Unravelling the genetic architecture of host adaptation in a collection of isolates from the wheat fungal pathogen Zymoseptoria tritici, collected in France between 2009 and 2010

Zymoseptoria tritici is an ascomycete fungus, responsible for Septoria leaf blotch disease on bread wheat, durum wheat and triticale. In bread wheat, 22 Stb resistance genes and more than 89 resistance quantitative trait loci, or QTL, have been genetically mapped, including the two cloned genes Stb6 and Stb16q. However, on the pathogen side, only two avirulence genes have been identified. With a view to gaining further insight into the genetic determinism of pathogenicity in this fungal pathogen, we constituted a collection of 772 Z. tritici isolates collected on bread wheat from 14 different regions in France. Assessing genetic diversity with 12 microsatellite markers revealed a non-genetically differentiated Z. tritici population, which is ideal to perform genome wide association studies (GWAS). We therefore selected a subset of 103 isolates and performed whole-genome sequencing on Illumina HiSeq 2000 (i.e. paired-end 100bp sequences). Mapping these sequences on the genome of the reference strain IPO323, we obtained a matrix of 1,463,638 high-quality SNPs from which a final set of 718,810 SNPs was used for GWAS. We performed quantitative pathogenecity assays on wheat differential cultivars, harbouring Stb1 to Stb15 resistances. We then applied GWAS and identified polymorphisms linked to pathogenicity, pointing at 58 candidate genes, including AvrStb6 and AvrStb9 that have been functionally characterized. Based on in planta RNAseq of Z. tritici infection course, we extracted 19 high-confidence candidates, of which we validated the implication of two distinct genes in quantitative pathogenicity using functional genetics approaches. In conclusion, we demonstrated that the genetic architecture of pathogenicity is polygenic with a large quantitative component, and points towards host specialization.