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Great British Success in ERA-CAPS

Categories: Arabidopsis, Brassica, Celebrating Basic Plant Science, epigenetics, funding, plant pathogens, UKPSF, Uncategorized

Tags: Arabidopsis, BBSRC, ERA-CAPS, funding, GARNet workshop, John Innes Centre, plant pathogens, UKPSF, wheat

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Published on: May 20, 2015

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:

Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

SEB 2014: The future is bright in the Plant Section

by Charis Cook

Categories: conferences

Tags: early career researchers, SEB, wheat

Comments: 1 Comment

Published on: July 1, 2014

Lisa and I are at the Society of Experimental Biology’s 2014 (SEB 2014) conference this week. The highlight so far was the first session, when the Plant Section gathered for talks from their President’s Medallist Cristobal Uauy and three Young Scientist Award Finalists: Beth Dyson, Caroline Upton, Stephanie Johnson.

Cristobal Uauy spoke first about his career and work on wheat genetics. He was frank about the difficulties of working with wheat, but said, “I’m not going to complain about how difficult it is to work on wheat, and blah blah blah … because actually it’s getting much better.”

This optimism was sustained throughout Cristobal’s talk. He aims to improve yield in wheat, and has found a trait that increases grain width by what looks like a tiny amount – but the difference adds up very quickly. Over 20 grains, you gain the equivalent of one whole grain. Scaled up to a field, this trait would give an extra 700 loaves of bread. This is certainly something to be proud of, yet Cristobal is excited about increasing this 5% difference to 20% or 30%. His current trait is the result of a mutation on just one copy of the gene – he hopes to find and modify its homologues on the other ancient genomes that make up the huge modern wheat genome.

Cristobal is keen to promote crop research. He pointed out that Arabidopsis dwarfs all other plant species at SEB meetings, yet the current focus on food security in the plant science community necessitates breakthroughs in crop science. At GARNet obviously we have Views on this, but as Cristobal said at the beginning of his talk, “A huge number of people all over the world eat wheat – so anything we can do to improve wheat will have a huge impact.”

Cristobal is a member of the SEB Plant Section Committee, and has started a new sub-group within the Plant Section entitled Crop Molecular Genetics. If you’re interested in getting involved, I’m sure he’d love to speak to you.

The Young Scientist Award Finalists also gave inspiring talks:

Beth Dyson measured metabolite, amino acid and organic acid levels in Arabidopsis plants grown in optimum and cold conditions. She has identified key mechanisms that enable photosynthesis to respond to low temperatures.
Caroline Upton’s research on barley roots is laying the groundwork in transparent soil methodology. She finds it far easier to analyse images from roots grown in transparent soil than the CT images she initially had to work with.
Stephanie Johnson outlined her PhD project on the molecular mechanisms that gives Stay-Green Sorghum its desirable trait. She spent 3 months with experts at the University of Queensland generating transgenic sorghum and is now waiting to confirm the hypothesis developed from her early models.

The President’s Medal and the Young Scientist Awards are both intended to reward and encourage early career excellence and the speakers were all worthy of this recognition. The UK plant sciences community rightly speaks out regularly about funding cuts and skills gaps, but this morning’s session was a refreshing celebration of the talent our community produces and nurtures.

ADAS Boxworth Open Day

by Guest Blogger

Categories: guest blogger

Tags: agriculture, brassica, guest blogger, wheat

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Published on: June 26, 2014

Charlotte White, crop physiologist at environmental and agricultural consultancy ADAS, reports from the ADAS Boxworth Open Day where science from ADAS is showcased alongside work funded by Defra and HGCA as well as private enterprises. It is a great opportunity for scientists, agronomists, farmers and seed/agrochemical representatives to network and discuss their needs and current work.

On the 3^rd of June ADAS Boxworth in Cambridgeshire opened its fields to welcome around 200 visitors. The rather wet morning, which made the behind the scenes setup soggy, dissipated in time for the mid-day opening and the afternoon was lovely and sunny. Visitors included farmers, agronomists, members of the seed and agrochemical industry, students and the farming press.

