Phytophthora infestans research
The James Hutton Institute and the University of Dundee has established itself as a leader in the study of late blight by integrating research, facilities, resources and skills into a coherent team. Our internationally recognised expertise focuses on a broad spectrum of research. This underpins both the long-term strategic objective of sustainable late blight control via host resistance and detailed applied research providing the industry with answers to current questions (for example, how do populations change and what are the major sources of primary inoculum?).
Our research on Phytophthora infestans can be grouped under six linked themes:
- P. infestans genomics
- pathogen biology
- potato-P. infestans interactions
- population biology and epidemiology
- host resistance: genetics, genomics and pre-breeding.
The James Hutton Institute has been active in genomics studies of P. infestans since 1998. We have prepared the highest quality bacterial artificial chromosome library and applied this resource in studies to understand the genome organisation of P. infestans. Involvement in a consortium of laboratories resulted in sequencing of over 90,000 expressed sequence tags (EST) and ensuing microarray analysis of 15,000 unigenes from P. infestans. The James Hutton Institute team has also led the application of real-time RT-PCR to quantify relative gene expression in P. infestans during infection of host plants. In recent years, the Institute team has been actively involved in a collaborative effort with the Broad Institute to sequence the genome of P. infestans.
Computational analyses of the large quantities of data generated through EST and genome sequencing and microarray analyses are being carried out at the James Hutton Institute. Recent bioinformatics studies have involved data mining for non-protein-coding RNAs, prediction of specific peptide motifs, rational protein engineering and comparative genomics.
The lifecycle of P. infestans is complex and involves several morphogenic transitions. We are specifically interested in identifying genes involved in transitions from lifecycle stages outside the plant (for example, germinating cysts, appressoria), to infection specific stages (for example, biotrophic structures called haustoria). We use data derived from transcriptional profiling and bioinformatics analyses to prioritise candidate genes for functional analysis by gene silencing and protein localisation through tagging with fluorescent proteins.
To overcome host innate immunity, P. infestans secretes numerous proteins to establish disease on potato (effectors). Some of these effectors are secreted into intercellular spaces while others are translocated inside host cells. P. infestans research at the Institute aims to determine which effector proteins are essential for pathogenicity, identify peptide motifs responsible for translocation inside host cells, understand the mechanisms of effector translocation, determine effector localisation and function inside host cells and identify triggers (avirulence proteins) of host resistance through genetics, genomics and high-throughput plant assays. Recent discoveries include the determination of effectors required for full pathogenicity, demonstration that a dual peptide motif RxLR-EER is required for translocation of some effectors inside host cells and identification of candidate avirulence proteins. More information on effector research at The James Hutton Institute can be found on the Effector Consortium pages.
Our main objectives are to examine the factors that drive change in P. infestans populations and the impact of change on the epidemiology and sustainability of blight management. The James Hutton Institute has one of the largest and most diverse collections of P. infestans isolates in Europe and new isolates from late blight surveys are continually being added to this collection. We have optimised a set of multiplex microsatellite markers that have proved to be important tools for monitoring population change. Collaboration with the Plant-Pathogen Interactions team means we can examine the frequency of different alleles of effector genes in populations and examine the mechanisms of how these alleles may influence recognition by R genes. Primary inoculum is the source of all new blight outbreaks and we are using the latest research tools to assess the significance of different inoculum sources such as oospores and tubers.
Staff in the CMS group work on multiple mapping populations segregating for resistance to major potato diseases including late blight. We utilise genetic mapping and genomic resources (for example, bacterial artificial chromosome (BAC) libraries) to positionally clone genes underlying the resistance phenotype. Cloning gene(s) responsible for durable resistance, such as field resistance, is one of our main priorities. In addition to traditional map-based gene cloning approaches we utilise allele/paralogue mining strategies, with the aim of identifying orthologues from known R genes that co-localise with the resistant QTL. The function of candidate genes is initially validated by transient, Agrobacterium tumefaciens based, overexpression in Nicotiana benthamiana and subsequent challenge with P. infestans and/or single pathogen effectors.
Furthermore, we utilise the Commonwealth Potato Collection (CPC) to identify new sources of resistance. Two different approaches are used: screening of CPC accessions with P. infestans isolates having a broad range of virulence, to identify accessions with durable resistance or with highly conserved or invariant P. infestans effectors to identify accessions that specifically recognise such effectors.
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