Towards a better understanding of the biology and genetics of Phytophthora rubi and phytophthora fragariae


CP 173 - Towards a better understanding of the biology and genetics of Phytophthora rubi and phytophthora fragariae

Start Date: 
Completion Date: 
Project Leader: 
Eleanor Gilroy, James Hutton Institute
CP 173
Industry representative: Ross Mitchell, Berry Gardens
AHDB Horticulture Cost: £70,500 
Summary: Demand for raspberries worldwide is at an all time high, worth an estimated £2 bn (UK £160 M). In the Northern Hemisphere, the Oomycete Phytophthora rubi thrives in relatively cold damp conditions causing root rot on raspberry. P.rubi is currently a poorly understood and understudied pathogen which is causing significant economic and environmental impact on softfruit production in the UK. Infested soil is forcing farmers (>70%) to adopt pot-based system with almost annual replenishment of the plants or growing alternative fruit crops.  Plant based resistance is the only way forward but this requires knowledge of the the effector arsenal by which pathogens will be recognised by the plant.  This project aims to study in detail the unusual lifecycle and disease progression of P. rubi and other closely related fruitcrop-infecting Phytopthoras. The student will develop P rubi transformation protocols generating transgenic strains that will allow the infection process to be closely monitoured in real time as well as improving upon infection methods on raspberry to allow better study of the roots during infection in resistant and susceptible cultivars. Using computational analysis sequences of interest from genomic DNA of P. rubi will be identified and assessed to allow us to better understand the current diversity and population structure of P. rubi in the UKs fields/nurseries. This PhD project aims to exploit expertise, experimental tools and systems at two crop institutes to better understand this pathogen. The student will spend significant time in two institutions and interacting with industry at annual events such as “Fruits for the Future”.
1. To transform P. rubi and P. fragariae with fluorescent marker to allow detailed study infection in roots in real time.
2. Determination lifecycle determinants and host specificity of P. rubi  and P. fragariae
3. To develop infection protocols that allow roots of host plants to be easily accessed and assayed
4. Use bioinformatics to identify potential effectors encoded and expressed by the P. rubi and P. fragariae genomes
Benefits to Industry
The academic partners will benefit through advancing the genomics of an important crop pathogen. Impact, generated through publications in respected journals and pilot data will further the chances of obtaining leveraged government funding to work on this research problem from BBSRC and innovate UK
For the non academic partners the benefits are multiple. First, the understanding of the pathogen infection cycle will aid resistance breeding for root rot, a primary objective of the JHI and EMS breeding programmes. This is important as in future it will lead to control of root rot through the deployment of natural resistance, in varieties with high fruit quality. Understanding more about the pathogenicity will aid the pyramiding of resistance genes and the deployment of other traits related to field resistance of root rot. Further understanding the life cycle of the pathogen and the key genes that it deploys in attack of host tissue may also lead to the identification of novel gene targets for control by chemicals. This is also important as part of integrated management. If identified the team will be in a position to exploit these findings through collaborative R&D.