Axis 2 - Understand the genetic and genomic determinism of Z. tritici adaptation and decipher molecular mechanisms of infection

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This second set of objectives is to understand the genetic and genomic determinism of Z. tritici adaptation to its hosts (species, variety) and its abiotic environment (climatic variables). We plan to characterize the allelic diversity of the genes identified within pathogen populations, validate their involvement in adaptation and study the molecular mechanisms involved in wheat infection by Z. tritici. These investigations include extensive research conducted with the support of BIOGER's bioinformatics platform. 

Key areas of investigation include:

2.1. Identification of the genetic and genomic determinism of Z. tritici adaptation, that we pursued on available material (fungal populations issued from field samples or from directed crosses) following linkage mapping (QTL) or association genetic (GWAS) approaches, on traits related to adaptation to durum wheat (PhD thesis of Ulysse Guilloteau) and to temperature (BASTAFUN project). These analyses are completed by genotype-environment associations (GEA) using climatic and geographic variables. For the genes involved in host adaptation, we would like to improve the identification of R-Avr pairs by pursuing our studies on genetics of resistance and implementing a new coGWAS approach (ERA-NET WHEATSECURITY, FSOV ATTILA and PEPR COBREEDING projects). Then, we would study the phenotypic consequences of allelic variability at the identified R-Avr pairs (on-going PhD thesis in collaboration with INRAE GDEC). Finally, we would use all this knowledge to monitor the evolutionary dynamics of genes involved in adaptation within populations of Z. tritici from contrasting environments, with potential applications in epidemiosurveillance.

2.2. Generation of high quality dual-transcriptomics data to profile genes expression simultaneously in the pathogen and its host. We would like use wild-type and mutant strains at pathogenicity genes to unravel the regulatory networks involving these pathogenicity genes and to detect differentially expressed genes in wheat. Acquiring high-quality transcriptomic data, especially at the early stages of infection, will enhance our understanding of pathogenicity in Z. tritici.

2.3. Validation of fungal genes potentially involved in adaptation and better understanding the molecular mechanisms involved in wheat infection by Z. tritici. We implement additional molecular tools in areas currently at the forefront of scientific research for the international community focused on Z. tritici. We are setting up the CRISPR-Cas9 tool on protoplasts to ease the functional analysis of genes/alleles involved in Z. tritici pathogenicity and adaptation. Cytology approaches in wheat protoplasts will be implemented to validate R-Avr interactions and to extend the functional analysis of genes of interest in planta.