduce a new response module that may be important during this key environmental response.

GARNet Research Roundup: March 7th 2019

This edition of the GARNet research roundup begins with a study into the genetic basis of fertility in barley led by Sarah McKim from Dundee. Second is a study from Oxford and Leicester that characterizes the proteolytic control of chloroplast import. The third paper from Levi Yant’s group at JIC and Nottingham that attempts to discover the influence of polyploidism on population genomic effects whilst the fourth paper from Juliet Coates’ lab in Birmingham uses the growth of Arabidopsis to assess the potential of algal biomass as a biofertiliser. The next two papers include co-authors from Oxford and Warwick respectively and investigate different factors that control seed viability in Arabidopsis and Brassica oleracea. The final paper includes Seth Davies from York as a co-author on a study that looks at control of the circadian clock in field-grown Arabidopsis.


Zwirek M, Waugh R, McKim SM (2019) Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytol. doi: 10.1111/nph.15548

Open Access

Current GARNet committee members Sarah McKim is the leader of this study in which first author is Monica Zwirek. They investigate the mechanism through which the barley VRS genes contribute to spikelet fertility. They undercover the epistatic relationship between five VRS genes that explains how they contribute to controlling fertility of lateral spikelets. Importantly they demonstrate that various vrs mutant combinations improve fertility in a variety of ways, information that will be useful during the generation of new varieties of barley.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15548

Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science. doi: 10.1126/science.aav4467

Qihua Ling and William Broad are the first authors on this study from the Universities of Oxford and Leicester. They investigate the role of proteolysis in the functional control of chloroplast-envelope translocases, which are required for the transport of proteins from nucleus-encoded genes into the chloroplast. They identify two newly characterised proteins that function in the same pathway as the known ubiquitin E3 ligase SP1. These novel proteins, SP2 and CDC48, are both required for the movement of ubiquitinated proteins from the chloroplast outer envelope membrane (OEM) into the cytosol, where they are degraded by the proteolytic machinery. This process of chloroplast-associated protein degradation (CHLORAD) maintains tight control of the activity of OEM proteins and is essential for organelle function.

http://science.sciencemag.org/content/363/6429/eaav4467.long

Monnahan P, Kolář F, Baduel P, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Šrámková G, Bohutínská M, Arnold B, Weisman CM, Marhold K, Slotte T, Bomblies K, Yant L (2019) Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nat Ecol Evol. doi: 10.1038/s41559-019-0807-4.

Patrick Monnahan at the John Innes Centre is first author on this study from the Yant lab that has recently moved to the University of Nottingham. In this collaboration with colleagues in the US, Austria, Sweden, the Czech Republic and Slovakia, they have performed large scale sequencing on 39 populations of Arabidopsis arenosa. These plants have differing levels of ploidy and they are attempting to understand how ploidy effects population genomics. They demonstrate that the ploidy effects are subtle but significant and that masking of deleterious mutations, faster substitution rates and interploidy introgression will likely impact the evolution of populations where polyploidy is common.


Ghaderiardakani F, Collas E, Damiano DK, Tagg K, Graham NS, Coates J (2019) Effects of green seaweed extract on Arabidopsis early development suggest roles for hormone signalling in plant responses to algal fertilisers. Sci Rep. doi: 10.1038/s41598-018-38093-2

Open Access

This work from the Coates lab at the University of Birmingham is led by Fatemeh Ghaderiardakani and looked into the potential of algal extracts as biofertiliser. They showed that at >0.1%, extracts taken from the common green seaweed Ulva intestinalis inhibit Arabidopsis seed germination and root elongation. At lower concentrations primary root elongation was promoted albeit with a complete loss of lateral root formation. Elemental analysis allows the authors to suggest that this effect was mediated via a novel mechanism involving aluminium. Overall the authors caution against the use of algal biofertilisers due to potential unforeseen negative effects on plant growth.


Viñegra de la Torre N, Kaschani F, Kaiser M, van der Hoorn RAL, Soppe WJJ, Misas Villamil JC (2019) Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds. Biochem J. doi: 10.1042/BCJ20180911.

GARNet Committee member Renier van der Hoorn is a co-author on this German-led study that investigates how the activity of seed-localised proteases can affect Arabidopsis seed germination. This study has clear real-world application regarding the storage of economically important seed stocks. They show that vacuolar processing enzymes (VPEs) become more active during aging whilst the activity of serine hydrolases declines alongside seed quality. This information has allowed the authors to develop protease-activity-based markers that will provide information about seed quality.


Schausberger C, Roach T, Stöggl WM, Arc E, Finch-Savage WE, Kranner I (2019) Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing. Biochem J. doi: 10.1042/BCJ20180903

William Finch-Savage from the University of Warwick is a co-author on this Austrian-led study that looks at the effect of aging on the quality of Brassica oleracea seeds stored at two oxygen concentrations. Higher O2 causes a more rapid decrease in seed quality through aging yet in contrast aging did not alter the impact of the hormone ABA on seed viability. This study enables the authors to uncover two mechanisms that control seed quality that appear to act through different mechanisms.


Rubin MJ, Brock MT, Davis SJ, Weinig C (2019) QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana G3 (Bethesda). doi: 10.1534/g3.118.200770

Open Access

Seth Davies from the University of York is a co-author on this study led by Matthew Rubin from the University of Wyoming. They looked at the growth of Arabidopsis thaliana recombinant inbred lines grown in field conditions and found an extremely nuanced relationship regarding how QTLs that influence the circadian clock respond to environmental conditions. For example the authors showed that plant growth in June, July and September is controlled by different QTL architecture, demonstrating the complex regulation of the circadian clock in these field growth plants.

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