How collaborative research is helping us to develop diverse genetic resources for wheat and legumes, supporting future food security and sustainable agriculture
Iam pleased to welcome you to this 37th edition of Advances. After a short publication hiatus, we are back with a magazine full of ground-breaking discoveries.
I may be biased but I am pleased that this edition focuses on the wonders of, and breakthroughs in, wheat research. BBSRC strategic wheat programme lead, Dr Simon Griffiths, describes the unlocking of the treasure-trove that is the Watkins collection. This gift from the past is crucial to future national and international wheat research and could be the key to revolutionising wheat for the 21st century.
From microbes in the soil to plants, and with research partnerships spanning institutes, countries and continents, we are more than the sum of our parts when we all work together. We hear from Professor Janneke Balk and Dr Sanu Arora about PCGIN, a collaborative network funded in the UK by Defra which is helping to boost and adapt pulse crops in response to climate change.
In a spirit of collaboration, we are asking our readers to support a new, ambitious fundraising campaign. With partners at The Sainsbury Laboratory, we are transforming our existing infrastructure to create a ground-breaking research and innovation hub, and we need your support to share our successes and expand our network. Please get in touch to help us out.
The John Innes Centre is a fantastic place to work, with many of us, myself included, staying for a large part of our careers. Others receive training, or stay for a shorter time, and many alumni go on to do incredible things. In this edition, Dr James Canham, co-founder of GetGenome, tells us how his time at the institute built his scientific network and shaped his career.
Our people and our mission to create a UK hub for plant and microbial science will ensure we continue to be at the forefront of plant and microbial research, supporting the health of people, plants and the planet for future generations.
Professor Graham Moore FRS Director of the John Innes Centre
About the John Innes Centre
John Innes Centre Advances Editorial & Content Team
Hannah Arnold, Adrian Galvin, Felicity Perry, Lauryn Williams
Photography Phil Robinson, Felicity Perry
Cover image: Wheat by Phil Robinson
The John Innes Centre is a world-leading research centre based on the Norwich Research Park. Funded by BBSRC, our mission is to generate knowledge of plants and microbes through innovative research, to train scientists for the future and apply our knowledge to benefit agriculture, health and wellbeing, and the environment. Subscribe to the Advances e-zine for free at: www.jic.ac.uk/advances
Time to rerun the wheat revolution?
A Defra-funded project led by the John Innes Centre and partners can revive the spirit of agricultural discovery for the age of climate change
Aremarkable project launched a century ago by unassuming plant scientist Arthur Watkins is reaping benefits for modern-day wheat researchers, as they seek solutions that will sustainably feed a projected global population of 10 billion people.
Researchers in the collaborative Wheat Genetic Improvement Network (WGIN) have been funded by Defra to use precision breeding techniques to deliver wheat that is more nutritious, disease resistant and better able to withstand drought, salinity and even slugs.
This fascinating project, a hybrid of ancient and modern, owes its existence to Watkins, a shy man who shunned the limelight in his day. The only grainy image that remains sees him leaning out of a first-floor window on the fringe of a departmental gathering.
“Watkins wasn’t a famous scientist at the time but, if you read the letters he sent to
his contacts across the British Empire, it is incredible how modern his thinking was,” said Dr Simon Griffiths, a group leader at the John Innes Centre and lead of the Delivering Sustainable Wheat Institute Strategic Programme (ISP).
“Watkins saw that the new systematic breeding in the early part of the 20th century was taking over and that 10,000 years of genetic diversity was rapidly being replaced by these new cultivars. His work in assembling what we now know as the A.E Watkins collection is truly visionary and only now are we beginning to see how influential he is,” continued Dr Griffiths.
Watkins was working at a time when science was fuelling dramatic changes in agriculture, as pioneers such as Sir Rowland Biffen applied the newly discovered laws of genetics towards gains in the field. Biffen was hailed a “wheat wizard” by the press of his day as grateful farmers welcomed higher yielding and better performing crops, the product
of crossing using a smaller gene pool.
These gains came at a cost which only a few appreciated at the time. As breeders of the day sought to use the new improved cultivars, they began to dispense with landraces, the locally adapted wheats that had been cultivated since bread wheat first emerged in the Fertile Crescent between 9,000 and 10,000 years ago.
With remarkable foresight, Watkins saw that the genetic diversity in the landraces was being lost to a bottleneck of new systemic breeding that narrowed the base from which new elite varieties were being selected.
Using networks across the British Empire, Watkins enlisted the support of British Embassy staff, soldiers and civil servants to collect landraces from local markets. Watkins’ letters advised his correspondents to avoid experimental wheat stations where the
RESEARCH
new systematic breeding was being practised, revealing an astute grasp of the dangers of this innovation. He wanted the wheat that had been grown since the dawn of agriculture, not that which had been grown since the dawn of genetics a few decades earlier.
Watkins’ far-flung correspondents gathered more than 1,000 bread wheat landraces of which 827 from 32 countries still exist today, curated and regularly regenerated at the BBSRC-funded Germplasm Resources Unit at the John Innes Centre.
It wasn’t until recently that wheat researchers appreciated the genetic goldmine that had been bequeathed by Watkins and his network. In an international collaboration in the spirit of Watkins, which appeared in the journal Nature, researchers DNA sequenced the historic collection and 220 elite modern wheats.
