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Agency: European Commission | Branch: H2020 | Program: RIA | Phase: SFS-05-2015 | Award Amount: 5.67M | Year: 2016

The world demographic growth and global climate change are major challenges for human society,hence the need to design new strategies for maintaining high crop yield in unprecedented environmental conditions.The objective of TomGEM is to design new strategies aiming to maintain high yields of fruit and vegetables at harsh temperature conditions, using tomato as a reference fleshy fruit crop.As yield is a complex trait depending on successful completion of different steps of reproductive organ development, including flower differentiation and efficient flower fertilization,TomGEM will use trans-disciplinary approaches to investigate the impact of high temperature on these developmental processes.The core of the project deals with mining and phenotyping a vast range of genetic resources to identify cultivars/genotypes displaying yield stability and to uncover loci/genes controlling flower initiation,pollen fertility and fruit set.Moreover,since high yield and elevated temperatures can be detrimental to quality traits,TomGEM will also tackle the fruit quality issue.The goal is to provide new targets and novel strategies to foster breeding of new tomato cultivars with improved yield.The main strength of TomGEM resides in the use of unique and unexplored genetic resources available to members of the consortium.It gathers expert academic researchers and private actors committed to implement a multi-actor approach based on demand driven innovation.Tomato producers and breeders are strongly involved from design to implementation of the project and until the dissemination of results.TomGEM will provide new targets and novel strategies to foster the breeding of new tomato cultivars with improved yield under suboptimal temperature conditions.TomGEM will translate scientific insights into practical strategies for better handling of interactions between genotype,environment and management to offer holistic solutions to the challenge of increasing food quality and productivity.

Howard M.,John Innes Center
Trends in Cell Biology | Year: 2012

Concentration gradients of morphogens are critical regulators of patterning in developmental biology. Increasingly, intracellular concentration gradients have also been found to orchestrate spatial organization, but inside single cells, where they regulate processes such as cell division, polarity and mitotic spindle dynamics. Here, we discuss recent progress in understanding how such intracellular gradients can be built robustly. We focus particularly on the Pom1p gradient in fission yeast, elucidating how various buffering mechanisms operate to ensure precise gradient formation. In this case, a systems-level understanding of the entire mechanism of precise gradient construction is now within reach, with important implications for gradients in both intracellular and developmental contexts. © 2012 Elsevier Ltd.

Rhizobia adopt many different lifestyles including survival in soil, growth in the rhizosphere, attachment to root hairs and infection and growth within legume roots, both in infection threads and in nodules where they fix nitrogen. They are actively involved in extracellular signalling to their host legumes to initiate infection and nodule morphogenesis. Rhizobia also use quorum-sensing gene regulation via N-acyl-homoserine lactone signals and this can enhance their interaction with legumes as well as their survival under stress and their ability to induce conjugation of plasmids and symbiotic islands, thereby spreading their symbiotic capacity. They produce several surface polysaccharides that are critical for attachment and biofilm formation; some of these polysaccharides are specific for their growth on root hairs and can considerably enhance their ability to infect their host legumes. Different rhizobia use several different types of protein secretion mechanisms (Types I, III, IV, V and VI), and many of the secreted proteins play an important role in their interaction with plants. This review summarizes many of the aspects of the extracellular biology of rhizobia, in particular in relation to their symbiotic interaction with legumes. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.

Sablowski R.,John Innes Center
Current Opinion in Plant Biology | Year: 2011

The shoot and root meristems contain small populations of stem cells that constantly renew themselves while providing precursor cells to build all other plant tissues and organs. Cell renewal, growth and differentiation in the meristems are co-ordinated by networks of transcription factors and intercellular signals. The past two years have revealed how auxin and cytokinin signals are integrated with each other and with regulatory genes in the shoot and root meristems. Small RNAs have also emerged as novel intercellular signals. Downstream of meristem regulatory genes, links have been made to cell division control and chromatin function. Protection of genome integrity, partly through programmed cell death after DNA damage, has recently been revealed as a specialised function in plant stem cells. © 2010 Elsevier Ltd.

Osbourn A.,John Innes Center
Trends in Genetics | Year: 2010

Microbes and plants produce a huge array of secondary metabolites that have important ecological functions. These molecules have long been exploited in medicine as antibiotics, anticancer and anti-infective agents and for a wide range of other applications. Gene clusters for secondary metabolic pathways are common in bacteria and filamentous fungi, and examples have now been discovered in plants. Here, current knowledge of gene clusters across the kingdoms is evaluated with the aim of trying to understand the rules behind cluster existence and evolution. Such knowledge will be crucial in learning how to activate the enormous number of 'silent' gene clusters being revealed by whole-genome sequencing and hence in making available a wealth of novel compounds for evaluation as drug leads and other bioactives. It could also facilitate the development of crop plants with enhanced pest or disease resistance, improved nutritional qualities and/or elevated levels of high-value products. © 2010 Elsevier Ltd.