On arrival visitors were welcomed with a complementary hog roast and could register for BASIS and NRoSO points. At reception there was a demonstration of electrical weeding, which had a lot of interest, along with updates on the SCEPTRE project, the fertiliser value of anaerobic digestate and the HGCA stand. There were then two routes: wheat followed by oilseed rape or oilseed rape followed by wheat. The majority took the latter.

The oilseed rape field had a number of Defra, HGCA and commercially funded project demonstration plots. These included optimising seed rates/row widths, and the project I was demonstrating, which looks at precision applications of late foliar nitrogen fertiliser to increase yield and feed value of the rape-meal (CC: described in this UKBRC factsheet). Dr Steve Ellis spoke about pollen beetle thresholds and neonicotinoids, while Dr Faye Richie was on hand to answer questions on oilseed rape diseases relevant to this season and give updates on the latest findings from the pathology group. The industry variety and product demo plots appeared to have a high yield potential and formed the perfect environment to catch up with sponsors and collaborators. As you turned the corner in the field it was a surprise to find Ken Smith stood in a soil pit promoting good soil management on behalf of HGCA, a topic which always generates a lot of interest and gets people talking!

The wheat field was across the farm road and had a similar mix of government, levy and industry funded project demonstration plots, industry stands and variety and product plots. Prof Roger Sylvester-Bradley explained the yield enhancement network (YEN), an innovation competition to help growers break existing cereal yield records. The demonstration plots, testing ‘innovative ideas’ to maximise grain filling, included irrigation, reflective soil strips and plot cooling (if you are interested in entering the YEN competition, visit the website). The triticale demo plots also received a lot of attention and Dr Sarah Clarke and Dr Daniel Kindred were on hand to discuss the benefits of triticale – it out-yields wheat as a second cereal – and to promote the LearN project, which is using a novel on-farm approach to investigate nitrogen monitoring and management. Jonathan Blake was there to discuss the HGCA Fungicide Performance work, and had some interesting demonstration plots to show yellow rust and septoria tritici control. In addition to these and other interesting research demonstration plots, national ADAS experts in weed, pest and disease management were around to answer all manner of questions. Visitors were kept lingering long after the 4pm close.

For me, it was a long and invigorating day and great to talk to farmers and agronomists about their experiences with late application of foliar nitrogen and to provide an update on the latest project findings, as well as seeing what everyone else in ADAS has been working on. Don’t worry if you missed it, keep your eye out for flyers for future open days!

Image credit: Charlotte White

Two services for plant scientists to consider

by Charis Cook

Categories: resource

Tags: Arabidopsis, NIAB, phenotyping, wheat

Comments: 1 Comment

Published on: January 28, 2013

Sometimes, experiments are too big, too expensive, or too specialist to do yourself or to negotiate a collaboration with someone who can. Fortunately there is a way for some of you to get those experiments done – but as ever, it involves competing for funding. Today I’ll highlight two service providers who are taking applications from researchers for a limited number of fully funded services.

The BBSRC are funding the Community Resource for Wheat Transformation at NIAB. NIAB scientists are wheat transformation specialists, and use a non-commercialized method with over 30% success rate – higher than standard Agrobacterium-mediated wheat transformation (Harwood, 2012). The ‘Community Resource’ is 50 single gene transformations, which researchers must apply for. Half of the transformations are reserved for model plant researchers wanting to test a gene of interest in wheat. The application form is fairly straightforward, requesting information about the proposed gene and research; and how it links to BBSRC food security targets. You need to apply by Thursday this week. If successful, the researcher provides NIAB with a gene in an Entry construct flanked by aatL sequences. NIAB performs the transformation, and delivers the researcher 30 inpendent transformed plants as either plantlets or T1 seed, having confirmed transgenesis by PCR or QPCR.