This computational ultra-marathon, taking up one million gigabytes of data, revealed that modern wheat varieties make use of just 40% of the genetic diversity found in the Watkins collection. The data showed that only two of the seven ancestral groups into which the Watkins Collections can be divided are represented in
wheat breeding.
“Wheat breeding began in France and Germany, and these European breeders built modern wheat on European landraces,” explained Dr Griffiths. “Until recently the breeding industry believed they had sampled a wide variety of the Watkins collection. It was a major surprise to discover that most of the collection – 60% – is untouched by modern breeding.”
The Watkins collection has started delivering its genetic treasure. Using the Breeders’ Toolkit, a suite of genomic resources provided by the Designing Future Wheat ISP, researchers and breeders have mined the collection for useful variation which is absent in modern wheat.
Genes controlling nitrogen use efficiency, mineral content, heat resilience, wheat blast resistance and slug resistance have already been identified. Some new wheat lines introgressed with Watkins diversity are to be part of the first field trials of gene edited wheat in the UK.
But to take full advantage of the Watkins Collection and other collections of wild relatives of wheat, Dr Griffiths believes we need a radical rethink of wheat breeding. That
spirit, he believes, underpins the five-year WGIN project.
“What we are saying in this project is that we are not sure breeders did a systematic job in the first place and we need to start again,” he explained. “When we sequenced
modern
Dr Simon Griffiths
Watkins (left in the right window) at Cambridge
the Watkins collection, we expected to find hundreds of useful variations compared with modern wheat. In fact, the variations run into many thousands. The methods we have developed in the Breeders’ Toolkit platform amount to searching for a needle in a haystack. Now we know there are thousands of potentially useful variations in Watkins that could be employed to the benefit of modern wheat. So, we need something different.”
John Innes Centre researchers, as part of their contribution to WGIN, will use the freedom afforded by the Precision Breeding Act to gene edit and trial the Watkins Collection. This means that the tall, pre-modern landraces will be edited to include valuable traits that emerged via systematic breeding in the 20th Century.
The edited landraces will contain genes that make wheat cultivars semi-dwarfed, so they stand firmer in the field; red grained, because red grains inhibit early sprouting in a UK climate; and hard textured for better milling.
“Put all these traits together in a landrace and you have a package which is UK wheat: modern wheat pedigrees with the landrace diversity that provides useful traits for our climate and weather just by making changes to three or four genes,” said Dr Griffiths.
Watkins’ correspondents gathered more than 1,000 bread wheat landraces of which 827 from 32 countries still exist today
This combination of modern cultivars packed with landrace diversity will allow breeders to select directly from these new modernised landraces, opening the 60% of genetic diversity which until now has been unavailable to modern breeding. “With the knowledge and tools we have and the passing of the Precision Breeding Act in England, we can do a better job than the breeders of the 20th century. The current methods we have developed are just taking the cherries – but you cannot do this on a scale of thousands,” observed Dr Griffiths.
“Our new programme will allow breeders to take the entire organism, the modern and old blend carrying all those thousands of genes.”
WGIN carries the same spirit of international collaboration as Watkins’ project did a century ago. While he may not have lived to see the Green Revolution, climate change or the effects of intensive plant breeding and farming, Watkins predicted that one day wheats of the past would still be needed. That day has now arrived.
What is the Defra Wheat Genetic Improvement Network (WGIN)?
Wheat is the major crop of the UK. In 2003, the Wheat Genetic Improvement Network started to connect commercial plant breeding activities and publicly funded plant and crop research institutes. The overall aim is to generate pre-breeding material carrying novel traits for UK wheat breeding companies and to deliver accessible technologies.
The project is led by Rothamsted Research and collaborators include the John Innes Centre, Bristol Genomics Facility and USA-based Arbor Biosciences.
As part of Defra funding for the next five years, the John Innes Centre will deliver work package two, which will deliver work to use precision breeding techniques to adapt landraces, making them accessible to the breeding industry.
Watkins in the field
The Watkins wheat collection in numbers
We dive into the numbers behind the Watkins collection, our vast archive of historic wheat seeds stored and regenerated in our BBSRC-funded Germplasm Resource Unit
Wheat was domesticated ~10,000 years ago
This was in the fertile crescent, a region in the Middle East that spans modern-day Iraq, Syria, Lebanon, Israel, Palestine and Jordan, together with the north of Kuwait, south-east Turkey and the west of Iran.
In the early 20th century, A.E. Watkins led an initiative to gather more than 1,000 landrace cultivars of bread wheat (Triticum aestivum L.) from
32 countries
around the world.
SYRIA
KUWAIT
JORDAN
PALESTINE
ISRAEL
LEBANON
IRAQ
Over time, some of the 1,000 original landraces have been lost or were found to be duplicates.
From this, the team made
8,000
recombinant inbred lines by crossing the Watkins to Paragon and in doing so they transferred
44,000 haplotypes (genes which are clustered together in the genome) which were not present in modern wheat.
Who Was A.E. Watkins?
A. E. Watkins worked in the plant breeding department at the University of Cambridge and was tasked with collecting wheat varieties from around the world to preserve the diversity found in the local landraces.
Watkins used his London Board of Trade connections to contact a network of collectors, who were stationed across the
Now, 100 years later
827
landraces are housed at the Germplasm Resource Unit at the John Innes Centre having been stored, regenerated and studied since the 1930s.
