Strawberry Research Report: 2015

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Published on: December 24, 2015

This is a brief summary of some of the work published in 2015 by UK Strawberry researchers and it is perhaps unsurprisingly dominated by work undertaken at East Malling Research. Richard Harrison leads two studies that focus on different aspects of the diseases that effect strawberry yield while Louisa Robinson-Boyer heads an investigation into the role that arbuscular mycorrhizal fungi might play in enabling future growth of strawberries in drier condtions.
Elsewhere we introduce a study that the outlines the developement of a commercial SNP-array that will hopefully aid marker-assisted breeding and finally is a Spanish-led investigation into a class of enzymes that contribute to fruit softening.

March
Antanaviciute L, Šurbanovski N, Harrison N, McLeary KJ, Simpson DW, Wilson F, Sargent DJ, Harrison RJ (2015) Mapping QTL associated with Verticillium dahliae resistance in the cultivated strawberry (Fragaria × ananassa). Hortic Res 2:15009  http://dx.doi.org/10.1038/hortres.2015.9 Open Access

Wilt score of resistance (blue) and suspectible (purple) varieties.
Wilt score of resistance (blue) and suspectible (purple) varieties.

Richard Harrison (East Malling) is the UK lead on this collaboration with Italian researchers in a study that investigates the QTLs that confer resistance to Verticillium dahliae, an important strawberry pathogen. A population of octoploid strawberries that was segregating for pathogen resistance was screened over three field seasons and multiple QTLs were identified. These resistance QTLs appear to be additive in this situation and their associated markers are abundant in cultivated strawberry germplasm. The authors state that genetic gain is clearly possible through marker-assisted breeding in Strawberry.

Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-Vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E (2015) Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC Genomics 16:155  http://dx.doi.org/10.1186/s12864-015-1310-1 Open Access

This international collaboration includes a UK industrial contribution from researchers from AffymetrixUK and describes the development of a SNP-array to aid marker-assisted breeding of allo-octoploid cultivated strawberry. Sequence variants were identified from the sequencing of 19 varieties of available octoploid germplasm along with a diploid progenitor. Following genotyping of over 300 octoploid accessions, SNPs were analysed using Affymetrix software. Ultimately the finished array has SNPs evenly distributed across 28 chromosomes with an average density of one marker/0.5cM. The authors state that this array will allow quality genetic analysis including generation of high density linkage maps and will aid strawberry researchers to identify QTLs and provide a platform for use in future marker-assisted breeding strategies.

April
Boyer LR, Brain P, Xu XM, Jeffries P (2015) Inoculation of drought-stressed strawberry with a mixed inoculum of two arbuscular mycorrhizal fungi: effects on population dynamics of fungal species in roots and consequential plant tolerance to water deficiency. Mycorrhiza. 25(3):215-27   http://dx.doi.org/10.1007/s00572-014-0603-6

Louisa Robinson-Boyer from EMR is the corresponding author of this study that investigated the ability of cultivated strawberry to grow in drought conditions after inoculation with zero, one or two species of arbuscular mycorrhizal fungi (AMF). They showed that both species of Funneliformis AMF were able to co-colonise roots but that their relative abundance varied under different water stresses (reduced irrigation by up to 40%). The authors found that colonisation was beneficial but that single species inoculation gave similar benefits to a mixed population, irrespective of the amount of irrigation. This shows that the presence of colonisation was of principle importance. Addition of AMF to plants under drought conditions restored growth to the levels observed in plants grown with normally watering. This demonstrated that the growth of cultivated strawberries in drought conditions significantly benefits from the presence of AMF and therefore might suggest a long-term strategy to improve future production of this crop in changing climate conditions.

June
Xu X, Passey T, Wei F, Saville R, Harrison RJ (2015) Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry. Hortic Res. 2:15022  http://dx.doi.org/10.1038/hortres.2015.22 Open Access

This second paper led by Richard Harrison looks into novel soil microbial pathogens that may be a causative agent for declining strawberry yield. Multiple soil samples were collected from four sites, two that showed yield-decline and two without. The authors defined operational taxonomy units (OTU) of bacterial and fungal origin and were able to assign yield decline to four potential factors: 1- Low abundance of helpful bacterial populations, such as Bacillus and Pseudomonas 2- lack of nematophagous fungus (Paecilomyces sp) 3- high levels of two potential fungal root-rot pathogens and 4- overall wet soil conditions. The authors will use this information to identify true causative agents that contribute to strawberry yield decline. Furthermore the authors highlight that this amplicon-based metagenomics approach is useful for profiling novel soil microbiota communities.

It is an exciting time for the Harrison lab as in collaboration with The Genome Analysis Centre, they have just obtained BBSRC funding for a project to sequence the octoploid cultivated strawberry.

