Weeding the Gems

Over the past few years, GARNet has kept track of papers (in the <a href="http://blog.garnetcommunity comparaison prix cialis.org.uk/arabidopsis-research-roundups/” target=”_blank”>ARR) that are published by UK researchers and feature Arabidopsis work of one sort or other.  When we look back over 2015 we documented 152 different papers featuring UK researchers, even though we probably miss one or two papers along the way.

When we look at the distribution of these papers it is unsurprising that Plant Physiology has the most papers given the size of each months edition. Other usually popular journals also feature toward the top: The Plant Cell, New Phytologist, Plant Journal and PLoS One. It is perhaps surprising that Journal of Experimental Botany (JXB) hasn’t had more Arabidopsis papers from UK researchers but this is likely due to the broader remit of that journal.

Overall approximately 70% of these papers are Open Access which seems to be good news for the communication of research from our Universities. Relatedly, in 2014 GARNet published a broader analysis of Publication Trends for Arabidopsis work that can be found here.

Note that only journals with two or more publications are included on this graph.

The very mention of differential equations or any other associated type of mathematics can be enough to have many biologists break into a cold sweat! I think it’s fair to comment that the prevailing opinion in the past has been that maths is ‘too complicated’ and that it doesn’t have ‘any relevance’ for their work.

However this idea is slowly changing with the appearance of more mathematic modeling in biological manuscripts and the need for cross-disciplinarity in grant applications. In basic terms, a partial differential equation aims to measure how parameters changes with respect to one another: which is exactly what any biologist is always studying. Therefore your research should, to a greater or lesser extent, be relevant for mathematical interrogation.

Therefore in order to facilitate interactions between biologists and mathematics, the ‘Mathematics in the Plant Sciences Study Group (MPSSG)’ was inaugurated in 2007 as part of the initial funding for the Centre for Integrative Biology (CPIB) at Nottingham University. Over the past 9 years these study groups have been extremely successful and have even directly led to a publication, which modeled the biomechanical parameters that are involved in anther opening (Nelson et al, New Phytologists, 2012, doi: 10.1111/j.1469-8137.2012.04329).

The 7^th MPSSG was held in Nottingham between Jan 4^th-7^th and took the same successful format as in other years. At the start of a meeting, three biologists presented a problem connected to their research, which had been selected by the organisers as being amenable for inclusion in this process.

As described below, these problems varied across the breadth of plant sciences so as to attempt to discriminate between the type of mathematics that might be applied to each case. After the initial presentations the biologists moved to seminar rooms where they were joined by a small group of mathematicians who are interested in modeling their problem. Over the course of the study group this evolved nicely as the mathematicians settled on a project that they were most interested in investigating. Most of these researchers were based in Nottingham although there were visitors from other UK and International universities.

On day one the discussions resembled a formal seminar session where the biologist led the mathematicians through the background of their problem. This is an interesting process as the mathematicians obviously had a very limited knowledge of each specific system, even though they might have some experience in modeling biological problems.

I observed this process for two of the study groups and it struck me that there was a tipping point at which time the mathematicians had taken onboard enough information about the problem to start to develop their own ideas. Suddenly at this point there were partial differential equations written on the whiteboard as the process began in earnest……

From this time onward the biologist plays a more advisory role whereas the mathematicians put in the hard work of transferring their initial equations into their analysis-program of choice. This is not a rapid process as the next two days are spent discussing and refining these models before the findings are presented on the final afternoon, just four days after most of the attendees will have first learnt about the topic!

The overall aim of the study groups is to begin to develop a model that can mathematically represent what is observed within the biological information.

In the initial stages of the process, I was somewhat surprised by how freely the mathematical ideas were discussed. In my experience, many biology-based discussions are often constrained by the need for an absolute requirement for the presence/absence/expression of a particular protein or gene in order to develop a hypothesis. However the mathematicians were unencumbered by this requirement and rather were able to throw ideas around, seeing what, if anything, would eventually stick. This ultimately might lead them blindly down closed alleyways but not always. Importantly it was clear that these discussions made the biologists look at their problem in a different way and each of the participating speakers had a list of future experiments that had resulted from these discussions.