Over the past ten years, an international team of researchers has selected, sequenced and analysed a core set of
119
landraces that capture the majority of the genetic diversity within the collection.
These landraces represent the
seven ancestral groups that capture the majority of the genetic diversity within the collection.
British Empire, asking each of them to find local landraces.
Watkins prudently instructed them not to go to the modern breeding stations, but to go to the more remote parts of the country or the local markets and to send these back to Cambridge.
Read more about A.E. Watkins on our website: www.jic.ac.uk
Science spotlight
A round-up of our recent research featured in scientific journals
Barley fine-tunes microbial root communities with sugary secretions
PLOS BIOLOGY
Different types of barley recruit distinct communities of microbes to grow around their roots by releasing a custom mix of sugars and other compounds into the soil.
Professor Jacob Malone, group leader, said: “Groups of microbes help some varieties to grow but not others, suggesting that breeding cereals to recruit beneficial, growth-promoting microbes may be possible in the future.”
Beneficial microbes that live on or around plant roots can provide nutrition, help the plant withstand stress, and protect it from pathogenic microbes. In return, the plant secretes a portion of the sugars it makes through photosynthesis, along with amino acids and other metabolites, into the surrounding environment.
The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. DOI: 10.1371/journal. pbio.3002232
An international research collaboration has shed light on the molecular basis of gene expression, the fundamental biological process that underpins how organisms use genetic information.
Smart soil bugs offer eco route to crop disease control
ELIFE
A method of controlling crop diseases using beneficial soil bacteria has emerged from a research-industry collaboration.
Researchers have shown that small molecules called cyclic lipopeptides, produced by certain strains of Pseudomonas bacteria, are important in the control of potato scab, a bacterial disease that causes losses to potato harvests.
Postdoctoral Researcher and first author of the study, Dr Alba Pacheco-Moreno, said: “By identifying mechanisms of potato pathogen suppression our study will accelerate the development of biological control agents to reduce the use of chemical treatments.”
Cyclic lipopeptides have an antibacterial effect on potato scab, and help protective Pseudomonas move around plant roots.
Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. DOI: 10.7554/eLife.71900
While much is known about ‘translation’, how a ribosome decodes mRNAs, a key outstanding question was how ribosomes find mRNA to begin with. Using an advanced microscopy technique, the research team captured the moment genetic information is translated into proteins, revealing a pathway on the surface of the ribosome that the mRNA takes to reach the decoding position.
Dr Michael Webster, group leader and first author of the study, intends to build on this new understanding to examine photosynthetic protein production in chloroplasts. This study included experts in: cryo-EM at the John Innes Centre and the IGBMC (Strasbourg); single-molecule kinetic analysis at the University of Michigan; and structural proteomics at the Technische Universitat (Berlin).
Molecular basis of mRNA delivery to the bacterial ribosome DOI: 10.1126/science.ado8476
Seemingly ‘simple’ mosses and ferns offer new hope for crop protection
Mosses, liverworts, ferns and algae may offer an exciting new research frontier in the global challenge of protecting crops from the threat of disease. These non-flowering plants are often regarded as unsophisticated compared to their flowering relatives. New research has found that bryophytes and mosses in particular have sophisticated immune receptors.
Using biotechnological techniques, researchers have revealed that nucleotide-binding and leucine-rich repeat (NLR) immune receptor domains which protect plants against pathogens are transferable
Secret recipe for versatile limonoids
between flowering and non-flowering plants.
This breakthrough in understanding offers a route to practical applications for crop protection and a source of new resistance genes against pathogens.
The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages.
DOI: 10.1093/plcell/koae113
Innovative research has uncovered the secret of how plants make limonoids, a family of valuable organic chemicals which include bee-friendly insecticides and have potential as anti-cancer drugs.
“By finding the enzymes required to make limonoids, we have opened the door to an alternate production source of these valuable chemicals,” explained Dr Hannah Hodgson, co-first author of the paper and a postdoctoral scientist. “Their structures are too complicated to efficiently make by chemical synthesis. With the knowledge of the biosynthetic pathway, it is now possible to use a host organism to produce these compounds,” she added.
The research team, a collaboration between the John Innes Centre and Stanford University, used ground-breaking methods to reveal the biosynthetic pathway of these molecules. Until now limonoids, a type of triterpene, could only be produced by extraction from plant material.
Complex scaffold remodelling in plant triterpene biosynthesis.
DOI: 10.1126/science.adf1017
Legendary legumes
Our researchers are supporting the development of new legume crops for the UK
Pea, bean and lentil belong to the legume family and have great promise as net-zero, climate-resilient crops for the future. They have the potential to be an important part of the solution to reduce the impact of agriculture and boost food production on our planet. However, to realise these benefits there are challenges to overcome. This is where John Innes Centre researchers and collaborators believe they can help.
Pulses provide a healthy source of protein, fibre, minerals and complex carbohydrates. But these plants have another astonishing feature – they form a close interaction with microbes that can harvest, or fix, nitrogen from the air and convert it to natural fertiliser. This beneficial plant-microbe arrangement means that most legumes can thrive without costly and damaging nitrogen fertilisers.