November
Paniagua C, Blanco-Portales R, Barceló-Muñoz M, García-Gago JA, Waldron KW, Quesada MA, Muñoz-Blanco J, Mercado JA (2015) Antisense down-regulation of the strawberry β-galactosidase gene FaβGal4 increases cell wall galactose levels and reduces fruit softening. J Exp Bot. http://dx.doi.org/10.1093/jxb/erv462 Open Access

This Spanish-led study includes UK representation from Keith Waldron at the Institute of Food Research. Softening of fruit is a significant issue when bringing strawberries to the market and is caused by an increase in the solubilization and depolymerization of pectins from cell walls. This study aimed to investigate the role that galactose-release plays in this process, a reaction that is catalyzed by β-galactosidase enzymes. One putative member of this enzyme family, FaβGal4 was identified using a novel strawberry expression array. The authors generated antisense transgenic strawberries that aimed to have reduced expression of FaβGal4. Two out of nine lines showed reduced expression of FaβGal4 (and also the related FaβGal1) that was coincident with fruits that were 30% firmer, analysed over three growing seasons. These plants have higher levels of galactose in their cell walls demonstrating that the role of the β-galactosidase enzyme was indeed inhibited in these lines. Therefore this indicates that the FaβGal4 gene represents an potential target for future breeding or transgenic strategies to generate strawberry plants that have firmer fruit.

Wheat Research Report: 2015

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Published on: December 23, 2015

In this Wheat Research Report we summarise some of the work published by UK wheat researchers in 2015. Given the importance of wheat for both UK and global food security there is plenty of UK work in this area that falls into a number of key areas:

– We highlight three pieces of research undertaken on the genome scale led by the Universities of Liverpool, Bristol and York, which aid to improve knowledge of the highly complex hexaploid wheat genome in order to improve future breeding efforts.

– On the phenotypic level we present studies led by both the John Innes Centre and NIAB that have identified wheat QTLs that are associated either with disease resistance or with the parameters that define grain yield.

– On the gene level researchers from Reading University investigate the role of the TIN gene on the water use efficiency associated with different levels of tillering.

– Elsewhere is a study that mixes digital imaging and field reconstructions with mathematical modeling to develop a methodology to assess the significance of the structure of the wheat canopy in final carbon gain.

– Finally we highlight a study that had high public awareness and that documents the results of a study in which transgenic wheat were generated with the aim of reducing aphid predation by production of a specific pheromone.

March

Griffiths S, Wingen L, Pietragalla J, Garcia G, Hasan A, Miralles D, Calderini DF, Ankleshwaria JB, Waite ML, Simmonds J, Snape J, Reynolds M (2015) Genetic dissection of grain size and grain number trade-offs in CIMMYT wheat germplasm. PLoS One. 10(3):e0118847. http://dx.doi.org/10.1371/journal.pone.0118847 Open Access

This is a collaboration between British, Argentinian, Mexican and Chilean researchers who investigated grain yield in a two CIMMYT varieties. Grain weight (GW) and number per unit area of land (GN) are principle components that determine grain yield and these components often show negative correlation. The CIMMYT varieties were crossed and a QTL loci was identified that showed increased GW but that did not change GN, therefore altering the usual trade off between these parameters. The authors suggest that this loci might be an attractive target for future marker-assisted breeding strategies aimed at developing higher yield wheat varieties.

June

Bruce TJ, Aradottir GI, Smart LE, Martin JL, Caulfield JC, Doherty A, Sparks CA, Woodcock CM, Birkett MA, Napier JA, Jones HD, Pickett JA (2015) The first crop plant genetically engineered to release an insect pheromone for defence. Sci Rep. http://dx.doi.org/10.1038/srep11183 Open Access

This study led by Johnathan Napier, Huw Jones and John Pickett at Rothamstead Research gained a large amount of pubilicity during its trial phase as it drew the attention of anti-GM campaigners. However for many commentators it represents an important point in the ongoing debate surrounding this technology as the public engagement undertaken by these researchers was effective in persuading the public that this was a worthwhile project. This paper reports on the findings from that study wherein hexaploid wheat was genetically engineered to produce a pheromone that aimed to reduce aphid predation. In lab experiments these pheromones were able to repel three species of aphids but in the field experiments these GM wheat showed no alteration in rate of predation. The authors suggest this might be due to erratic climatic conditions or unexpectiedly low overall insect numbers but they recognise that more work needs to be done to identify a class of pheromones that might work in this experimental system. In many ways this study is an important confirmation of the scientific process and should help persuade the general people that GM scientists are undertaking all the necessary controls before organisms with a novel genetic maekup are released into the environment.

October

Burgess AJ, Retkute R, Pound MP, Foulkes J, Preston SP, Jensen OE, Pridmore TP, Murchie EH (2015) High-Resolution Three-Dimensional Structural Data Quantify the Impact of Photoinhibition on Long-Term Carbon Gain in Wheat Canopies in the Field. Plant Physiol. 169(2):1192-204 http://dx.doi.org/10.1104/pp.15.00722 Open Access

This collaboration between crop scientists and mathematicians at the University of Nottingham and those at the University of Manchester investigates the importance of photoinhibition in the overall carbon gain of hexaploid wheat. This parameter has proven difficult to accurately assess due to the lack of data about the detailed architecture of the constantly fluctuating wheat canopy in the field. In this study they compare the canopies of three wheat species using a novel method that involves digital 3D reconstruction. This enables measurement of a range of parameters that subsequently allows an accurate assessment of light distribution throughout the canopy. This data feeds into a mathematical model that predicts that photoinhibition alone can contribute to a substantial reduction in carbon gain. The authors conclude that their model allows them to predict that even moderate changes to leaf angle at the upper levels of the wheat canopy can result in a large number of lower leaves attempting to photosynthesize in a severely light-limited location. When this information is allied to improved field phenotyping it might be possible to select for plants that have a maximal leaf arrangement. When these differences in canopy efficiency are scaled up then the changes in carbon gain will prove to be highly significant in absolute terms.