The Centre for Plant Integrative Biology at the University of Nottingham and the National Plant Phenomics Centre at Aberystwyth University is just one of 14 participants in the European Plant Phenotyping Network (EPPN; Ruth blogged about the centre in Julich a few weeks ago). Researchers can apply for access to CPIB (or another European EPPN installation) to do a phenotyping experiment. ‘Access’ includes:

free access for eligible user groups to research facilities;
support for travel;
on-site logistic support by the infrastructure staff;
access to knowledge and know-how at the research infrastructures necessary to complete the proposed experimental work

The wheat genome – the best thing since …

by Charis Cook

Categories: Summary for non-specialists, systems biology

Tags: wheat

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Published on: December 4, 2012

When Anthony Hall trailed the wheat genome paper (Brenchley et al.; published on Thursday) at last week’s GARNet Tools and Technologies workshop, I knew it was excellent blog fodder. When I sat down to read the paper on Friday though, it seemed like a bad choice for a blog post. This is no restricted-access, wordy paper with obvious aspects to highlight in an accessible way; it is open access and describes the bread wheat genome, comparing it to related species concisely and clearly. However, in many ways this paper is important, even a landmark, because of what is not in it. So instead of highlighting the paper, I will attempt to explain why it was all over plant science social media and science news sites, and why it deserved far more coverage from the general media.

First, the bread wheat (Triticum aestivum) genome was, to steal a phrase from the Annals of Botany blog, the Everest of crop genomes. Sequencing it was difficult due to its enormous size. It is a hexaploid, essentially containing the genomes of three separate grass species. First of all Triticum urartu hybridized with a Sitopsis species to form tetraploid species Triticum dicoccoides, which eventually hybridized with Aegilops tauschii around 8000 years ago (for more information, see WheatBP). Both hybridization events increased the ploidy of the offspring. In 2010, the draft sequence of this huge genome was released, and analysing it must have seemed almost impossible. In the end, the genome took the team just two years to analyse – and that is what is published. It is an amazing achievement, which took a multinational team of scientists many years. The analysis showed that the genome contains 94 – 96 000 genes. The team were able to identify the parent species of many gene families and track their development over time.

Second, this work and other high profile ‘big data’ stories celebrate groundbreaking achievements in biological sciences. Sequencing technologies and analysis techniques have advanced beyond recognition since the human genome was sequenced in 2003. Many sequencing methods were used in the wheat genome project, all of which are either out of date or have been upgraded since – so sequencing more wheat genomes in a project similar to ENCODE or the 1001 Genomes project will take far less time. Similarly the computing power needed to analyse 17 gigabase-pairs of DNA sequence was unheard of in 2000, but 12 years later it is not only here, but improving. The bread wheat genome marks wheat’s entry into the ‘big science’ era.

Third, and most importantly, wheat is one of the most important plants on earth. It makes up 20% of the calories consumed by humans (statistic from Brenchley et al.). When crops fail, it affects everyone. This year saw poor weather in wheat regions across the globe, leading to warnings of unprecedented rises in the price of bread in the UK. Plant scientists are working with agriculturalists to improve crops and reduce the risk of harvest failure, but a 2011 Science paper (Lobell et al., 2011) commented that in some regions, the negative effects of climate change offset the technological advances that should increase crop yields. A fully sequenced and analysed bread wheat genome is a great asset for crop scientists working on developing breeds that may, for example, be able to withstand draughts and floods, and contain higher levels of nutrients.

The wheat genome sequence is not only a triumph for crop scientists. The more information there is out there on wheat ‘omics,’ the easier it is for Arabidopsis researchers to transfer their knowledge to wheat and improve the ‘impact’ of their projects – or find out in advance that for that particular gene or process, cross-over is impossible.

The sequencing of the Arabidopsis thaliana genome was completed in 2000, causing a paradigm shift in plant research. In 2005 Bevan and Walsh published an overview of the progress made in the first five years after the annotated genome was published, including the establishment of large stocks of the gene disruption lines now taken for granted. The sequencing of the wheat genome opens up new avenues of research for crop scientists and I am looking forward to seeing the results in the coming years.

There are instructions on how to download and use the wheat genome sequence at MIPS.

Highlighted paper: Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F. X. Mayer, Keith J. Edwards, Michael W. Bevan & Neil Hall (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491, 705–710 doi:10.1038/nature11650

Image credits: Great Harvest by MMNoergaar and Challah by ladySorrow, both via stock.xchng.

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