With a long history of genetic research and an international collection of diverse pea germplasm, the John Innes Centre is well placed to study how both the nutritional traits and environmental resilience of pea can be improved. In addition, germplasm collections of other legumes, mainly lentil and common
bean, have recently been added.
The Defra-funded Pulse Crop Genetic Improvement Network (PCGIN), led by group leaders Professor Janneke Balk and Dr Sanu Arora, is a five-year programme with £3 million funding and involves five different UK partner organisations. It aims to understand the genetic variation for specific traits in pulse crops and develop new genetic resources. This will form the basis of a toolkit for plant breeders who develop new varieties of pea, faba bean and lentil for farmers in the UK.
One of the PCGIN-funded tasks taken on by Professor Balk and Dr Arora, in collaboration with Professor Lars Østergaard, who recently moved to the University of Oxford, is to create a new genetic resource for pea.
To generate a large population of lines with small genetic changes, they have used a conventional breeding technique called ‘induced mutation’, that creates small changes in a plant’s DNA by exposing a plant or seeds to chemical or physical stresses.
Sequence analysis so far indicates that the new pea lines have small genetic changes in
virtually all of the 30,000 genes in the genome. If such a change disrupts a gene function, this will manifest itself in altered traits and link the trait to specific genes, which is very useful for plant breeders.
In 2024, 3,000 plants were grown in our glasshouses to give a glimpse into the range of traits in this pea population. Observations of visible traits (leaf morphology, plant size, flower colour and seed shape) are stored in an accessible database. A DNA sample has been collected from each plant and the seeds will be carefully archived.
Did you know?
Nearly half of the protein in the human diet comes from plants, mostly pulses, which are the dried, edible seeds of legumes.
Legumes are gluten-free and have a low glycaemic index, making them a good choice for the health of the planet and human health.
This is the start of a community resource that will enable the development of improved legume crops which are more nutritious, resilient to evolving pests, diseases and a changing climate.
For Professor Balk this is a novel experience: “For most of my career I have been focused on investigating and understanding the function of the proteins involved in iron transport and storage in plants. The work we’re doing here to create a resource that can support the long-term development of a crop is new to me and I’m enjoying the process.”
Researchers who want to study a specific trait can find plants of interest and order the seeds. Also, if they are interested in a specific gene, the TILLING service at the John Innes Centre can screen DNA samples for mutations. The plan is to sequence the genomes from all 3,000 plants, but this will require additional funding.
The identity of the pea used for creating the new mutant population was chosen carefully.
Professor Balk explained: “The line we have used is the John Innes ‘lab rat’ of pea – JI2822. It has a short seed to seed generation time, and it only grows to around 50cm tall. This makes it perfect for this type of study where we need lots of plants and many generations.
This is an exciting development that could have a hugely positive impact on human health in the long term
Her initial priority is to screen a subset of the mutant pea population for resistance to root rot and downy mildew pathogens.
“In addition to morphological traits, we have also started to screen for nutritional changes, such as increased iron. Tegan Tyzack, a PhD student, found an iron-accumulating plant in the first set of 400 plants and is taking this further to find the genetic cause.
Increasing the iron content of plant-based foods is important for human health in the long term, as many people switch to diets with less meat,” said Professor Balk.
Dr Arora, co-lead of PCGIN, and her team focus on understanding the genetic basis of disease resistance in the context of a changing climate, and developing more resilient legumes.
Dr Arora explains, “Working with a crop like pea comes with many challenges, from limited funding and genomic resources, to being part of a relatively small community of researchers. But, over the years, PCGIN has
More about PCGIN
been a fantastic programme for developing resources accessible to the entire community. The next step is to enable the cultivation of crops like lentil and Phaseolus (or common bean, used for baked beans) in the UK.”
“Working together with industry, farmers, food producers and the government, we hope to be able to improve diverse legumes so that they become viable crops for the UK, supporting sustainable agriculture, and producing healthy food,” Professor Balk concluded.
The Defra-funded Pulse Crop Genetic Improvement Network is a consortium of UK research organisations led by the John Innes Centre. PCGIN supports researchers and industry to provide improved breeding material that will better enable the development of climate resilient pea, faba bean and other pulses in the UK.
The partners involved are the University of Reading, NIAB in Cambridge, the Institute of Biological, Environmental and Rural Sciences (IBERS) at Aberystwyth University, and PGRO, the Processors and Growers Research Organisation, Peterborough.
Dr Sanu Arora and Professor Janneke Balk
CGI of the proposed net-zero carbon laboratory building at the Norwich Research Park
Healthy Plants, Healthy People, Healthy Planet (HP3) is the joint vision of the John Innes Centre and The Sainsbury Laboratory to secure a safer, healthier and more sustainable future through plant and microbial science. It provides a long-term strategic vision for our research, outlining how we will address key global challenges, such as food security, sustainable agriculture and human health. The Next Generation Infrastructure (NGI) is the construction programme enabling us to deliver this vision, including creating a new net-zero laboratory building and insectary, as well as a state-of-the-art plant growth facility and specialist glasshouses. An ambitious fundraising campaign is underway to secure a further £35 million investment to support the full cost of our exciting development.
Securing the future of food and health
Nature has the answers, help us deliver the solutions
The John Innes Centre (JIC) and The Sainsbury Laboratory’s (TSL) ambitious vision, Healthy Plants, Healthy People, Healthy Planet (HP3) aims to deliver solutions to global challenges and secure a safer, healthier, and more sustainable future, through the power of plant and microbial science.
