We strive to increase the sustainability and equity of global agriculture and increase resilience to future climate change.
To achieve this we focus our research on:
- Sustainable nutrient capture - Improving crop plant access to sustainable sources of nitrogen and phosphorus, replacing the need for inorganic fertilizers.
- Reducing losses from pests and diseases – Finding sustainable ways to reduce yield losses from pests and diseases.
- Improving crop breeding – Developing technologies that increase the pace and impact of crop breeding
- Increasing yield potential through improved photosynthesis – Raising the potential yield ceiling through enhancing photosynthetic efficiency.
Sustainable crop nutrition – Giles Oldroyd
The availability of sources of nitrogen and phosphorus are major limitations to crop productivity. This is primarily addressed through the application of inorganic fertilisers to augment these limiting nutrients. However, the use of such fertilisers is the greatest cause of pollution from agriculture in high and middle-income countries, while access to inorganic fertilisers is restricted for farmers in low-income countries, who suffer resultant losses to their potential yield. In natural ecosystems many species of plants acquire nitrogen and phosphorus through associations with beneficial fungi and bacteria, but the use of these beneficial microbial associations is currently very limited in agriculture. Through a detailed understanding of how plants associate with beneficial microorganisms, we aim to broaden their use in agriculture to facilitate sustainable productivity and to ensure such benefits are accessible to the world’s poorest farmers.
Engineering nitrogen fixation
Nitrogen-fixing bacteria associate with legumes in specialised organs, nodules, that create an environment to maximises the activity of nitrogenase, the enzyme responsible for nitrogen fixation. Through genetic dissection in the model legume Medicago truncatula, we provide a detailed understanding of how legumes associate with nitrogen-fixing bacteria and are using this foundational knowledge to engineer crops, particularly cereals, to associate with these beneficial bacteria. Nitrogen-fixing cereals have much potential to deliver sustainable and secure food production systems, with potential for significant yield improvements to the poorest farmers of the world.
Enhancing nutrient capture
Plants associate with an array of microorganisms that facilitate nutrient capture from the environment, providing sources of phosphate, nitrate, water and some micronutrients to their host plants. Despite their widespread use in natural ecosystems, the application of beneficial microbial associations in agriculture is limited. Through understanding the processes that drive their establishment, we are developing crop lines that make more effective use of beneficial microbial associations, providing sustainable ways to deliver nutrients to crops.
Cereal symbioses - Uta Paszkowski
The mutually beneficial arbuscular mycorrhizal (AM) symbiosis is the most widespread association between roots of terrestrial plants and fungi of the Glomeromycota. The association receives increasing scientific attention because of the nutritional benefit it confers to plants, its ubiquitous occurrence among contemporary plant species and, as a result of its evolutionary antiquity, an ancestral relationship to other plant interactions. We focus on molecular mechanisms underlying the formation and function of AM symbioses in rice and maize. We aim to develop our knowledge of these associations to optimize the incorporation of the AM-symbiosis into sustainable agricultural practices.
Establishment of AM symbioses relies on the continuous orchestration of signals to achieve recognition and coordination of the interacting organisms. We have identified genetic determinants of the rhizosphere dialogue from rice and maize. Their functional characterization will shed light on the communicative signal exchange, “sending” and “receiving”, that impacts on the plant’s reprogramming for symbiosis and therefore on the effectiveness of AM symbioses in rice and other cropping systems.
Symbiotic phosphate acquisition
Phosphate (Pi) acquisition of crops via AM symbioses gains increasing importance due to limited Pi reserves and demand for environmentally sustainable agriculture. We found that 70% of the Pi acquired by aerobically- grown rice is delivered via the symbiotic route. We would like to understand the functioning and regulation of this pathway under laboratory and field conditions to exploit the symbiosis and develop rice cultivars better adapted to low-input rice agro-ecosystems.
Arbuscules, the heart of the symbiosis
'Arbuscules' are fascinating fungal feeding structures, produced inside root cortical cells by arbuscular mycorrhizal fungi. Arbuscules are built by consecutive dichotomous hyphal branching, ultimately adopting a complex tree-like shape at microscopic scale. As the arbuscule develops, the hostplant cell undergoes fundamental architectural adaptations to accommodate the intracellularly expanding fungus. For instance, the plant cell dramatically increases membrane biogenesis to envelope the growing hyphal structure in the so-called peri-arbuscular membrane. The hugely enlarged membrane surface area between the two organisms appears ideal for the exchange of signals and nutrients. Remarkably, despite what seems a considerable metabolic investment, arbuscules collapse after a few days, and host cell architecture is restored to that of a non-colonized cell. Therefore, the life of an arbuscule is marked by the highly dynamic continuum of development and collapse without static intermediate stages. To capture arbuscule formation and turnover in 4D, and at ultrastructural resolution, we combine advanced multiphoton confocal imaging of living mycorrhizal rice roots with high resolution electron microscopy.