Hendriks PW, Kirkegaard JA, Lilley JM, Gregory PJ, Rebetzke GJ (2015) A tillering inhibition gene influences root-shoot carbon partitioning and pattern of water use to improve wheat productivity in rainfed environments. J Exp Bot. http://dx.doi.org/10.1093/jxb/erv457 Open Access
Wheat Tillering
Peter Gregory (Reading) is the UK lead on this UK-Australian collaboration where researchers investigate the role of the wheat TILLING INHIBITION (TIN) gene during measurements of water-use in rainfed environments. They used near-isogenic lines (NILs) that varied in expression of TIN to show that the root-shoot ratio increased two-fold following tillering in plants with expression of TIN. Following a range of measurements the authors are able to conclude that water use efficiency was increased in TIN-containing lines, resulting in increases in grain yield. Although TIN was associated with increased biomass, the significant influence of both genetics and environment means that the requirement remains for careful assessment of TIN-containing progeny.

Winfield MO, Allen AM, Burridge AJ, Barker GL, Benbow HR, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, King J, West C, Griffiths S, King I, Bentley AR, Edwards KJ (2015) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool Plant Biotechnol J. http://dx.doi.org/10.1111/pbi.12485 Open Access

This wheat SNP genotyping project involves researchers from Bristol and Nottingham Universities alongside those from the JIC and NIAB together with industrial assistance from Affymetrix. This highly descriptive study identifies a large number of SNPs useful for subsequent genotyping of hexaploid wheat and for SNP-tracking following introgression from different genetic stocks. Following initial sequencing, markers have been validated using an ultra-high-density genome array. In the spirit of open access, all the sequence information defined by this project is available at:

http://goo.gl/e4oEhs (Putative varietal SNPs from CerealDBs)

http://goo.gl/VdN5NW (Putative SNP probes from CerealDBs)

 

Harper AL, Trick M, He Z, Clissold L, Fellgett A, Griffiths S, Bancroft I (2015) Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat. Plant Biotechnol J. http://dx.doi.org/10.1111/pbi.12486 Open Access

Transcript Contribution from B+D genomes. From Plany Biotech journal
Transcript Contribution from B+D genomes. From Plant Biotech journal

Ian Bancroft at the University of York is corresponding author on this work that is a collaboration between his own lab and that of Simon Griffiths at the JIC. They have used de novo expression data together with a new genetic linkage map to develop an ordered set of nonredundant transcripts for each of the three A,B D subgenomes of hexaploid wheat (between 40K-60K unigenes from each sub-genome). An RNAseq dataset obtained from young leaf tissue was mapped to this reference sequence in order to define the relative expression of each homoeologues variant. This showed no dominance for a particular sub-genome but rather the most highly transcribed genes were distributed throughout each sub-genome. Assessment of wider genome areas was able to define regions where one genome was dominant over the other two as well as regions where one genome was repressed compared to the other two. This study offers further insights into the expression relationships between each sub-genome and adds to the other recent methylation data (outlined below) that offers a different insight into the nature of the hexaploid wheat genome.

 

December

Gardiner LJ, Quinton-Tulloch M, Olohan L, Price J, Hall N, Hall A (2015) A genome-wide survey of DNA methylation in hexaploid wheat Genome Biol 16(1):273 http://dx.doi.org/10.1186/s13059-015-0838-3 Open Access

Anthony Hall leads this University of Liverpool study that analyses the wheat genome by bisulfite sequencing to identify the differential methylation that occurs throughout the three sub-genomes of allohexaploid wheat. The authors correlate sub-genome specific promoter methylation with altered expression from each particular sub-genomes. They also conduct an experiment demonstrating that temperature has an impact on gene expression across all of the sub-genomes. Although there is significant variation between sub-genomes the authors show that patterns of methylation in the D-genome is conserved with regions in its diploid progenitor Aegilops tauschii.

 

Gordon A, Basler R, Bansept-Basler P,, Fanstone V, Harinarayan L,, Grant PK, Birchmore R, Bayles RA,, Boyd LA, O’Sullivan DM (2015) The identification of QTL controlling ergot sclerotia size in hexaploid wheat implicates a role for the Rht dwarfing alleles Theor Appl Genet. 128(12):2447-60 http://dx.doi.org/10.1007/s00122-015-2599-5

This academic-industry collaboration is led by researchers at NIAB and the University of Reading and tackles an aspect of plant biology that is of great interest to those interested in developing disease resistance wheat varieties. This study looks at infection success of Claviceps purpurea, which is fungal pathogen that infects a range of temperate grasses and is therefore economically important. Claviceps infection produces a sclerotia within the seed and, when ingested, can cause significant illness in mammals. Two varieties of winter hexaploid wheat were identified that showed more resistance to Claviceps so these were crossed to produce a doubled haploid mapping population. Following phenotypic assessment of sclerotia development, QTLs were identified that mapped to reduced height (Rht) loci and therefore indicates that semi-dwarf varieties may display resistance to Claviceps infection.