For 110 years JIC has been using its knowledge of plants and microbes for the benefit of society and global development. TSL pioneers ground-breaking research in plant health, advancing crop disease solutions for global food security, with a legacy of world-renowned discoveries.
Purpose driven solutions from cutting-edge science
We must address the critical challenges facing society and the planet:
• Feeding the world – we must create a better food future, to sustainably produce enough healthy, nutritious food to feed a growing population.
• Climate change – we need to support agricultural transformation to reduce the impact of food production on the climate, soil and the environment.
• Improving global health – we can use plants and microbes to improve human health, by producing healthier foods and medicines from nature.
JIC and TSL are striving to build the best plant and microbial science laboratory infrastructure in the world at the Norwich Research Park. It
A once-in-a-generation opportunity, for all future generations
Sir
Tom Hughes-Hallett, Chair of the Governing Council, John Innes Centre
will bring together the interdisciplinary teams required to deliver solutions to these global challenges.
Together with our funding partners, we are investing in the future to transform our existing capabilities and develop a net-zero carbon laboratory building.
This ground-breaking research and innovation hub will supercharge our global ability to translate scientific knowledge into practical solutions, while sharing our knowledge, facilities, networks and experience with others nationally and internationally.
We’ve launched a £35 million fundraising campaign to complete delivery of our ambitious vision, and your philanthropic support is needed to fully realise this potential.
If you would like to discuss areas of mutually beneficial interest, please contact: Angela Bowen, Director of Development. Angela.bowen@jic.ac.uk
+44 (0) 7714 051 310
CGI of the proposed net-zero carbon laboratory building CGI of the proposed glasshouse corridor
Working in partnership with nature
In the long term, science and biodiversity will benefit from our infrastructure programme
Over the next five years, the Next Generation Infrastructure (NGI) programme aims to establish a world-leading hub for UK plant and microbial research, transforming the capabilities of the John Innes Centre and The Sainsbury Laboratory, at the heart of the Norwich Research Park.
This programme will redevelop our campus, with ambitions to create a net-zero carbon laboratory building (with certification under the UK Net Zero Carbon Buildings Standard) and insectary, as well as a state-of-the-art plant growth facility and specialist glasshouses. Alongside new buildings, we will also refurbish existing buildings and create a functional landscape, with spaces for working and socialising, and habitats for nature.
The new buildings, renovations, and demolition will inevitably change the existing site and surrounding green spaces and infrastructure. However, the programme is committed to enhancing biodiversity, with new developments asked to achieve a minimum Biodiversity Net Gain of 10%. We are committed to achieving a greater gain than the minimum requirements and are predicting a much greater uplift.
New Landscapes
Our aim is to create a welcoming, natural landscape that works for science and biodiversity.
To achieve this, we will embed a range of initiatives, including introducing more pollinator-friendly native plants, the creation of a rain garden, attenuation ponds and new hedgerows, alongside protecting healthy, mature trees and wildlife corridors where possible.
Significant trees will be protected before, during and after the construction phase, and the new landscape includes a net gain of 40 trees on site.
Our team is working with ecologists and arboriculturists to mitigate the effects of construction. Having completed a full biodiversity survey of the site, some of their recommendations that we will implement include: the use of coppicing instead of hedge/
tree removal, hand-digging near root protection zones, the use of matting on temporary access routes to prevent soil compaction, and the use of sensitive lighting during construction to avoid disturbing foraging wildlife, such as bats and hedgehogs.
The NGI programme will also produce a Habitat Management and Monitoring Plan, which will outline how land will be managed over the next 30 years to maintain the gain in biodiversity.
CGI of the proposed main lab building from the UEA approach
MKA ecologists carrying out bat surveys
Tick tock, internal clocks
The role of circadian rhythms in humans and animals has long been studied, but new discoveries are shining a light on the vital role of daily and seasonal biological cycles in plants and microbes, and how changes in the environment might affect this important internal time-keeping
‘Ice bucket challenge’ reveals that bacteria can anticipate the seasons
SCIENCE
Bacteria use internal circadian clocks to anticipate seasons, according to research utilising an ‘ice bucket challenge.’ Dr Luísa Jabbur, who recently joined the John Innes Centre as a BBSRC Discovery Fellow, headed a study at Professor Carl Johnson’s laboratory at Vanderbilt University, where cyanobacteria populations were subjected to different artificial day lengths at a constant warm temperature then plunged into ice for two hours. Samples exposed to shorter days achieved survival rates up to three times higher than those exposed to longer days – providing first-time evidence for evolution of photoperiodism in bacteria.
Bacteria can anticipate the seasons: Photoperiodism in cyanobacteria.
DOI: 10.1126/science.ado8588
Clue to parasite’s infection mechanism
PNAS
Circadian rhythm field trials get the green light
PNAS
Most knowledge about plant circadian rhythms comes from laboratory experiments where inputs can be tightly controlled. An ongoing collaboration between UK and Japanese research teams has helped inform how plants combine clock signals with environmental cues under naturally fluctuating conditions in landmark field experiments. The John Innes Centre and Kyoto University monitored plant gene expression over 24-hour cycles as light and temperature varied, producing statistical models to help predict plants’ responses to fluctuating temperatures.
