Exploitation of the knowledge on Oomycete effectors to drive the discovery of durable disease resistance in cultivated plants – EFFECTOORES

Plant pathogenic Oomycetes cause important losses in agriculture. Tomato late blight caused by Phytophthora infestans, sunflower downy mildew caused by Plasmopara halstedii and grapevine downy mildew caused by Plasmopara viticola are three economically important diseases caused by Oomycetes. Disease control is achieved with the systematic use of fungicides, which increases production costs and is a concern regarding the environment and human health. An alternative to the use of chemicals is using natural resistance. One of the main issues concerning the use of natural resistance is its durability. Indeed, attempts to use natural resistance in tomato were soon abandoned because the resistance was overcome by P. infestans; the current use of resistance genes against P. halstedii in sunflower is threatened by the emergence of new resistance-breaking isolates; resistance-breaking isolates have been described for P. viticola despite the limited use of natural resistance in grapevine. Finding broad-spectrum a priori durable resistance against pathogens would open the doors to efficient, environmentally friendly and cost-effective disease control, guarantying the quantity and quality of the production and making an important contribution to the competitiveness of European agriculture.
Plant disease resistance proteins recognise pathogen-encoded factors, so called avirulence genes, and trigger defence responses leading to pathogen arrest. Most Oomycete avirulence proteins known up to date do belong to the RXLR family of effector proteins, small secreted proteins containing an N-terminal RXLR-dEER motif. Thus, data mining of genomic resources can lead to the identification of candidate Oomycete avirulence genes. Indeed, the repertoire of RXLR effectors from P. infestans has been characterised in silico through mining of its complete genome sequence, and identification of RXLR effectors from P. halstedii and P. viticola are in progress, thanks to the availability of cDNA sequence as well as partial genome sequencing. RXLR effectors form a large fast-evolving family. It is not then surprising that most individual resistance genes deployed against Oomycetes have been overcome by the pathogens. In this context, it has been proposed to use the most conserved components of the repertoire of Oomycete effector genes as a way to accelerate the identification, the functional characterization and the cloning of potentially broad-spectrum resistances. This approach has already been applied to the potato/P. infestans interaction, and led to the rapid characterization of new plant resistance genes.
The proposed research aims to use the knowledge in Oomycete effector genes to identify a priori durable resistance genes against plant pathogenic Oomycetes in three cultivated plants of economic importance in France: tomato, sunflower and grapevine. The proposal is divided in 5 different objectives:
1. Identification of conserved effectors through high-throughput sequencing of pathogen isolates;
2. Detailed analysis of effector variability in pathogen populations;
3. Identification of essential effectors through analysis of effector gene expression;
4. Identification of putatively durable resistance genes through transient expression of conserved effector genes in resistance sources;
5. Identification of pathogen avirulence genes through transient expression of effector genes in plants carrying known resistance genes.
The proposed research will produce knowledge about effector variability from three Oomycetes and provide data for comparative genomics between pathogens. From the applied point of view this project will result in the identification of resistance genes with the potential of providing durable resistance, as well as the detection of eventual redundancies in resistance sources (e.g., resistance sources carrying the same resistance genes). The proposed research will thus allow a better utilisation of genetic resources for plant disease resistance.