Omics-enabled detection and studies of phytophthora capsici disease in the field

Lead Research Organisation: University of Dundee


Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.




10 25 50
Description iCASE PhD studentship scheme
Amount £95,042 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2015 
End 09/2019
Description James Hutton Institute collaboration on project 
Organisation James Hutton Institute
Department Cell and Molecular Sciences
Country United Kingdom 
Sector Public 
PI Contribution We have held regular meetings to discuss projects on our understanding of Phytophthora gene expression during infection of plants. we have generated a combined P. infestans and P. capsici Y1H library for our collaborators and screened motifs (present in both organisms) for interactors (transcription factors). in addition, we have tried to over-express P. infestans TFs in P. capsici to get to grips with possible roles in infection.
Collaborator Contribution Complementary efforts toward understanding these processes allowed us to test the possible roles of regulators in two distinct Phytophthora species. these efforts include expression profiling of P. infestans and P. capsici candidate transcriptional regulators and comparative analyses.
Impact Comparative gene expression analyses and datasets for candidate TFs. Candidate DNA motifs present in either P. capsici, P. infestans or both
Start Year 2013
Description iCASE studentship 
Organisation Enza Zaden
Country United Kingdom 
Sector Private 
PI Contribution Phytophthora capsici is a devastating pathogen capable of infecting important crops worldwide. Disease in the field can lead to eradication of crops and large financial losses if left untreated. Current diagnosis of the pathogen from the field is time consuming, difficult and requires highly trained specialists to handle and process samples. A more efficient diagnosis method is needed to ensure farmers can effectively maintain and manage their crops. Working with recently isolated P. capsici strains from the field is beneficial for both phytopathologists and plant breeders to identify the mechanisms used by the pathogen to cause infection and to develop resistant, commercial crops. To bridge the gap between laboratory and field knowledge, successful diagnosis and isolation of the pathogen is necessary. A genome of a single isolate of P. capsici has been sequenced and is publicly available. I have used this genome - as well as sequencing three other field isolates using three different sequencing technology - to use an omics approach to address the diagnostic issues that are currently faced. Here, I have employed two bioinformatic pipelines to aid the diagnosis effort to diagnose P. capsici from the field. The first (OEDs), designs diagnostic primers that are species-specific; and the second (PDP), designs primers that can discriminate within the species, resulting in isolate-specific primers. We conclude that both pipelines can design discriminatory diagnostic primers, but more sequence data and validation is required. These pipelines show great promise for diagnosing eukaryote plant pathogens found in the field.
Collaborator Contribution Enza Zaden were our formal collaborators and partners in this project. As part of the iCASE agreement, they hosted the PhD student, Rory McLeod, in their research department where he looked at virulence of P. capsici on elite pepper breeding lines. In addition, they have made the following contributions: Supervision and management of student, including regular site visits make available greenhouse facilities and breeding materials for experimentation Sequencing (MiSeq) of 4 P. capsici isolates (in-house) Provide access to breeding locations in Indonesia (through Ewindo)
Impact Grant proposal (IPA). Failed.
Start Year 2015
Title Improved Pipeline for the design of species and isolate specific primers 
Description Modification of existing pipelines to handle sequence data from eukaryote microbes. OEDS: This pipeline takes (publically) available genome sequences for a range of pathogens (within the Phytophthora genus) and identifies regions of genomes that are unique to a given pathogen. By using sequences from multiple isolates within a species, the pipeline can automatically design species-specific primers for validation and deployment in the lab and field respectively. PDP: Primer Diagnostic Pipeline (PDP) is a modular pipeline derived from the Find Differential Primers pipeline. The published pipeline has seven steps - validate input config file, concatenate sequences, identify features, predict primer locations, cross amplification, BLAST screen and classify. PDP has the ability to produce diagnostic primer candidate-specific at species, sub-species and isolate level (depending on the dataset). The sub-species-specific primers can group particular isolates together whilst distinguishing them from other isolates. 
Type Of Technology Software 
Year Produced 2019 
Impact We have deployed and conducted some limited tests on the rapid design and evaluation of primers that are species-specific and/or can discriminate between isolates of a given pathogen. 
Description Research talk & Visit to Enza Zaden 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Research talk and exploration of future collaboration with EZ staff. Discussion has led to one successful iCASE application (see portfolio) and one BBSRC-IPA grant application (not funded).
Year(s) Of Engagement Activity 2014
Description Scientific Talk at Enza Zaden 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Presentation of work towards understanding P. capsici biology to a breeder audience (Enza Zaden Company) in the Netherlands
Year(s) Of Engagement Activity 2018