All in a life’s work

Professor Paul Nicholson recently received the British Society for Plant Pathology’s RKS Wood prize in recognition of his contribution as a researcher and mentor.  

The prize is named in honour of Professor RKS Wood, who was at the forefront of the discipline Physiological Plant Pathology. It celebrates excellence in plant disease biology and its application in the protection of plants against pathogens.  

Here Paul explains the threat of two challenging crop pathogens, and what his group at the John Innes Centre is doing to identify potential new mechanisms by which we can help plants defend themselves.  

“It was a great honour for me and my group at the John Innes Centre to receive the award and I very much enjoyed sharing our work with the BSPP at its Presidential meeting in Newcastle. 

I was nominated by one of my former PhD students Professor Fiona Doohan, now a leading researcher based at University College Dublin.  

Fiona and I both work on the fungal pathogen Fusarium graminearum which causes Fusarium head blight, (FHB), a disease affecting the head of cereals such as wheat, maize and barley. Fiona’s group are looking for clues within the genes induced in Fusarium-resistant lines of wheat in response to the fungus and the toxin it produces. Some of these biosynthetic gene clusters produce antifungal compounds in response to infection and so may be candidates for engineering or identifying new alleles for breeding in resistance. 

My group’s work complements this fundamental science: we work on Brachypodium distachyon, a diploid species of grass related to wheat but with a simpler genome. Wheat is a polyploid species, meaning it has multiple sub genomes as a result of hybridization. Where Brachypodium has two copies of each gene, wheat could have up to 6. 

Our approach is to simplify the situation, from polyploid wheat, where the multiplicity of genes makes research more difficult, and to use Brachypodium to simplify validation of genes of interest. This means, for example you can knock out (disable) one gene using gene editing or mutagenesis, and clearly identify the activity of that gene from the phenotype.  

It gives us a way of seeing the mechanism and identifying whether that gene or a cluster of genes in wheat has a role in disease resistance.  

What can we look forward to in the future from the Nicholson group on fusarium research?  

We are looking to reduce disease by identifying and eliminating susceptibility factors present in the host plant that aid the infection of the pathogen. By removing these negative effects, the disease resistance of the plant is strengthened. 

In the past decade, we have studied the role of phytohormones, such as auxin, ethylene, and brassinosteroids. In almost every case we see that if you take away the molecular pathways to those signalling molecules, you increase resistance to fusarium infection.  

We have found that those pathways are enhancing susceptibility, so one of our big efforts is to try to understand whether we can see and isolate genes that are involved in susceptibility. We identified susceptibility associated with a single chromosome arm of one of the 21 chromosomes in wheat. Over the years we have narrowed the search down to a smaller region of 22 genes – and we are now going through those 22 genes to find out which one might be responsible for susceptibility. 

Knocking that one gene out could give us a significant increase in resistance. That is exciting, and we know there are other loci in wheat – other regions in the genome that enhance susceptibility – and we are collaborating with a group in the US on this.  

Why should we be concerned about fusarium?  

Although Fusarium head blight (FHB) causes yield losses in major crops such as wheat, maize and barley, it is of particular concern because the fungus produces toxins that contaminate the grain and pose a health threat to humans and animal consumers. The threat is present in the UK due to changes in agricultural practice which have seen more maize grown as biofuels. It was discovered some time ago that a maize-wheat rotation was bad for farmers because there is a significant risk that the wheat could be contaminated by spores released from maize stubble left over from the previous year’s crop.  

It is a major disease particularly in in the US where a huge multi-million-dollar programme running for decades is still struggling for an answer. I do not think there is one answer; all we can do is identify ways of enhancing resistance.  

Wheat blast is another major disease of crops which the Nicholson group is working on.  

When wheat blast hits, it is devastating. The amount of inoculum can be so high that farmers can get almost total loss of the crop. It is believed this disease was brought into Brazil on a grass species from Africa and from there has spread, with outbreaks in Bangladesh, India and Zambia. It is not in the UK but there is a risk where you have hot, humid conditions you can get this disease – so climate change may lead to it becoming a potential threat in the UK.  

My group has been using a gene discovery platform called AgRenSeq developed by (former John Innes Centre researcher) Dr Brande Wulff. We use computational technology to search for disease resistance genes in a collection of wheat lines collected from across the globe by (John Innes Centre researcher) A. E Watkins in the 1930s. By using the gene discovery platform, researchers can relate sequence variation at a certain location in the genome to whether lines carrying that sequence are resistant or not. Using this system we have identified a new gene for resistance to blast that can complement the only source of resistance currently widely deployed against this disease. 

Wheat lines developed by CIMMYT (International Maize and Wheat Improvement Center) already carry a piece of DNA from a wild species which resists blast. We aim to give CIMMYT DNA markers to detect the presence of the new resistance that we have identified within their breeding stock. If they have lines carrying this resistance, then they will have two sources of resistance, and hopefully the fungus will not mutate to overcome both. 

The RKS Wood prize was recognition of more than 30 years of work. What lies in store for plant pathogen researchers starting out now? 

The publication of the wheat genome – and the pan genomes combined with computational power to scan sequences, means we can make rapid advances. 

That is all down to those in the wheat community who have come together and realized the need to develop these revolutionary tools. With those resources combined with precise phenotyping it should make progress much more rapid. We can hand that information over to fundamental scientists who want it to investigate mechanisms and pathways and most importantly to the breeders who can introduce the beneficial aspects to their crops and varieties without endangering yield or other important agronomic traits.” 

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