Brassica Research Report: 2015

The Arabidopsis Research Roundup has been put to bed for 2015 so in the leadup to the Christmas we’ll take a look at some of the papers that have been published in 2015 by UK researchers working ondifferent plants.
Today we focus on Brassica species and by looking at papers from throughout 2015 this selection touches on a broad selection of research areas. Chronologically first is a study from Nottingham University that looks at the ability of Brassica rapa to take up specific elements, such as Zn, Ca and Mg. Secondly is a study that documents the parameters that make different cultivars of Brassica napus useful in biorefining. Thirdly we highlight where Brassica oleracea has been used both in preference to, and alongside Arabidopsis in a study that investigates meiotic recombination. Next is a study that investigates the relationship between leaf colour and insect herbivory. Finally we highlight a recent publication from the John Innes Centre that demonstrates the ability to generate gene-edited B.oleracea.
The varieties of Brassica
March

Blasco B, Graham NS, Broadley MR (2015) Antioxidant response and carboxylate metabolism in Brassica rapa exposed to different external Zn, Ca, and Mg supply.
J Plant Physiol. 176:16-24 http://dx.doi.org/10.1016/j.jplph.2014.07.029
Martin Broadley and Neil Graham from Nottingham University lead this study that investigates antioxidant response and carboxylate metabolism in Brassica rapa. The authors looked at these parameters in the presence of varying amounts of zinc, calcium or magnesium in experiments that aimed to simulate the response to deficiency or toxicity of these elements. Plants grown with high concentrations of these elements showed increased shoot biomass, hydrogen peroxide, total ascorbate and increasing activity of enzymes involved in removal of antioxidants. This indicates that B.rapa is particularly sensitive to high levels of these elements. The information provided in this study represents important baseline measurements that will aid the future characterisation of B.rapa TILLING lines, generated by the RevGenUK service at the JIC.

July

Wood IP, Wellner N, Elliston A, Wilson DR, Bancroft I, Waldron KW (2015) Effect of Brassica napus cultivar on cellulosic ethanol yield. Biotechnol Biofuels. 8:99. http://dx.doi.org/10.1186/s13068-015-0278-z Open Access
Keith Waldron (Institute of Food Research, JIC) leads this collaboration with the University of York that investigates how the sugar composition of Brassica napus alters its ability to be used as a source for biorefining. They found significant differences in the saccharification and fermentation yields after the processing of straw obtained from 17 different B.napus cultivars. Surprisingly glucan-rich straw was not correlated with higher saccharification or ethanol yields but rather the non-cellulosic components were more reliable indicators of substrate quality, with the amount of pectins and arabinogalactans having the greatest impact on saccharification. Ultimately this study finds that pectin concentration is most likely to determine to effectiveness of the cultivar in the production of bioethanol. This is important information for the future development of different dicot species for use in this aspect of biorefining.

July

Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372 http://dx.doi.org/10.1371/journal.pgen.1005372 Open Access

Immunolocalisation of proteins during meiotic recombination in Brassica.
Immunolocalisation of proteins during meiotic recombination in Brassica.

Chris Franklin (Birmingham) is the leader on the UK-US-Austrian collaboration that looks at the role of the PCH2 protein during meiotic recombination. Although much of this study uses Arabidopsis mutant plants, the initial immunoprecipitations that led to identification of novel factors were performed using pollen mother cells from Brassica oleracea. Subsequently some important imaging also takes place in B.oleracea. The authors use structured illumination microscopy (SIM) to investigation the localisation of synaptonemal complex formation during meiosis and the close relationship between Arabidopsis and B.oleracea allowed the authors to use to same reagents fo these experiments. This paper was featured in an Arabidopis Research Roundup earlier in the year.

September.

Green JP, Foster R, Wilkins L, Osorio D, Hartley SE (2015) Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea). PLoS One 10(9):e0136884 http://dx.doi.org/10.1371/journal.pone.0136884 Open Access

This collaboration between York and Sussex Universitites is led by Sue Hartley and Daniel Osorio and look into the role that leaf colour plays in the defence response in wild cabbage. This aspect of plant physiology has been proposed as being important in defence against insect herbivory but this is the first instance where real data from wild populations has been obtained on this topic. The authors found that variation in leaf colour and brightness corresponded to particular glucosinolate levels as well as of the ability of certain herbivores to colonise the leaves. As might be predicted, leaves with lower levels of glucosinolate coincided with faster growth rates of lepidopteran larvae. However in a controlled experiment neither adult butterflies or adult aphids showed a preference for leaves of different colours. This therefore might suggest that although in the field herbivores may benefit from colonising leaves with lower defence chemicals (and an altered colour), the adults do not have the ability to select for these particular leaves, indicating that selection of leaves is either down to chance or other uninvestigated parameters.

November.

