Key Research Achievements

Between 2006 and 2011 JIC scientists and our collaborators have published over 750 papers with a total of more than 8,400 citations. Our scientists regularly publish in the high impact general science journals (see Scientific Output section).

Below we describe examples of research outputs (2006-2011) that have provided new insights and understanding well beyond the fields of plant and microbial research.

The regulation of gene expression

The discovery of long antisense transcripts that guide chromatin modification provides fundamental new insights into the mechanisms of gene regulation by chromatin modification.
Breakthroughs have been made in understanding the molecular basis of developmental responses to environmental conditions, such as overwintering and responses to ambient temperature, showing that chromatin plays a key role .
Using novel cell biological approaches, JIC scientists identified a link between the cell cycle and chromatin modification. This knowledge provides the foundation for understanding the molecular basis of plant adaptation to the environment, and it underpins future efforts to optimise crop yield by adaptation to sub-optimal and changing growing conditions.
Continuing the pervasive importance of chromatin, Ph1, a key locus controlling chromosome pairing during meiosis, was identified in wheat that modifies chromatin. This leads to opportunities to manipulate recombination in wheat to increase genetic diversity in this key crop through new breeding technologies.

Understanding the complex interplay of plants and beneficial microbes

The engineering of nodulation in the absence of rhizobia with a gain-of-function in a calcium dependent kinase.
Deeper knowledge of nodule initiation has been made by understanding the transcriptional networks controlling host nodulation genes.
A transgenic legume expressing a calcium-sensing protein was used to define the parameters of calcium signalling required for nodulation and to identify mycorrhizal-fungus induced calcium responses.
Symbiotic auxotrophy was shown to occur in rhizobia in the legume symbiosis. This work provides understanding for engineering of non-nodulating species for symbiotic N fixation to reduce dependence on N fertilisers.

Deeper insights into the arms race between pathogens, pests and their crop plant hosts

The genome sequences of powdery mildews were defined, providing an essential platform for the dissection of this important disease.
The first two effector proteins, which target components of the host defence system, were isolated from the barley powdery mildew fungus and genetic components underpinning invasion strategies of rice blast disease were characterised.
The first effector proteins of insect pests have recently been identified and this opens the door to the characterisation of important aphid pests.
Novel mechanisms of basal resistance in the plant have been characterised and the means by which bacterial pathogens overcome them have been revealed.
Genetic markers were identified to enable breeders to select for two major eyespot resistances (Pch1 and Pch2) in wheat.
Collectively this research provides the foundation for identifying genes that combat key diseases of crops, such as potato late blight and fungal diseases of cereals, which cause massive crop losses. This will allow breeders to compete more effectively in the arms race against pathogens to maximise crop yields.

Metabolite pathways

The discovery of gene clusters for synthesis of secondary metabolites in plants presents new opportunities for natural product pathway discovery and crop improvement.
Methods for crop improvement through mutation breeding have been developed using pathway engineering.
These led to the testing of specific phytonutrients in promoting health and the establishment of a spin- out, Norfolk Plant Sciences, to develop preventive approaches to chronic disease.
Similar levels of understanding of biosynthetic pathways in microbes, primarily in the Actinomycetes, have identified new mechanisms of coordinating expression that now form the basis for the development of novel therapeutics for control of infectious diseases.
The development of transcription factor decoy technology has led to the founding of Procarta Biosystems, a new spin-out company.

Increasing crop yields and product quality within a sustainable production framework

Plant growth and development, and ultimately yield, depends on the supply of nutrients, and a key challenge is to discover how to maintain high levels of growth in limiting nutrient conditions.

Breakthroughs have been made in understanding the links between carbohydrate availability and plant growth and the underlying regulatory pathways.
Novel insights on sulphate assimilation were obtained by identifying naturally- occurring alleles of known genes, potentially influencing sulphur use and stress defence.
Fundamental new insights into the functions of microtubules in primary and secondary cell wall formation guide future research in the cellular basis of organ formation.
Mechanisms for controlling stem cell behaviour, organ size and fruit development have been discovered and new families of plasmodesmal proteins affecting cell-to-cell communication were identified.
Important progress has been made in understanding legume and oilseed seed quality traits and in providing genetic markers and novel germplasm to breeders.
Novel variation for starch properties in wheat and barley has been identified and characterised, and grain from pre-breeding lines of barley developed in collaboration with NIAB is under test by industrial end-users.

Natural variation in traits within and between species

Studies of floral symmetry and flowering have revealed the molecular basis of this variation. This knowledge provides insights into the relationships between genetic variation and adaptation, directly supporting future research aimed at developing new breeding methods that directly utilise genetic variation.
Extraordinary technical advances in genome sequencing and bioinformatics continue to provide new foundations for research relevant to food security. John Innes Centre scientists and collaborators have made important leading contributions to deciphering, analysing and applying genome sequence assemblies. The sequences of several oomycetes, including the Irish potato famine pathogen Phytophthora infestans, were determined in collaboration with the MIT Broad Institute.
Tools based on the genome sequences of Brassicas have been developed for genetics and genomics of Brassica crop species in collaboration with Beijing Genome Institute and the J. Craig Venter Institute.
The genome sequence of Brachypodium, a pooid grass closely related to wheat was generated in collaboration with the DOE Joint Genome Institute and the sequence of the model legume Medicago has been partially led by JIC. This provides a comparative framework for assembling and analysing next generation sequence coverage of bread wheat produced in collaboration with the Universities of Liverpool and Bristol.
These genome resources directly support future work in Brassica and wheat breeding and gene isolation. Functional genomics resources have been developed in model legumes, Brassicas and other plants as part of RevGenUK. This has supported research in the discovery of metabolic pathways, signalling pathways in symbiosis, and to manipulate dehiscence in oilseed siliques.
T-DNA mutant populations have been developed as functional genomics resources in Brachypodium to support grass research.
Future developments include integrating these resources into a high-throughput platform for TILLING reverse genetics (RevGen) in collaboration with TGAC.

Chemical synthesis and systems biology

Chemical synthesis of carbohydrate and glycopolymer mimetics through ‘click chemistry’ has been applied to the development of novel enzyme inhibitors and anti-trypanosomal agents.
Chemical and chemoenzymatic methods for the generation of sugar nucleotides have been central to the elucidation of lipopolysaccharide biosynthetic pathways in human respiratory pathogens Bordetella pertussis and Pseudomonas aeruginosa.
A new pathway from trehalose to α-glucan in Mycobacterium tuberculosis has been discovered,opening the way to new tuberculosis therapies.
Synthetic biology approaches have led to the development of plant virus-derived technology for high-level production of metabolic enzymes and therapeutic proteins.