A discovery first made in plants has inspired important insights into the malaria parasite’s (Plasmodium falciparum) infection mechanism. Professor Antony Dodd’s group discovered that a sigma factor is necessary for gene regulation in chloroplasts, leading them to wonder whether comparable proteins exist in Plasmodium falciparum
A collaboration between Tokyo Institute of Technology, Nagasaki University, and the John Innes Centre identified a Plasmodium sigma factor (ApSigma) that binds to the apicoplast genome and regulates gene expression. The results suggested that ApSigma is essential for the parasite’s survival, offering a future target for malaria drug discovery.
Coordination of apicoplast transcription in a malaria parasite by internal and host cues.
DOI: 10.1073/pnas.2214765120
Circadian and environmental signal integration in a natural population of Arabidopsis.
DOI: 10.1073/pnas.2402697121
Complexity of bacterial clocks
SCIENCE ADVANCES
A collaborative team at Ludwig Maximillian University Munich, the John Innes Centre and Leiden University revealed that soil bacteria have internal clocks, synchronising activities with the 24-hour day and night cycle. The discovery was made by probing gene expression as evidence of clock activity in the bacterium Bacillus subtilis, clearing the way for exciting new research – from precise timing of antibiotic use, to bioengineering smarter gut and soil microbiomes. In future, the team will be studying all aspects of the functioning of this bacterium’s clock, supported by an €8.3 million ERC Synergy grant.
The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems.
DOI: 10.1126/sciadv.adh1308
International Innes
The greatest breakthroughs in science often emerge from connections forged across boundaries. This map reveals a web of just a small number of the global scientific collaborations and projects fostered by our researchers to tackle humanity’s challenges. From urban research hubs to remote field stations, this map is a story of shared knowledge, innovation and collective discovery
MARPLE
Locations: Ethiopia, Kenya, Nepal, Pakistan, Türkiye and South Africa
The MARPLE diagnostics methodology, developed at the John Innes Centre in collaboration with CIMMYT, is a portable near real-time diagnostics system for the devastating wheat rust pathogens. Using the handheld MinION nanopore sequencer, built by Oxford Nanopore, the MARPLE system analyses pieces of the pathogen’s genome to determine which strains are present in the region and can generate results in just two days. This information can be immediately integrated into early warning systems and disease management decisions, making it ideal for responding to crop disease emergencies.
Circadian rhythms
Locations: Japan, Germany and the Netherlands
Professor Antony Dodd, group leader, leads a lab that investigates the adaptation of plants and microorganisms to fluctuating environments, focusing on circadian regulation and signal transduction. The John Innes Centre, LMU Munich, and Leiden University secured an ERC Synergy Grant to take forward their ground-breaking research. Their project, MicroClock, follows the recent discoveries by this collaboration of biological or circadian rhythms in the non-photosynthetic soil bacterium Bacillus subtilis
Biosynthesis
Locations: Chile and the USA
Professor Anne Osbourn, group leader and Fellow of the Royal Society, investigates plant natural product biosynthesis.
Professor Osbourn’s team at the John Innes Centre tracked down and mapped the elusive genes and enzymes needed to produce the useful molecule QS-21, naturally produced by the Chilean soapbark tree (Quillaja saponaria) and used to make vaccines more effective. The team collaborated with American genomics experts to determine the genome sequence of soapbark. Professor Osbourn’s team then elucidated the entire QS-21 pathway and reconstituted it in Nicotiana benthamiana, a wild relative of tobacco. This led to a collaboration, supporting a group in California to engineer this pathway into yeast.
CHILE
UNITED STATES
Purple tomatoes
Location: USA
Genetically modified, high-anthocyanin purple tomato seeds are available for home gardeners to purchase for the first time in the United States, having launched in February 2024. More than 1,200 seed packets sold within 48 hours of launch, and 9,600 sold in the first week. First produced by Norfolk scientists nearly two decades ago, the seeds are now produced by Norfolk Healthy Produce, a subsidiary of Norfolk Plant Sciences founded by Norwich Research Park scientists Professor Cathie Martin FRS and Professor Jonathan Jones FRS.
The Centre for Microbial Interactions
Location: UK
The Centre for Microbial Interactions represents one of the world’s largest concentrations of microbiologists on a single site, with more than 100 microbiology research groups based at the Norwich Research Park. Six partner institutions, the John Innes Centre, The Sainsbury Laboratory, Earlham Institute, Quadram Institute, the University of East Anglia (UEA) and the Norfolk and Norwich University Hospital, have collaborated to launch and fund the centre, one of the most globally important sites for microbiology.
The Watseq consortium
Location: China
A five-year collaborative, cross-institutional collaboration with the Agricultural Genomics Institute at Shenzhen completed whole genome sequencing of the A.E. Watkins Landrace Collection, a historic collection of locally adapted strains of wheat which are no longer grown anywhere in the world. Complementing next generation gene discovery populations developed and characterised in BBSRC’s cross institutional wheat programme, Watseq data showed that modern wheat lacks 60% of the beneficial traits available in Watkins. This is delivering new varieties of wheat to sustainably feed a growing global population.