Lawrenson T, Shorinola O, Stacey N, Li C, Østergaard L, Patron N, Uauy C, Harwood W (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease Genome Biol. 16:258. http://dx.doi.org/10.1186/s13059-015-0826-7 Open Access

An example of successfully gene edited Brassica. From Genome Biology
An example of successfully gene edited Brassica. From Genome Biology

This is a collaboration between Wendy Harwood, Cristobal Uauy, Nicola Patron and Lars Ostargaard from the John Innes Centre and the Sainsbury Lab in Norwich. Over the past few years, CRISPR-Cas technology has been presented as important technology to be used in the future generation of gene edited crops. However only a few studies have been published to date where this technology has been effectively used. This paper describes the use of CRISPR-Cas to generate specific mutations in both barley and Brassica oleracea. Across both species they identified targeted mutations in 10%-25% of the first generation plants although interestingly they were also able to identify B.oleracea mutants in the T0 generation. They also observed off-target activity in both species even though the designed guide RNAs contains mismatches with the incorrectly edited sequences.
This is important work demonstrating that this type of gene editing can be used to rapidly generate stable mutants in crop species. The creation of mutants in off-target genes is a potential concern from a regulatory perspective although can be viewed as a positive factor for targeting multigene families that do not have appropriate identical target sequences.

Arabidopsis Research Roundup: December 18th

The final Arabidopsis Research Roundup of 2015 contains a bumper crop of papers that again highlights the diversity of research occuring in UK plant science. Justin Goodrich from the University of Edinburgh kindly provides an audio description of work that identifies a novel role for a member of a transposon gene family. Elsewhere are studies about a specific aspect of the biochemistry of crytochromes as well as confirmation of a role for DNA gyrases in Arabidopsis. Paul Dupree (Cambridge) leads a study into the mechanism of ascorbic acid production while Heather Knight is the UK representative in a study about cell wall composition. We also present an investigation into the mechanism and subsequent expression changes that occur following infection with different isolates of the Turnip Mosaic Potyvirus. Finally are two short studies from Ive de Smet (Nottingham) and Matt Jones (Essex).

Liang SC, Hartwig B, Perera P, Mora-García S, de Leau E, Thornton H, de Alves FL, Rapsilber J, Yang S, James GV, Schneeberger K, Finnegan EJ, Turck F, Goodrich J (2015) Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2. PLoS Genet. 11 e1005660. http://dx.doi.org/10.1371/journal.pgen.1005660 Open Access

Justin Goodrich (Edinburgh) is the lead of this collaborative study between UK, German and Australian researchers that investigates the role of the evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) genes during plant development. These homeotic genes influence gene expression by causing epigenetic chromatin changes, usually in the form of histone methylation. Previously the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene was found to act as a genetic suppressor the Arabidopsis PcG gene, LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In this study ALP1 is shown to genetically interact with members of these two gene families and its activity is necessary for the activation of several floral homeotic genes. Surprisingly the ALP1 gene is shown to encode for a transposase of the PIF/Harbinger class, which is conserved throughout land plants. The authors suspect that the transposase activity has been lost in the angiosperm lineage, where the gene obtained a novel function. Interestingly ALP1 can interact with the core PrC complex, which most notably participates in H3K27me3 methylation and therefore appears to act, along with other proteins such as EMBRYONIC FLOWER 1 (EMF1), as a plant-specific accessory component that controls histone modification. The authors speculate that this novel function might have arisen as a “means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity”. Over the coming years it will be interesting to discover if other transposon-encoded genes share novel functions and this study represents an important lesson for researchers not to ignore transposon sequences as ‘junk’ DNA that they might feel can clutter up their analysis!

Justin Goodrich kindly provides an audio summary of this paper:

van Wilderen LJ, Silkstone G, Mason M, van Thor JJ, Wilson MT (2015) Kinetic studies on the oxidation of semiquinone and hydroquinone forms of Arabidopsis cryptochrome by molecular oxygen FEBS Open Bio. 5:885-892 http://dx.doi.org/10.1016/j.fob.2015.10.007 Open Access

This study is a collaborative effort between researchers from Imperial College and the University of Essex, led by emeritus biochemistry Professor Michael Wilson and is an in vitro analysis of the oxidation of the Arabidopsis cryptochrome (CRY) photoreceptor in the presence and absence of an external electron donor. They show that a more complex model than previously thought is required to explain the mechanism by which the CRY-associated flavin molecule is oxidised. The authors propose that the final steps in this reaction require cooperative interaction between partners in a CRY homodimer or between separate CRY molecules.

Evans-Roberts KM, Mitchenall LA, Wall MK, Leroux J, Mylne JS, Maxwell A (2015) DNA Gyrase is the Target for the Quinolone Drug Ciprofloxacin in Arabidopsis thaliana. J Biol Chem. http://dx.doi.org/10.1074/jbc.M115.689554 Open Access

Antony Maxwell from the Biological Chemistry department from the John Innes Centre is the UK academic lead on this UK-Australian study. This group has previously shown that Arabidopsis contains three proteins thought to function as DNA Gyrases (AtGYRA, ATGYRB1, ATGYRB2) although they could not provide direct evidence that are were involved in DNA supercoiling. This study moves the work on by identifying mutant plants that are resistant to the drug ciprofloxacin and contain a point mutation in AtGYRA. Furthermore ATGYRA heterologously expressed in insect cells has supercoiling activity. Therefore the authors unequivocally show that plants encode an organellar-targeted DNA gyrase that, like bacterial gyrases, is a  target for ciprofloxacin. This work has important consequences for our understanding of plant physiology and in the future development of novel herbicides.

