Tasks carried out during the course of EvolMAX and the main results are as follows:
To identify effector genes, we have sequenced 78 P. oryzae isolates from one recombining population of the rice-infecting lineage using short-reads. Using full-genome data, we confirmed previous lines of evidence that the studied population is mainly sexual whereas the rice-infecting lineage is mostly clonal throughout its distribution range. Moderate to high levels of recombination found for this population enabled the identification of loci involved in virulence using a genome-wide association mapping approach (GWAS). In addition, we performed gene annotation, and identified secreted proteins.
We performed pathogenicity tests to assess isolate virulence profiles. We used 64 isolates of the studied recombining population and inoculated their spores onto 16 rice varieties and isogenic lines which differed from each other by different major resistance genes. To identify loci involved in virulence, we tested for associations between genotypes and virulence profiles of the 64 P. oryzae isolates for each rice variety or line tested. Out of 16 rice varieties or isogenic lines, six had balanced scores. For the rice variety Toride1, the pathogen’s gene that triggers a response that prevents infection was already known (AVR-Pizt) and therefore, the analysis for this variety represented a control GWAS. The target gene was correctly found within the genomic region associated with virulence, validating the power of this approach. For three other varieties and isogenic lines (LTH, Maratelli, IRBL19-A), a shared genomic region was associated with virulence. In the genomic region of interest, homologous relationships for core genes were identified. To escape recognition, adapted pathogens generally loose or modify their effectors that match to the plant resistant genes present in the host population. Consistent with this expectation, we compared patterns of absence/presence but also haplotypes of these orthologous genes to virulence profiles to pinpoint precisely the genes involved. This approach allowed us to identify two candidate genes that were also predicted as effectors. By using a P. oryzae population with substantial recombination, we were able to conduct in a timely manner what is, to our knowledge, the first proper genome-wide study of virulence phenotypes in P. oryzae. Functional validation and further analysis of the candidate genes will be the next step in collaboration with S. Cesari and T. Kroj at the Plant Health Institute of Montpellier.
For comparative genomics of effector repertoires among lineages associated with different cereal hosts, we compiled whole-genome raw data for 642 P. oryzae isolates from 28 plant genus. Half (321) of the 642 isolates were sequenced in our lab at the Plant Health Institute of Montpellier and the remainder is from public databases. Raw genomic data included short-read and long-read sequencing data for 595 and 47 unique isolates, respectively. Genome assemblies of short-read sequencing data were performed for the 595 isolates so far.
Regarding the dissemination of the action, three abstracts at conferences and a seminar at the Plant Health Institute of Montpellier have been presented. Two high impact peer-reviewed articles are expected. Photographs of our experiments were shared with National Research Institute for Agriculture, Food and Environment (INRAE) to illustrate research conducted in the Institute. A photograph showing the rice sprouts used in our pathogenicity tests was awarded a prize. Also, we made a video to show to the general public our daily scientific work and how we tackle major agricultural and environmental challenges. Additional outreach activities included exhibitions at the French Science Festival, discussions about the project with high-school students at two events and with the lay public at the European Researcher’s nights in 2020 and 2021.