CHINA
JAPAN
ETHIOPIA
NEPAL
SOUTH AFRICA UNITED KINGDOM
KENYA
PAKISTAN
TÜRKIYE
Taking root in Norwich
With staff and students from more than 36 countries, we are proud to be an inclusive institute. We asked colleagues what they love about Norwich and working at the John Innes Centre
Dr Myriam Charpentier, group leader
“Working at the John Innes Centre is a unique experience for anyone passionate about plant science and innovation. We are part of an inspiring, diverse community where ideas flow freely, and cutting-edge research takes centre stage. Collaboration with talented colleagues from around the world fosters fresh perspectives and drives discoveries. It is a place where curiosity-driven science is celebrated."
Dr Alba Pacheco-Moreno, postdoctoral researcher
“When I was applying for PhD positions, the project that was offered here captivated me. I loved the place, the people and the city. The plan was to stay only four years but more than seven years later and I'm still here!
“Norwich and the research park has a lot to offer, both professionally and personally. The level of science that you can do here is among the best in the world in plant sciences, and will positively impact opportunities to grow your career. At the same time, Norwich itself is a lovely place to live. Going for a walk around its medieval streets is quite unbeatable, I would say.”
Professor Tung Le, group leader
“Back in 2006, the John Innes Centre was the only place in the UK that offered me a full scholarship as an international student to do a PhD. Without this rotation programme, I could not have pursued further education, and would not have met my wife!
"When I finally came here, I discovered my talent and enjoyment of lab work, and was supported by fantastic mentors. I chose to come back to Norwich in 2016 to start my own independent lab, after a stint in the USA as a post-doc. I wanted to have access to the great facilities, great science and being surrounded by like-minded people - that combination can’t go wrong!”
Dr Anne Edwards, research assistant
“I came to Norwich in 1987 to do a PhD on oxidative stress in peas, a Pea-h-D if you will. It was a long train journey from South Wales, and as I arrived I rolled into thick Norfolk fog. Not long after, the Great Storm arrived, the worst in more than 200 years! Weather aside, I immediately felt at home.
“Now I live just outside Norwich and enjoy visiting the city to explore its many historic buildings. I love the Norfolk countryside with its diverse wildlife (though I do miss mountains as
it is so flat!)
“John Innes has a great atmosphere. It is a very exciting and friendly place to work, and no two days are the same in the laboratory. We are very lucky to have fantastic support services to assist with tasks, including growing plants, making media, mending equipment and so much more.
“Norwich is a very fine place to live and work – but beware! Once you are here you will not want to leave.”
Why Norwich?
Norwich has been the home of the John Innes Centre since 1967 (then the John Innes Institute), and is a fine city in which to live and work
City life
Norwich was rated one of the best places to live in the UK in the Sunday Times 2024 guide. Described as a ‘cosmopolitan city’ with modern and medieval architecture where ‘literary pedigree meets liveability’, it also has one of the oldest and largest outdoor markets in the country. Home to theatres, museums, galleries and concert venues, Norwich was named the UK’s first UNESCO City of Literature in 2012.
Norwich Research Park
Norwich Research Park is one of five BBSRC-funded UK Research and Innovation Campuses, bringing together four independent internationally renowned research institutes: the John Innes Centre, Quadram Institute, Earlham Institute and The Sainsbury Laboratory. It is also home to the University of East Anglia, Norfolk and Norwich University Hospitals NHS Foundation Trust and a community of more than 30 businesses. It is one of the largest single-site concentrations of research in food, genomics and health in Europe.
Nature and landscape
Norwich is the only city in England set in a national park, the Norfolk Broads. The spectacular Broads are the UK’s largest navigable man-made waterway, and the John Innes Centre even has a boat you can hire to use. Norwich is also only 20 miles away from the beautiful Norfolk coastline, which spans 90 miles of sandy beaches, soaring cliffs, shingle, saltmarshes and estuaries. The coast is easily accessible by car, train or bus, and is perfect for walking, cycling, bird watching, or just sitting in a country pub.
Connectivity
The city has excellent transport links to local destinations like Cambridge, and a direct train can get you to central London in just two hours. Norwich also has a convenient international airport, only 2.5 miles away.
Affordable housing
According to ONS, the average house price in Norwich was £243,000 in September 2024. The average monthly private rent in Norwich was £1,048, with the average rent for a one-bedroom property at £705 per month.
Awards & achievements
Many of our scientists have been recognised with prestigious accolades, in recognition of their outstanding achievements within the international research community, as well as for their impact on plants, people and the planet
Professor Saunders sweeps the board
Diane Saunders OBE has been decorated for her outstanding scientific achievements and dedication to women in STEM. In 2022, Diane received the Royal Society Rosalind Franklin Award and Lecture in recognition of her long-term achievements in plant pathology. The following year, she was awarded the British Society for Plant Pathology (BSPP) RKS Wood Prize, and in 2024 was awarded Officer of the Order of the British Empire (OBE) in the King’s Birthday Honours.
Professor Howard receives the 2022 Institute of Physics Rosalind Franklin Medal
Professor Osbourn elected as a member of the National Academy of Sciences
Anne Osbourn OBE FRS has been elected as an international member of the National Academy of Sciences (NAS), one of the United States’ highest honours. Her discovery that biosynthetic pathways are organised in clusters in plant genomes like ‘beads on a string’ has accelerated the ability to find new biological pathways and chemistries for potential medicine and useful compound development.