Sawake S, Tajima N, Mortimer JC, Lao J, Ishikawa T, Yu X, Yamanashi Y, Yoshimi Y, Kawai-Yamada M, Dupree P, Tsumuraya Y, Kotake T (2015) KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis The Plant Cell http://dx.doi.org/10.1105/tpc.15.00379

Paul Dupree (Cambridge) is the British lead on the UK-Japanese collaboration that investigates the role of the GDP-mannose pyrophosphorylase (GMPP), VITAMIN C DEFECTIVE1 (VTC1) enzyme in catalysis of the rate-limiting step in the production of ascorbic acid (AsA). They identify two novel pyrophosphorylase-like proteins, KONJAC1 (KJC1) and KJC2 that stimulate VTC1. Mutant analysis showed that these proteins are necessary for normal growth that coincides with control of AsA production via stimulating GMPP activity. Yeast 2 Hybrid  analysis is indicative of a direct interactin between KJC and VTC1 proteins. In future, it will be interesting to investigate the role of these proteins in plants that are more relevant to human consumption of AsA.

Sorek N, Szemenyei H, Sorek H, Landers A, Knight H, Bauer S, Wemmer DE, Somerville CR (2015) Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor MONGOOSE1. PNAS http://dx.doi.org/10.1073/pnas.1521675112

Heather Knight (Durham) is the sole UK representative on this manuscript that is led by the lab of Chris Somerville from the University of California. In this work the authors identified suppressors of the Arabidopsis cobra mutant, which have defects in cellulose formation. The appropriately named mongoose (mon1) mutant partially restored cellulose levels and also restored the esterification ratio of pectin to wild-type levels. MON1 was cloned to the MEDIATOR16 (MED16)/ SENSITIVE TO FREEZING6 (SFR6) locus and single mon1 mutants are resistant to cellulose biosynthesis inhibitors. Concomitantly, transcriptome analysis demonstrated that a set of ‘cell wall’ genes are misregulated in mon1/med16/sfr6, including two encoding pectin methylesterase inhibitors. Overall the authors suggest that cellulose biosynthesis is closely linked to esterification levels of pectin and offer a number of possible explanations for this functional relationship.

Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, López-González S, Jenner C, González-Melendi P, Elena SF, Walsh J, Ponz F (2015) Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns Mol Plant Microbe Interact. http://dx.doi.org/10.1094/MPMI-05-15-0111-R

The UK contributor to this Spanish-led study is Carol Jenner, who at the time was a research fellow at the University of Warwick. This study highlights the morphological changes that occur in Arabidopsis plants infected by different isolates of Turnip mosaic virus (TuMW). The UK1 and JPN1 versions of TuMW were shown to have highest levels of sequence divergence in the P3 cistron and following the generation and use of viral chimeras, it is this region that was identified as the major viral determinant of plant developmental changes. However when the P3 gene was constitutively expressed in Arabidopsis it did not cause any development effects, which highlights the importance of performing infection studies in a whole-plant context. Latterly the authors performed transcriptomic and interactomic analysis, showing that infection with the most severe UK1 strain primarily causes changes, perhaps unsurprisingly, in genes involved in transport and in the stress response.

Czyzewicz N, De Smet I (2015) The Arabidopsis thaliana CLAVATA3/EMBRYO-SURROUNDING REGION 26 (CLE26) peptide is able to alter root architecture of Solanum lycopersicum and Brassica napus. Plant Signal Behav http://dx.doi.org/10.1080/15592324.2015.1118598

This work was performed in the lab of Ive De Smet, who is a BBSRC research fellow at the University of Nottingham. In this short communication they show that overexpression of the Arabidopsis AtCLE26 peptide is able to induce architectural change in the agriculturally important crops, Brassica napus and Solanum lycopersicum. Having previously shown that AtCLE26 is similarly active in Arabidopsis, Brachypodium and Triticum, these experiments further demonstrate that small peptide signaling plays an important role in root development across plant lineages.

Litthauer S1, Battle MW1, Jones MA (2015) Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signal Behav. http://dx.doi.org/10.1080/15592324.2015.1126029

Matt Jones (Essex) leads this accompanying study to the more substantial project previously published in Plant Journal. This manuscript reports that phototropin photoreceptors are not involved in the nuclear accumulation of evening-phased circadian transcripts. In addition they show that even in phototropin mutants, the rhythms of nuclear clock transcript accumulation are maintained under fluctuating light regimes.

Arabidopsis Research Roundup: December 9th.

This December 9th Arabidopsis Research Roundup includes four rather different studies. Firstly we include an excellent audio description from David Salt about a new type of GWAS analysis that his lab was involved in developing. This allowed identification of new genetic loci involved in molybdenum signalling. Secondly Isabelle Carre’s group from Warwick presents a study into the interactions that define the functioning of the circadian clock. Thirdly Mike Blatt leads a study that models stomatal opening and finally we include an investigation of the DOG1 gene, that includes a contribution from Fuquan Liu.

