PTDC/ASP-PLA/29189/2017, LISBOA-01-0145-FEDER-029189
The epidemic resurgence of several fungal plant diseases has been occurring repeatedly over the last decade posing a major threat to agro-ecosystems and global food security. The devastating impact of these diseases gives a deep sense of urgency to breeders, farmers and end users to improve pathogen surveillance and control measures. These concerns have catalyzed a change in the game towards focusing on pathogen research, in complement to plant resistance, and using integrative genomics to probe virulence mechanisms. A better understanding of the processes driving rapid pathogen adaptive evolution, leading to improved surveillance systems and diagnostic tools, is instrumental for designing more efficient and durable disease management strategies. Focused on the devastating coffee fungal pathogen Hemileia vastatrix, responsible for the present major threat to Arabica coffee production all over the world, this project intends to apply a pathogenomic approach to dissect the molecular basis of virulence divergence and the mechanisms underlying evolution of pathotypes, providing ground to understand how host resistance genes are overcome, and to develop molecular tools for high-throughput discrimination of pathotypes. An important first step towards the achievement of this goal will be to generate a high-quality reference genome and annotation for this pathogen. Making use of population genomic resources and data generated in previous projects developed by the PI or other authors, comparative genomic, genome-wide association and transcriptomic analyses will be combined to identify SNPs, genomic changes and candidate genes, namely positively selected and candidate effector genes, that can be linked to virulence profiles of coffee pathogens. This focused strategy aims at uncover genetic determinants underpinning virulence that at the same time can be used as markers to track pathotypes at international level through diagnostic assays. At the end of this project, it is expected that diagnostic assays are made available to accurately and routinely monitor the standing H. vastatrix pathotypes and their movement within an international coffee rust survey program, promoting the establishment of a web platform for coffee disease surveillance.
The genetic information and tools generated by this project will contribute to guide the much-needed design of sustainable practices to control pathogen emergence and spread and prolong the life-span of resistant commercial cultivars, but also to expand the global knowledge on the molecular features underlying virulence mechanisms and evolution for one of the major important groups of plant pathogens, listed in the “Top 10”.