This award recognises Martin Howard’s pioneering work in applying concepts from statistical physics to molecular biology. His group has helped to unlock diverse biological questions around cell memory systems, cell size control and spatiotemporal protein patterning. He has also introduced physics-based thinking to biologists.
Dr
Borrill
receives President’s Medal Award from The Society of Experimental Biology
This prestigious award honours outstanding early-career scientists. Philippa’s celebrated research focuses on firstly, how genes are switched on and off in wheat’s complex genome, and secondly, improving the nutritional content of wheat, especially iron and zinc.
Royal Society Fellows
Professors Graham Moore, Director, and Saskia Hogenhout, group leader, have been elected as Fellows of the Royal Society. Graham has made outstanding contributions to wheat research, which have provided insight into the pairing and crossover control between related wheat chromosomes. Saskia has pioneered research on the functional characterisation of virulence factors from non-culturable bacteria and interactions of sap-feeding insect vectors with plants.
Professor Le awarded Lister Fellowship
In recognition of his group’s innovative research, Tung Le was awarded the highly prized Lister fellowship, which will allow new lines of investigation that may benefit antibiotic discovery. His research group studies Streptomyces, soil bacteria which are the source of most clinically used antibiotics. Exploring the genomic and functional diversity of Streptomyces is crucial to fully unlocking their potential.
EMBO membership
Three John Innes Centre researchers have been elected as members of the European Molecular Biology Organisation (EMBO) since 2022.
Professor Anne Osbourn was elected in 2022, Professor Saskia Hogenhout the following year, and in 2024 Professor Martin Howard was elected.
Additionally, Dr Susan Schlimpert was accepted into the EMBO Young Investigator Programme in 2022, which supports outstanding early career group leaders.
Dr James Canham
After working and studying at the John Innes Centre from 2014-2022, James now works at GetGenome – a charity he co-founded that delivers equitable access to genomics technology, training, and education. We caught up with him to ask about his career so far, from maintaining golf courses to delivering genomic support to researchers around the world
What got you interested in science?
It was simply curiosity. When I worked on golf courses, I was fascinated by the environmental aspects of the role. Ultimately, the grass on the course is subject to many challenges, including pathogens, heat and drought. For me, the answer was to learn as much as possible to mitigate the impact on the course. This led me to complete a foundation degree in sports turf science. It included some plant science, but I needed to know more, which meant immersing myself back into full time education.
What brought you to JIC?
During my time at the University of East Anglia, studying for an MSci in Plant Sciences, I applied for a position at the John Innes Centre helping PhD student Tom Vincent in Professors Tony Miller and Dale Sanders’ lab. Tom was collaborating with Professor Saskia Hogenhout, focusing on calcium signalling in plants during a plant-aphid interaction.
For my undergraduate research project, I stayed in the Miller-Sanders lab, and investigated similar calcium responses, but this
time, during nitrate sensing in plants. I then did my Masters with Saskia and then my PhD, asking the question: ‘Can plants perceive insect herbivores and know them to be a threat?’
What is your current job role?
I am one of the cofounders of GetGenome, a non-profit housed within The Sainsbury Laboratory (TSL). We empower scientists by democratising genomics technology and training. That’s our mission.
How did your time at JIC influence your career?
During my Professional Internships for PhD Students (PIPS) placement, I spent time at the AfriPlantSci summer school in Kenya. A participant who worked for a government agency explained they were investigating a coconut disease outbreak in neighbouring regions. I supported their research through genomics, which highlighted the barriers to accessing genomics when trying to collect high-quality DNA in 35°C with limited resources. I began to think about ways to formalise what later became GetGenome’s mission – to
democratise genomics and to provide these technologies and skills to researchers globally. I later discovered that Professor Sophien Kamoun, a group leader at TSL, had gone further than I had to begin to address inequity. We joined forces.
What’s the most rewarding aspect of your job? I get to support so many researchers. Sometimes I send them ten whole genome sequences of organisms that have amazing potential. I can only imagine how transformative it must be to receive the genome of an organism you’ve studied for a decade or more!
Once researchers get this data, we encourage them to engage in open science and disseminate their findings. If research is shared, we benefit everybody, from researchers, to policy makers, to the general public.
Our organisation starts with the researcher and branches out like a tree, empowering scientists to make a difference, to generate their own impact and ultimately form a network of shared opportunities.
What advice would you give to current staff and students?
Our organisation starts with the researcher and branches out like a tree, empowering scientists to make a difference
Build meaningful working relationships. Some of them won’t flourish, but others could be life changing. If you put yourself out there, you’ll meet somebody who will inspire you and that could change everything. Achieving a goal depends on the support and collaboration of others – you never reach it alone.
Still image of a calcium wave (light blue) that has travelled from a wounded leaf along the veins of Arabidopsis thaliana to reach distant leaves.
Image credit: Dr Annalisa Bellandi and Professor Christine Faulkner
John Innes Centre researchers have shown that calcium waves are a secondary response to a wave of amino acids released from a wound. These findings challenge established thinking on long distance plant signalling molecules and the mechanisms by which information travels through plants from a site of stress.
John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK t: (+44) 1603 450000 comms@jic.ac.uk www.jic.ac.uk
If you would like to partner with us in the translation of our science, visit https://jic.link/getinvolved