Forsberg SK, Andreatta ME, Huang XY, Danku J, Salt DE, Carlborg Ö (2015) The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance PLoS Genet. e1005648. http://dx.doi.org/10.1371/journal.pgen.1005648 Open Access.

Current GARNet Chairman David Salt (Aberdeen) is the UK lead on this collaboration with the lab of Orjan Carlborg from Uppsala in Sweden. The novelty of this paper is in the development of a new technique to measure Genome-Wide Association using the variance in SNP differences instead of using the mean. Professor Salt explained this vGWA technique in the attached audio-file, which is especially useful for people not so familiar with GWAS. Using this vGWA technique the authors were able to re-analyse an old dataset to gain additional understanding of how certain genetic loci are regulated to explain differences in the production of the essential nutrient molybdenum. Overall this paper introduces an analysis technique that can hopefully be used by other members of the community to analyse/re-analyse their data with increased rigour.

This is the 10minute audio file where David explains the paper:

Adams S, Manfield I, Stockley P, Carré IA (2015) Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLoS One.10(12):e0143943. http://dx.doi.org/ 10.1371/journal.pone.0143943 Open Access

This collaboration between the Universities of Warwick and Leeds is led by Isabelle Carré and investigates the Arabidopsis circadian clock. They analysed the in vivo interactions of the LATE ELONGATED HYPOCOTYL (LHY) protein with promotors of other clock components. This uncovered a novel regulatory loop between LHY and the CIRCADIAN CLOCK ASSOCIATED-1 (CCA1) gene. Furthermore they show LHY acts as a repressor of all other clock components, clearly placing this protein as a key regulatory component of the Arabidopsis clock.

Minguet-Parramona C, Wang Y, Hills A, Vialet-Chabrand S, Griffiths H, Rogers S, Lawson T, Lew V, Blatt MR (2015) An optimal frequency in Ca2+ oscillations for stomatal closure is an emergent property of ion transport in guard cells. Plant Physiol. http://dx.doi.org/10.1104/pp.15.01607 Open Access

Mike Blatt is the corresponding author for this collaboration between Glasgow, Cambridge and Essex Universities. There are a good number of UK researchers who investigate the factors that regulate stomatal opening and this study looks at the role of calcium oscillations in this process. They have used the Arabidopsis OnGuard model that faithfully reproduces the optimum 10minute period of Ca2+ oscillation in guard cells. They used experimentally derived kinetics to describe the activity of ion transporters in the plasma membrane and tonoplast. Overall they discovered that the calcium oscillations are actually a by-product of the ion transport that determines stomatal aperature and not the overall controlling factor.

Cyrek M, Fedak H, Ciesielski A, Guo Y, Śliwa A, Brzeźniak L, Krzyczmonik K, Pietras Z, Liu F, Kaczanowski S, Swiezewski S (2015) Seed dormancy in Arabidopsis thaliana is controlled by alternative polyadenylation of DOG1 Plant Physiol. http://dx.doi.org/10.1104/pp.15.01483

Fuquan Liu (Queens, Belfast) is the UK contributor to this Polish-led study focused on the DOG1 gene, which is a key regulator of Arabidopsis seed dormancy. Previously it had been shown that the C-terminus of DOG1 is not conserved in many other plant species. The DOG1 transcript is alternatively polyadenylated and the authors show that Arabidopsis mutants that lack current 3’ RNA processing also show defects in seed dormancy. The shorter version of DOG1 is able to rescue the dog1 phenotype, which allows the authors to propose that DOG1 is a key regulator of seed dormancy and that the phenotypes of RNA processing mutants are linked to the incorrect processing of this specific mRNA species.

HVCfP Annual Meeting

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Published on: December 2, 2015

The High Value Chemicals in Plants (HVCfP) Network in a BBSRC-funded NIBB (Network in Industrial Biotechnology and Bioenergy) that is centered at the University of York. At the end of October, Cambridge Cottage at Kew Gardens hosted the HVCfP Annual Meeting that brought together over 80 interested members of the network to discuss recent research developments and their resulting commercial potential.

The schedule was comprised of invited keynote speakers as well as talks from contributors who have taken advantage of the funding opportunities provided by the network. These include the Proof of Concept (PoC) fund that are worth up to £50K as well as smaller Business Innovative Vouchers (BIV) (previously £5K, now increased to £10K). Funding opportunities are ongoing through the life of the NIBB so please check out funding (https://hvcfp.net/funding/) page for information about previous awards and current open calls.

The meeting kicked off with two keynote talks, firstly from Monique Simmons, deputy director of Kew Science who introduced the wide variety of resources associated with the Botanic Gardens. Over the past year, Kew has undergone a significant reorganization and has a renewed remit for interaction with the scientific community. Perhaps of greatest interest to GARNet readers will be the Kew DNA bank (http://apps.kew.org/dnabank/homepage.html) that contains over 40K samples from around the globe, the majority of which are available to order, either in aliquots suitable for PCR or in larger quantities if necessary.