More detail about the three problems presented in this study group can be found on the MPSSG website but in summary:

– Biosynthesis of Casparian strips: How to build a micron-scale bridge out of a lignin polymer? Presented by Dr Guilhem Lenaic (University of Aberdeen).

The molecular participants that play a role in the generation of the casparian strip (CS) are not well studied. Guilhem works in the lab of GARNet chair Professor David Salt and introduced the genes that are involved in this process and importantly, the patterns of CS that develop in different mutant plants. Simply put, the CS is a band of lignin that surrounds root endodermal cells ‘like an belt’ and plays an important role in water uptake, which is of clear importance not only for the growth of an individual plant but has broader relevance for issues of water use efficiency. The CS develops through a series of patterning steps that have at been, in part, genetically determined. Therefore the mathematicians attempted to develop a model that generated these patterns by parametrising the activity of different proteins as well as a monolignol lignin precursor molecule.

Ultimately they made some process developing both 1D and 2D models although, as with all the problems from the study group, there was still work to do. Arguably the best line from the presentation, used to account for a stray equation and was described as “classic-MPSSG”, was “oh yes…..that line was written on the whiteboard by John King…..but then he left….”.

– Modeling Leaf-Sheath Interactions in Grasses. Presented by Dr Douglas Cook (NYU Abu Dhabi).

This problem introduced the biomechanical interaction between a maize sheath and the leaf that wraps itself around the sheath, providing protection and mechanical strength to the underlying tissue. The leaf surrounds the sheath prior to internode elongation, so when the sheath start to elongate there is a frictional interaction between sheath and leaf. This can result in ‘slippage’ when the forces between sheath and leaf build up. Dr Cook mentioned that can is an economical important parameter as without the protective influence of the leaf, the maize stalk is weak and can be more easily bent.

Initially the mathematicians presented this problem as being equivalent to the interaction between two cylindrical tubes. Over the course of the workshop a number of models were developed, not all of which were successful but which highlighted the important trial-and-error nature of many of these interactions. A nice analogy for this process was the comparison to the seismic activity that builds up between tectonic plates. A favourite comment from the early discussions occurred when the sheath was described as an “infinite cylinder”…. certainly not the type of language commonly heard when discussing plant science problems!

– Hyperspectral image analysis of plants, presented by Dr Andrew French (University of Nottingham)

Imaging with a hyperspectral camera (that records a complete breakdown of the reflectance spectra for each pixel in an image) provides a researcher with a large amount of data (5seconds=1Gb) but much of this is extraneous for use in any one particular biological problem. In this problem Dr French presented the idea that this type of data could be used to detect minute changes in the colour of leaves that are a prelude to visible signs of disease. Therefore the task for the mathematicians was to devise a way of analysing the spectral data to define a new indice that represents a relationship between wavelengths that has the most utility for this type of analysis. I did not directly observe any of the interactions of this group but they appeared to make good progress. In their final presentation the description of their methods was the most mathematically dense of the three problems (at least to a naïve observer such as myself). However the group had clearly put together some ideas that could be developed in future.

The final step in the process is to collate the information from each study group into a report, which will be published on the CPIB website. Later on this will hopefully yield further interactions and potential grant writing opportunities between the biologists and mathematicians involved in the meeting.

Please look out for a summary of the final reports in the next edition of the GARNish newsletter, to be published in the summer. From a biologists perspective I would encourage anyone who is wary of interacting with mathematicians, computer scientists or modellers to bite the bullet and make that connection. Even though your system ultimately might not be the most amenable to a modeling approach, the interaction will help you develop ideas that will undoubtedly drive your research forward in unexpectedly directions. Basically it is a no-lose interaction!

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.

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.

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

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 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.