TRACING THE EVOLUTION OF A PATHOGEN-HOST ARMS-RACE TO PREDICT DURABILITY OF RESISTANCE IN RICE – PHRACE

To cause disease in rice, Xanthomonas oryzae bacteria use DNA-binding proteins called TAL effectors (TALEs) that induce plant susceptibility genes upon binding to their promoters. Broad-spectrum resistance to this devastating pathogen has been achieved by employing strategies to prevent the bacteria from exploiting susceptibility genes. However, the arms-race between plants and bacteria is a fast-evolving process, and resistance breakdown is a worrying prospect. To predict durability of resistance in rice, this proposal aims to trace the evolution of the arms race between rice genomes and Xanthomonas DNA-binding TALEs. First, a wide panel of rice-X. oryzae interactions will be used to generate a large set of phenotypic, genomic and transcriptomic data. The panel will include several compatible (disease) and incompatible (resistance) interactions encompassing the diversity of both the Oryza genus (wild and cultivated rice accessions) and the X. oryzae species. The “-omics” data will be integrated to generate functional classifications for all rice genes according to how they respond to X. oryzae and its TALEs. Then, by analyzing how the gene functional classifications change in susceptibility/resistance transitions, this project will address how rice genomes responded to the action of TALEs through evolution, including how resistance arises and how it breaks down. Second, a wide set of X. oryzae genomes will be used to investigate the bacterial side of the arms race. A combination of phylogenetic and in-silico evolution analyses will be used to determine evolutionary rates of TALEs, and to identify the processes through which they gain the ability to target rice susceptibility genes. The study of the rice genome vs TALE interaction offers a unique opportunity to study an arms-race at the whole genome level. This project will inform how plant genomes respond to bacterial attacks and vice-versa, which will help guide strategies for durable resistance in crops.