Kumar S.V.,John Innes Center | Wigge P.A.,John Innes Center
Cell | Year: 2010

Plants are highly sensitive to temperature and can perceive a difference of as little as 1°C. How temperature is sensed and integrated in development is unknown. In a forward genetic screen in Arabidopsis, we have found that nucleosomes containing the alternative histone H2A.Z are essential to perceiving ambient temperature correctly. Genotypes deficient in incorporating H2A.Z into nucleosomes phenocopy warm grown plants, and show a striking constitutive warm temperature transcriptome. We show that nucleosomes containing H2A.Z display distinct responses to temperature in vivo, independently of transcription. Using purified nucleosomes, we are able to show that H2A.Z confers distinct DNA-unwrapping properties on nucleosomes, indicating a direct mechanism for the perception of temperature through DNA-nucleosome fluctuations. Our results show that H2A.Z-containing nucleosomes provide thermosensory information that is used to coordinate the ambient temperature transcriptome. We observe the same effect in budding yeast, indicating that this is an evolutionarily conserved mechanism. © 2010 Elsevier Inc. All rights reserved.

Agency: European Commission | Branch: H2020 | Program: ERC-STG | Phase: ERC-2016-STG | Award Amount: 1.71M | Year: 2017

Yellow rust (YR) disease is a major threat to cereal crops and grasses worldwide, causing significant losses to the global wheat harvest each year. The long-term aim of this research is to develop new varieties of wheat with enhanced resistance to YR. To do this, it is essential to understand host specificity - the ability of the pathogen to specialize on particular grass hosts, coupled with the ability of the host to resist infection by different strains of YR. I recently pioneered a field-based pathogenomics approach to enable a comprehensive evaluation of the genetic diversity of YR. This new method provides unparalleled resolution of the pathogen population that can identify gene families associated with the ability to cause disease on all the major hosts of YR in Europe, namely wheat barley, rye, triticale and cocksfoot grass. Using this approach, I previously uncovered a genetically distinct population of YR on triticale and showed that these isolates contained gene clusters that were specifically expressed in all isolates identified on triticale and had no or negligible levels of expression in all wheat YR isolates. In this ERC project, I will use the pathogenomics approach to collect an extensive dataset of YR on all its major hosts, aiming to characterise genomic regions and the genes they encode to understand the underlying regulatory mechanisms that drive host specialization and adaptation. I will then assess changes at the transcriptomic level in closely related host-specialized YR races to provide insights into how pathogens adapt to new hosts. In parallel, I will identify host targets of effectors from YR to resolve the underlying molecular processes that are targeted by the pathogen to enable successful host-specific colonization. I will then disrupt the function of these host targets using precision genome editing to determine their contribution to YR pathogenicity and reveal novel susceptibility genes that are essential for pathogen progression.

Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 707.60K | Year: 2017

The Dean group studies the control of flowering time in the reference plant, thalecress (Arabidopsis thaliana). Several flowering pathways converge to regulate a gene called FLC and variation in expression of this gene contributes enormously to natural variation in flowering time of Arabidopsis types collected from around the world. Winter conditions switch off expression of the FLC gene, removing the brake to flowering, and thus accelerating the flowering process. This induction of a plants flowering process by exposure to the prolonged cold of winter is termed vernalization. Genetic, molecular and computational analysis of vernalization in thalecress has shown it involves a cellular memory mechanism, one that also occurs during development of our own bodies. In the plant, cold switches off expression of FLC and this repressed state is maintained by Polycomb proteins that add methylation groups to proteins associated with FLC DNA. These modifications are passed from the mother to the daughter DNA strand to maintain the repressed state of the gene through the development as epigenetic regulation and similar mechanisms keep many thousands of genes switched off (silenced) during vertebrate development. A key question in the epigenetic field is what determines whether a specific gene becomes silenced or not. Recent work in the Dean lab has made progress in this question through characterization of a change in the sequence of the FLC gene that blocks the silencing by cold. This then enabled the factor that binds to that specific region to be identified. Use of a tagged version of the factor then enabled isolation of a range of proteins that were in many cases unexpected and which suggested what might be involved in the silencing switch. This proposal aims to follow up these findings to fully describe the multiple factors required to specify a gene for epigenetic silencing. Understanding from a study such as this can provide concepts important to epigenetic regulation across many genomes.

Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 3.51M | Year: 2017

Agriculture is facing the crucial challenge of adapting crop productivity to changes in the climate. More variable weather patterns require the development of crops that are able to perform more robustly under a wider range of environmental conditions. At the same time, climate change also provides new opportunities for increasing the length of the UK vegetable growing season and increasing food security by reducing imports of fresh produce during the winter, but this requires breeding new varieties that are able to produce robustly at different times of year. The BRAVO consortium aims to meet these challenges through close interactions between academia and industry. To achieve this goal, we have brought together world-leading experts in both Arabidopsis and Brassica plant reproduction from research institutes and universities within the UK. As the result of a series of meetings between consortium members and stakeholders from the oilseed rape and vegetable Brassica industries, optimisation of flowering and coordination of developmental transitions in the production of high-quality seeds were identified as important common targets. These transitions that occur during plant reproduction such as to flowering, fertilisation, inflorescence growth, seed production, dispersal, and subsequent seed performance are now known to be managed by environmentally responsive gene networks built on a foundation of common components first described for their ability to control flowering time. The goal of BRAVO is to provide a mechanistic understanding of the role of flowering time gene networks in the control of Brassica reproductive developmental transitions from vegetative growth through to seed production and seed vigour. Because these networks control environmental responsiveness, this knowledge can be exploited to increase robustness in the performance of oilseed and vegetable Brassicas. A key challenge is how to optimise individual traits when the same flowering time gene network has been optimised by evolution over millions of years for multiple functions, each of which is important for crop performance. In this proposal, we will combine genomics and phenomics technologies with approaches in developmental genetics and mathematical modelling to link genotype to phenotype for master regulators of key transitions during Brassica reproductive development. Through exploitation of available genetic resources, we will reveal the architecture of flowering time gene networks in Brassicas and how they have been modified in the past by plant breeders to cause trait variation, life history variation and climate adaptation. This will allow us to develop a predictive framework for designing strategies to vary specific crop characteristics without harming others, and to generate and test novel genetic variation with potential uses in future trait enhancement. In parallel we will establish and exploit resources such as a gene expression atlas and targeted gene disruption which will allow the Brassica research and breeding communities to expand knowledge on important biological processes and use the outputs form BRAVO collectively to improve Brassica crop performance. Long-term improved and sustainable Brassica crop performance can only be achieved through fundamental understanding of biological processes. The composition of the BRAVO consortium allows the combination of excellence in Brassica research with knowledge transfer from the closely related Arabidopsis model species. The project builds on and expands academia-industry interactions through industrial membership on the projects Supervisory Board, industry engagement and practical involvement in case studies, frequent consortium meetings and annual stakeholder events. We believe this project provides a unique opportunity to align industry priorities with excellent fundamental research programmes in order to help secure the future yield of Brassica crops in the UK and worldwide.

Agency: GTR | Branch: BBSRC | Program: | Phase: Fellowship | Award Amount: 1.01M | Year: 2017

Calcium signalling is essential for growth and development, in both plants and animals. In animals nuclear calcium release is a potent regulator of neuronal gene expression and of cell proliferation. Nuclear calcium signalling is also known to be essential in legumes to promote associations with nitrogen fixing bacteria and phosphate delivering arbuscular mycorrhizal fungi. Legumes are among the worlds most important agricultural food crops that are beneficial to billions of farmers and consumers worldwide and provide an essential aspect of natural soil enrichment of organic nitrogen compounds. The mechanisms of plant nuclear calcium signalling were poorly understood. During my work I have used the symbiotic associations in legumes as a platform to dissect plant nuclear calcium signalling. Using a wide range of approaches, I discovered a number of ion channels located at the nuclear envelope that are responsible for symbiotic nuclear calcium release. Among them, I defined the first plant nuclear-associated calcium channels encoded by cyclic nucleotide gated channels (CNGC15s). The CNCG15s sit at the nuclear envelope in a complex with a potassium permeable channel (DMI1), also required for the generation of the symbiotic nuclear calcium signals. Interestingly, CNGC15s and DMI1 are conserved across all land plants, including non-symbiotic species, strongly suggesting that they have other functions during plant development. Consistent with this I have found a number of defects in Arabidopsis lines mutated in CNGC15 and DMI1, that include root developmental defects. I propose that my research in legumes has revealed the generic plant machinery involved in the regulation of nuclear calcium release. By studying the components that regulate nuclear calcium release I will be able to understand when and where nuclear calcium signalling is important. My proposal will focus on the role of nuclear calcium signalling during root development, both root growth and associations with symbiotic microorganisms. Consistent with a function for CNGC15 and DMI1 in root development I have observed nuclear calcium responses in Arabidopsis root meristematic cells during their response to the phytohormones auxin and cytokinin. These calcium responses are mechanistically different from the nuclear calcium signals observed in legumes during symbiotic associations. My proposed research integrates molecular biology, genetics, cell biology, chemistry, electrophysiology and mathematical modelling to investigate how CNGC15-DMI1 regulates nuclear calcium release leading to plant developmental processes. It will use a large collection of Arabidopsis mutant and transgenic lines, that I have already generated, with a panel of nuclear calcium sensors allowing detection of nuclear calcium signals in an array of Arabidopsis mutants. My work will dissect the functions that nuclear calcium signalling plays in root developmental processes and how diverse nuclear calcium signals are encoded. Finally, through a combination of transcriptomics and mutant screens, I will be uniquely poised to decipher the downstream signalling components associated with nuclear calcium signalling during root development.

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