For this analysis, they gathered nearly all of the RNA-seq data available for wheat from public repositories and incorporated new samples from others within the IWGSC. This dataset of 850 samples gave them a unique resource to start exploring gene expression in wheat at a global scale. These samples (and more which have been added since 2018) are available through the open-source platform wheat-expression.com. They also developed co-expression networks from these samples and investigated how the three subgenomes in wheat coordinate their expression, a study that was published back to back with the IWGSC RefSeqv1.0 paper in Science in 2018.

Philippa’s research focuses broadly on two themes: understanding gene regulation in polyploid wheat and the genetic control of senescence and nutrient remobilization. In the first area, her group just started a new project exploring how subgenome expression patterns differ between wheat cultivars. They aim to understand the mechanisms controlling these expression patterns, with a view to promoting beneficial patterns for crop improvement. In the second area, they are working to identify genes that influence senescence and nutrient remobilization in wheat, with the aim to improve the nutritional value of the grain without a detrimental effect on yield. They are using a combination of reverse genetics and genomics to identify and characterize novel genes, and to understand how these genes work together to coordinate this complex developmental process. Philippa presented this research in an IWGSC webinar last November.

What motivated you to become a plant scientist? How did you become involved in genomics?

When I was at school I was interested in biology, and genetics particularly. I had some great lecturers in Plant Sciences at the University of Cambridge who made plants very interesting, with their broad diversity, complex cellular processes, and relevance to food security, and there seemed to be plenty left to discover! Once I started my PhD at the John Innes Centre, I wanted to identify the downstream targets of a specific wheat transcription factor involved in senescence, but to do this I had to teach myself how to analyze genomic data and how to code. It was a steep learning curve, but it has been an exciting and interesting area to work in. Doing this analysis made me realize that genomic resources were lacking in wheat compared to other species, and I was keen to do something to improve the situation for wheat researchers and breeders.

How did you come to work on wheat? And why bread wheat?

At the start of my PhD I knew I wanted to work on a crop, because of their importance to agriculture, but I wasn’t sure which one. I was fortunate to do a rotation PhD program where I could work in three different labs in the first year to find out what interested me the most. All of these projects involved cereals in one way or another. I decided to work on bread wheat because it is the most widely grown crop in the UK and already at that time there were some hints that genomic resources for wheat were advancing, making certain scientific questions more accessible. Nowadays I also use durum wheat as a model, for example to generate mutants more quickly than is possible in bread wheat.

What would you say are the benefits of being part of an international consortium?

Working in an international consortium allows you to address scientific challenges which would be impossible to approach as one research group, or even in a national effort. The wide range of expertise, skills and (importantly for genomics) data that can be obtained through international collaborations allows us to ask and answer complicated biological questions and generate resources that will be useful for a wide range of users. For me personally I learnt a lot through working with the IWGSC, both scientifically but also about project management on such a large scale.

You participated to the development of several functional genomics resources for the wheat community, can you tell us about these resources?

When I won a BBSRC fellowship, I was fortunate to have the scientific freedom and opportunity to contribute to several functional genomic projects. For example, I contributed to the TILLING mutant sequencing project led by Ksenia Krasileva, Jorge Dubcovsky and Cristobal Uauy by investigating whether we could use this mutant resource to knock-out all the genes in an entire pathway (very nearly but not quite for the case of starch synthesis which was my interest at the time). In my fellowship research, I was working to identify novel genes regulating senescence and I realized a gene expression atlas would be very useful to help prioritise candidate genes. Talking with Ricardo Ramírez-González who was also in Cristobal Uauy’s lab we realized this was a problem we could solve – and www.wheat-expression.com was born. This website is a gene expression atlas for wheat, which now has >1,000 RNA-seq samples, all categorized according to their tissue, age, cultivar and stress condition. All the data can be freely downloaded, and the site has been used by >20,000 people around the world. To encourage the uptake of these and other resources we built a training website ( www.wheat-training.com ) which provides step by step guides and background information which could be useful to existing and new wheat researchers. Seeing these resources used so widely is very rewarding to me.

The IWGSC regularly releases updated versions of its high-quality reference sequence of bread wheat (RefSeq). What other resources are still needed to meet the needs of wheat scientists and breeders?

We are getting to a stage where we have many of the resources we need, but the challenge remains to integrate these all in an easy to use and accessible way. Many different databases are starting to tackle this challenge and it will be interesting to see how this data integration progresses over the next few years. Another challenge will be how to keep track of version changes of the assemblies and annotation versions – how can we make sure that results we publish today using the current assemblies are easy to translate into new assemblies in the coming years to maximize the value of this information?

According to you, what are the next challenges for the application of genomics in wheat breeding?

We now have many of the tools and resources, but we need to work together to find the best ways to apply them in breeding programs. To do this it will be important to train and work with molecular breeders who can take genomics into the real-world process of wheat breeding.

In your opinion, what will be the biggest advances in wheat research in the next 5-10 year?

In the next 5-10 years cloning and characterizing genes in wheat will be readily accessible to many research groups, which will accelerate our understanding of the genes regulating biological processes. I think that wheat is becoming an attractive system to work with, even for researchers who have not traditionally worked in this area, so more groups will be working with wheat. Whilst some may view these new researchers as competition, I think there will be opportunities to forge new collaborations, bring additional expertise into the wheat field and to accelerate progress in wheat improvement through our shared interest in food security. For this reason, I hope we will also see these discoveries being translated into breeding programs to benefit wheat production.

You established your own research group three years ago, what advice would you have for other scientists interested in doing the same?

This is a tricky question and I don’t think there is one recipe for success. For me being surrounded by excellent and supportive colleagues from whom I could learn and collaborate with to raise my science to the highest levels possible was essential. I would recommend taking advantage of opportunities that arise – I didn’t plan to get involved with the IWGSC during my fellowship at JIC but it has been one of the best things I did in my career. However, it is also important to focus on the research you want to do, and not to get distracted by too many different projects. I believe that luck is also involved in getting the chance to establish your own research group. Whilst you need to work hard and smart, your research niche needs to be in demand which may be outside your control.

What are your future plans?

Having started my lab three years ago we are now gaining momentum with several projects. I am very excited about the science we are doing and the discoveries we are starting to make. I look forward to sharing our results soon!

About Philippa 

Publication date: 05/24/2021