Scientific research is always working at the frontiers of knowledge, but plant genomics technologies have had a dramatic impact on plant science even by our standards. The wide availability of sequencing technologies has been a rare step-change that has unlocked knowledge in a way nobody in the field could have imagined twenty years ago. Knowledge which could make a considerable contribution to food security in the face of changing climates.
Understanding plant immunity
My group at The Sainsbury Laboratory focuses on understanding the evolution of immunity in the grasses, and particularly host-range dynamics. We are especially interested in understanding the genetic factors which determine the pathogen’s ability to infect one host but not another, when those two hosts are very closely related to each other. A large proportion of our work is focused on wheat. As well as work on host-ranges, we are building an understanding of immunity in wheat and how its subgenomes interact. We also have a range of biotechnology projects with industrial partners for exploiting novel sources of resistance for crop improvement.
Plant immunity is based on membrane receptors and intracellular immune-receptors. We have been studying the evolution of recognition and response mechanisms in grasses, with a particular focus on the role of the intracellular immune-receptors (nucleotide binding leucine-rich repeat proteins -NLRs). Grasses (monocots) have been under-investigated, as compared to eudicot species, so, as we have been developing an understanding of NLR activation and signaling, and have been looking out for novel components of the immune system in grasses.
The grass has never been greener for plant genomics research
There are a lot of great people doing excellent work in this field and it’s a particularly exciting time in the grasses. Previously the grasses were inaccessible, mainly due to the size of their genomes. The maize genome is about three gigabases, barley is five gigabases and wheat is seventeen gigabases. So these genomes were previously impossible for individual groups to access and required large consortiums. Now, the price of sequencing has reduced substantially and discoveries that would have taken 20 years can take four years or fewer. This is one of the best moments in time to be mining natural variation in barley and wheat.
What makes plant genomics research so exciting, and what really accelerates projects, is the ability to apply a number of different tools, technologies and strategies to understand the genome we are working with. It’s all about selecting the right tool or strategy from the toolkit to identify and understand genetic variation. Map-based cloning and mutagenesis-based approaches remain fundamental to my group’s research, and crucial advances come with sequencing mutants and immediately identify the causal gene underpinning a phenotype.
We can also employ gene disruption technologies such as TALENs and Cas9. It’s really about using all the tools that are available to solve the problem. When it comes to translating the resistance gene into the target crop (often that target is wheat), we’ll do both small-scale experiments and also, with industrial partners, large scale pipeline development that leverages high-throughput transformation pipelines using the target crop.
What I’m particularly excited about is the way Nanopore and PacBio sequencing have transformed our ability to resolve complex regions of the genome which have previously been an insurmountable hurdle. The genes encoding immune-receptors are often extremely complex. We might, for example, have four copies of the same gene which are all almost identical to each other and the differences would collapse with traditional technologies but an approach that applies Nanopore and Cas9 can enable precise sequencing of particular regions and therefore resolve these regions.
Engineering resilience has never been more imperative
Ultimately, the impact that I want our group to have is in reducing global dependence on pesticides and building resilience into food systems to end hunger and poverty. The urgency of developing resilient crops and food systems is so crucial given climate change. As climates change, pathogens will evolve and move into new zones. The fungal disease Wheat Blast demonstrates this pattern and seriousness of the situation: it was a major problem in South America, it has now moved to Bangladesh. If it moves to India, and particularly if it moves to the wheat growing region in the north, the entire region which depends on wheat as a major food source, will likely face a crisis in food supply.
We want to engineer plant immunity and so enable food security in the face of these kinds of evolving pathogens through putting resilience into the seed. We need to be able to do this even as pathogens evolve rapidly in changing climates. The availability of sequencing technologies has enabled us to reduce the time-limiting step of phenotyping in the field, radically transforming our ability to access and harness natural variation and will continue to do so.
I would love to see greater training and collaboration across genomics and bioinformatics to be able to manage and understand the data we can now access in order to develop the resilience we are going to need. In order to respond rapidly to changing pathogens, it would be fantastic to see a developing network of specialists in disease resistance across the globe who can bring their expertise in resistance to bear on emerging problems and develop solutions.
Matthew Moscou is Group Leader at The Sainsbury Laboratory, Norwich, UK.