Nutrient Perception and Capture – Jeongmin Choi
Nutrients are major building blocks of biological machinery and biochemical processes governing the existence of life. Therefore, every organism needs to ensure nutrient provision by obtaining them from the environment while recycling them within the body. This requires highly complex biological communication systems linking organelles, cells and organs. To do so, a nutrient serves a dual function; a metabolite and a signalling molecule. As sessile organisms, plants developed sophisticated systems to maintain the nutrient sensing and signalling mechanism to maintain nutrient homeostasis to ensure their survival at a limited time and space. My lab focuses on discovering new molecular mechanisms underpinning nutrient sensing and signalling mechanisms in plants. The research outcomes could help us maximize the crop nutrient use efficiency to ensure global food security at low financial and environmental costs.
In nature, plants are not alone; they are constantly in close contact with microorganisms. The collective evidence from paleontological, phylogenomics and evolutionary studies support that plants have been associated with beneficial microbes to maximize nutrient uptake and other ecological benefits. We will explore the role of nutrients by studying arbuscular mycorrhizal symbiosis in rice as a model system.
Phosphorus and nitrogen signalling in arbuscular mycorrhizal symbiosis
In poor nutrient conditions, plants launch phosphorus and nitrogen signalling pathways to maximize nutrient uptake while maintaining homeostasis. And this is the condition where the plant and microbe symbiosis occurs. We will explore how these nutrient sensing and signalling pathways are integrated into the core program of the arbuscular mycorrhizal symbiosis.
Plasticity of host susceptibility to arbuscular mycorrhizal symbiosis
Arbuscular mycorrhizal symbiosis is a highly dynamic process that requires biochemical communication and careful assessment of nutrient economics in both symbiotic partners. Especially, plants develop ways to regulate the symbiosis as they invest up to 20% of the carbon fixed by photosynthesis to farm the microbes. In addition to nutrient status, many environmental factors also regulate the host susceptibility of AM symbioses. Understanding factors and mechanisms regulating the process will help us utilize symbiosis in a dynamic and broader range of environments especially facing global climate changes.
Plant-parasitic interactions - Sebastian Eves-van den Akker
The overarching theme of our group is to combine genomics and molecular biology to understand fundamental questions in host:parasite biology. The group focuses on plant-parasitic nematodes because: i) they are a threat to food security in developed and developing countries, and ii) underlying this threat is a wealth of fascinating biology that until very recently has been largely unexplored.
The 'readers' and the 'regulators'
What distinguishes plant-parasitic nematodes from many other plant pathogens is the presence of specialised gland cells that produce effectors. Discrete subsets of the effector repertoire are delivered into the plant in waves, over the course of several weeks. This project aims to understand this spatio-temporally controlled "parasitism programme": how the parasitism process is regulated over time, in the nematode and in the plant. We anticipate a small number of regulators that control the concerted action of a large number of effectors – if we can disrupt the few regulators, we can simultaneously disrupt hundreds of effectors.
We recently discovered the "DOG box": a promoter motif that unifies hundreds of otherwise sequence-unrelated effectors that are expressed in the same gland cell. The DOG box is our first insight into the regulation of the parasitic process. The fact that a single DNA motif unifies these effectors, implies the existence of a 'reader' and/or 'regulator': likely a protein, or protein complex, which coordinates tissue specific-expression through sequence-specific binding to the DOG box. We are characterising these 'readers' and 'regulators' of parasitism.
Discovering nematoide effectors
Plant-parasitic nematodes have the remarkable abilities to suppress plant-immunity, and to cause existing plant cells to re-differentiate into a novel tissue. The extent of host-plant manipulation is rapid and profound: the cell cycle is arrested at G2, and the number and/or size of almost every sub-cellular organelle is drastically increased (Nuclei, endoplasmic reticulum, mitochondria, and plastids).
In a recent effort we have identified a comprehensive list of one of the 'toolboxes' that cyst nematodes use to manipulate their host. It is thus likely that within this effector repertoire lie genes that can dictate the outcomes of plant organelle development. This project aims to understand the targets and molecular detail of such effectors.
Plant-parasitic nematode genomes and transcriptomes
Over the last few years, we have sequenced genomes and or transcriptomes for nematode species that straddle almost every major phylogenetic bifurcation that gave rise to the sedentary endoparasites: the most economically important species. Most notably this includes the completion of the G. rostochiensis genome consortium. We have ongoing genome projects for a number of cyst nematode species, most recently including the Heterodera schachtii genome consortium, and are always looking for interesting species to analyse.
A current focus of our genomics research is to understand the genetic mechanisms that underlie the juxtaposition of genomic variability and stability in effectors.