David Hughes from Syngenta followed up with an excellent talk about the current situation surrounding the debate around Genetically Modified Crops. He gave his thoughts on why this ‘debate’ has gone on for almost 20 years even without any reliable evidence about the negative effects of developed crops. He thought the negative public response could be summed up by three emotions.

Essentialism: is the ‘essence’ of the original organism transferred to the crop

Naturalism: ‘Synthetic’ is evil, ‘natural’ is good.

Disgust: If something is not ‘100% safe’, then it must be bad.

David also advised that the power of narrative is a much more effective technique than the use of potentially bland scientific evidence, which usually falls on deaf ears amongst the public.

 

The day included two talks from commercial members of the HVCfP network that provided a contrast to the majority academic talks. They included a presentation from James King of Oxford Biotrans (http://oxfordbiotrans.com/), a company that is attempting to exploit biocatalytic routes to develop novel compounds. Their focus is on the use of cytochrome P450s and one of their initial challenges is to enzymatically produce nootkatone, which provides the flavor and scent from grapefruit. They aim to produce this compound via the intermediate Valecene, which can be collected from oranges. The unpredictable grapefruit harvest and the difficulties in isolation of endogeous nookatone mean that Oxford BioTrans suggest that using enzyme catalysis might be a more cost effective method for isolation of the high value product. The other SME that presented was Neem Biotech, which is located in the South Wales Valleys, a place not usually associated with biotechnology. Their major product is Vetrinol, which includes garlic extract and that is used for boosting the bovine immune system.

Cathie Martin discussing Cavity Spot

The remainder of talks featured researchers involved in PoC or BIV projects. These were all rather fascinating (especially for a researcher usually preoccupied by Arabidopsis) as they introduced novel compounds and non-model organisms that were ‘unusual’ to many in the audience. Cathie Martin (JIC) is well known for her work with purple tomatoes but here she presented her attempts to isolate the compound from Mugwort leaf extract that is responsible for reducing cavity root spot disease, which is caused by Pithium species of Oomycete. This work was performed in collaboration with ‘Root Crop Consultancy’ and resulted from an observation that carrots grown in the presence of mugwort were less susceptible to cavity spot disease.

Three talks that described research funded by PoC grants came from Gary Loake (Edinburgh), Luis Mur (Aberystwyth) and Mike Beale (Rothamstead) who each highlighted work aimed at to improve production from organisms already used to produce medicinally useful compounds. Gary Loake is hoping to develop the use of cambial meristematic cells (CMC) to improve paclitaxel biosynthesis from Taxus (Yew) (for review of CMCs http://www.sciencedirect.com/science/article/pii/S1871678415000205). The Taxus CMCs are able to produce plenty of paclitaxel so to improve this aspect they have analysed expression profiles in an attempt to identify the transcription factors that are important in this process. The ultimate aim would be to use synthetic biology approaches to potentially modify the expression of these TFs in order to maximise paclitaxel production.

Aberystwyth University has a strong tradition of research in Avena species (Oat) so Dr Mur is using these resources in order to understand and maximise the production of Avenanthramide, which has well-established medicinal benefits. The HVCfP money has funded the use of HPLC to analyse their germplasm for altered production of Avenanthramide. Broadly they have found that domesticated hexaploid Avena species have higher levels of the compound compared to wild diploid varieties. They are now conducting expression analysis in order to understand the molecular reason for these alterations.

Mike Beale is taking advantage of the National Willow Collection (NWC) to undertake a phytochemical and pharmacological screen in order to identify novel compounds. Willow (Salix) is famously the original source of aspirin so Dr Beale and colleagues are using NMR and MS in an attempt to analyse unpurified extracts from 200 species of Willow. By screening against a battery of cancer cell-lines, fungi and bacteria, they hope to identify extracts that can be further interrogated to find compounds of interest.

The other two talks resulting from BIV-funding were both focused on algae, although with organisms of different sizes! David Bailey from IOTA Pharmaceuticals outlined their plans to exploit the potential of using the macroalgae Sargassum muticum (seaweed) as a production chassis while Paul Knox (Leeds) and John Dodd (AlgaeCytes) described their early work to identify novel polysaccharides found in microalgae.

HVCfP_Davey
Matt Davey discussing Living Stones

The meeting ended with a series of flash presentations given by representatives of GARNet, the Liverpool GeneMill, the University of Essex Cell screening facility and finally from Matt Davey (Cambridge). His talk highlighted the incredible potential that is provided by plant species as he is developing commercial relationships to study the UV absorption properties of Living Stone species (Lithops). Initial experiments have shown that direct UV light is very successfully absorbed by Lithops species and this is of interest to the cosmetic industry.

Although much of the research presented in this meeting is in its infancy, the HVCfP Network can be pleased with the process it has made. With another set of PoC and BIV funding recently announced the network is supporting research in a wide range of organisms aimed at producing a varying array of compounds. The network has been providing funding since 2014 so the first set of PoC funding is now coming to an end. The true success of the network will be realised over the next two years, determined by the amount of follow-on funding that can be obtaining to support the research conducted in these seed-projects. We will watch this space with interest….

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