The contribution of horizontal gene transfer to plant-parasitism by nematodes
We have known for some time that the genomes of plant-parasitic nematodes have acquired genes from non-metazoans by horizontal transfer. Many of these genes encode cell-wall degrading/modifying enzymes that appear to be involved in host invasion.
Genome wide analyses of horizontal gene transfer have identified several other classes of genes that may be involved in other parts of the infection process. This project will investigate how the biochemistry of proteins encoded by horizontally acquired genes change following transfer, and how these functions contribute to plant-parasitism.
Transformation of the global study of plant-parasitic nematodes
With the help of BBSRC funding, we recently established the transformation of plant-parasitic nematodes consortium with the goal of coordinating efforts from groups around the world to deliver credible strategies for subsequent development; ultimately leading to a robust transformation method. Recent support from the Isaac Newton Trust/Wellcome Trust/University of Cambridge is allowing us to progress in this area. We are always interested to discuss and test ideas to make transformation for plant-parasitic nematodes a reality.
We are developing novel breeding technologies in legume crops to enhance the production of new cultivars adapted to changing climatic conditions, as well as having sustainable yields. Legumes are economically and agronomically important crops in the UK and worldwide due to their proteinaceous seeds and their ability to enhance soil fertility, making them important crops in rotation and intercropping with cereals. We work on legumes of importance to both high- and low-income countries.
We focus on meiosis, a cell division during sexual reproduction resulting in gametes, egg and sperm. During meiosis parental chromosomes exchange parts in a process called recombination, or crossover. As a result, traits from both parents are reassorted before being passed on to offspring. This leads to new qualities in crops, such as yield, nutrient content, resilience to pests and adaptation to abiotic stresses and is the basis for selective breeding. The current challenges for researchers and crop breeders lie within the limitations of meiotic recombination. Not all characteristics are equally amenable to meiotic reassortment, which leaves up to a third of the genetic material unavailable for breeding and results in lengthy and costly breeding programmes. Breakthroughs in the field including our recent work have identified mechanisms that control trait reassortment. We aim to deepen our mechanistic understanding of meiotic recombination control and translate the wealth of this knowledge into impactful breeding.
How can we boost trait reassortment in crops?
Trait reassortment during meiosis results from crossovers which start as double-strand breaks on the genomic DNA and are repaired in a multistep process highly conserved across all eukaryotes. In plants only ~5% of meiotic double-strand breaks are repaired as crossovers, while the remaining ~95% are repaired as non-crossovers with limited impact on trait reassortment. Working in model plants, we and others have discovered crossover modifiers: pro- and anti-crossover factors that compete against each other during meiotic double-strand break repair, mismatch-repair factors, proteins that determine chromosome organisation during meiosis, epigenetic marks and chromatin. Modulating expression of crossover modifiers individually or in combinations is a way to boost crossovers and expedite crop pre-breeding because increasing the number of possible trait combinations translates into fewer generations of plants and individuals required to obtain cultivars with desired qualities. We are now working to identify best strategies to boost crossovers in legume crop pre-breeding using soybean as a model. In the longer term, we are aiming to develop these strategies into widely accessible breeding technologies.
What determines a crossover?
Despite discoveries of crossover modifiers and tremendous progress in understanding of what controls meiotic crossovers, there are two big unanswered questions in the field: i) what makes crossover ‘hotspots’ – several-kilobase-long genetic intervals where crossover frequencies are 10- to 100-fold higher than in the crossover-suppressed ‘coldspots’ and ii) how to efficiently ‘unlock’ genetic variation in crossover-suppressed heterochromatin-rich regions that in crops can harbour up to 20-30% of functional genes. We aim to address these questions by CRISPR-based engineering where we test whether targeted recruitment of pro-crossover factors to the DNA or erasure of crossover-inhibiting heterochromatin marks, can ensure crossovers. We aim to find out whether this approach can lead to de novo crossovers both in ‘hotspots’ and ‘coldspots’. We hope that in the future this knowledge can become game-changing in crop breeding allowing us to incorporate previously ‘locked’ traits into breeding programmes and to overcome linkage drag, or co-inheritance of agronomically useful and undesired traits.
Why are reproduction, meiosis and crossovers affected by temperature?
Elevated temperatures affect spermatogenesis and reduce fertility in humans, insects and plants. In crops sperm (pollen) abortion leads to yield losses. Meiosis, one of the key components contributing to fertility, and crossovers are temperature-sensitive, however, mechanisms behind this are poorly understood. Adaptation to temperature stress can occur naturally: some wild relatives of cultivated crops, for example, cowpea, maintain fertility under elevated temperatures. We hypothesize that this adaptation is, at least in part, due to adaptation of meiosis to heat and further hypothesize that temperature-sensitivity of meiosis can be modulated genetically. We are using forward genetics approaches in Arabidopsis and cowpea to identify mechanisms behind the sensitivity and adaptation of meiosis, crossovers and fertility to elevated temperatures. In the longer term we aim to use this mechanistic understanding to develop climate-smart crops.
Interested in joining the lab?
We welcome highly motivated scientists who would like to join our lab. If you are interested in joining us, please contact Natasha Yelina directly at email@example.com. We particularly encourage prospective post-doctoral scientists eligible for competitive schemes (EMBO, Marie Curie or HFSP). Crop Science Centre is a friendly workplace and a world-leading hub for plant and crop science with strong links across the Cambridge plant science community that includes Department of Plant Sciences, Crop Science Centre, The Sainsbury Laboratory (SLCU) and NIAB.
The crop pathogen immunity group – Lida Derevnina
One of the most important challenges in plant breeding is increasing plant resistance to biotic stresses. Pathogens and pests threaten global food security by limiting crop production. To fend off invading organisms, plants have evolved complex multi-layered immune systems, comprised of cell surface pattern recognition receptors (PRRs) and intracellular immune receptors, largely members of the nucleotide binding and leucine-rich repeat containing (NLR) family. The emerging paradigm is that these receptors can function in networks to detect invading pathogens and activate immunity. Understanding how plant immune receptor networks function and how they have evolved to counteract pathogens and pests will enable the development of novel strategies for disease resistance breeding.
To date, most cloned plant disease resistance genes encode for NLR proteins. NLRs perceive pathogen secreted molecules, termed effectors, and initiate a robust immune response, known as NLR-triggered immunity (NTI). In the Solanaceae plant family, a major phylogenetic clade of NLRs form a complex immunoreceptor network that mediates immunity to diverse pathogens (i.e viruses, bacteria, oomycetes, nematodes, and insects). In this network, NLRs are functionally specialised as sensors that detect pathogen effectors, or helpers, known as NLR-Required for Cell death (NRCs), which trigger downstream immune responses. NRCs form redundant central nodes within the network and display distinct and overlapping sensor specificities. The NRC network emerged ~100 million years ago and includes up to half of all NLRs in some plant species.
We aim to functionally characterise the NRC network and determine the molecular basis of NLR network mediated immunity. Mapping NLR network architectures will boost our capability to breed for disease resistance against multiple diverse pathogens. We will apply our findings to enhance resistance to economically important Solanaceous crops (e.g. potato) against pathogens that infect them (e.g. potato cyst nematode).
How do sensor and helper NLRs function together?
NRCs are core signalling hubs within the NLR network. They function in a partially redundant manner with a large number of sensor NLRs to mediate resistance against diverse pathogens. The determinants of sensor – helper specificity in NLR networks are unknown. We will carry out comparative genetic and biochemical studies of orthologous sensor and orthologous helper NLRs that carry distinct specificity spectrums. We will use this knowledge to decipher the molecular mechanisms that underpin sensor – helper interactions and determine how these NLRs function together to confer disease resistance.
How do NLR networks contribute to immmunity in roots?
Roots are major plant organs, they encounter the highest density of microorganisms and represent important entryways for soilborne pathogens. Despite this, our knowledge of how the root immune system functions to initiate defence responses is lacking. We aim to determine how the NLR network mediates immunity to root infecting pathogens by studying the role of root-specific helper NLR hubs. These helper hubs are highly and often exclusively expressed in plant root tissue, however, their role in mediating immunity to root infecting pathogens are unknown.
How do pathogens interfere with NLR network mediated immunity?
Pathogens secrete effectors that modulate plant processes in order to facilitate host infection and colonisation. Some of these effectors inadvertently activate the plant immune system by being perceived by NLRs, resulting in NTI. A subset of effectors can function as suppressors of immunity and promote virulence leading to host susceptibility. Our recent work revealed that pathogens can target the NRC network by suppressing NTI (Derevnina et al 2021). These effectors proved to be fantastic molecular probes and provided insights into how the NLR network functions. Studying effectors with immunosuppression activity can, therefore, help improve our understanding of how pathogens successfully overcome NLR network mediated immunity and lead to the identification of novel components and processes involved in the plant immune system. We will decrypt the biochemical activities of effector suppressors to improve our understanding of the functional principles and evolutionary dynamics that underpin plant immune receptor networks. This knowledge can then be leveraged to guide new approaches for disease resistance breeding to maximise crop protection, for example, by engineering NLRs that evade pathogen suppression.
Interested in joining the lab?
We welcome inquiries from highly motivated scientists seeking to work in plant-pathogen interactions. If our research piques your interest, please contact Lida Derevnina directly at firstname.lastname@example.org for further discussion. We particularly encourage inquiries from prospective post-doctoral scientists eligible for competitive fellowships (e.g., EMBO, Marie Curie, HFSP, JSPS).