Zymoseptoria tritici is the causal agent of Septoria tritici blotch, a major pathogen of wheat globally and the most damaging pathogen of wheat in Europe. A gene-for-gene (GFG) interaction between Z. tritici and wheat cultivars carrying the Stb6 resistance gene has been postulated for many years, but the genes have not been identified. We identified AvrStb6 by combining quantitative trait locus mapping in a cross between two Swiss strains with a genome-wide association study using a natural population of c. 100 strains from France. We functionally validated AvrStb6 using ectopic transformations. AvrStb6 encodes a small, cysteine-rich, secreted protein that produces an avirulence phenotype on wheat cultivars carrying the Stb6 resistance gene. We found 16 nonsynonymous single nucleotide polymorphisms among the tested strains, indicating that AvrStb6 is evolving very rapidly. AvrStb6 is located in a highly polymorphic subtelomeric region and is surrounded by transposable elements, which may facilitate its rapid evolution to overcome Stb6 resistance. AvrStb6 is the first avirulence gene to be functionally validated in Z. tritici, contributing to our understanding of avirulence in apoplastic pathogens and the mechanisms underlying GFG interactions between Z. tritici and wheat.

Botrytis cinerea is a major crop pathogen infesting >220 hosts worldwide. A cryptic species has been identified in some French populations but the new species, B. pseudocinerea, has not been fully delimited and established. The aim of this study was to distinguish between the two species, using phylogenetic, biological, morphological, and ecological criteria. Multiple gene genealogies confirmed that the two species belonged to different, well-supported phylogenetic clades. None of the morphological criteria tested (spore size, germination rate, or mycelial growth) was able to discriminate between these two species. Sexual crosses between individuals from the same species and different species were carried out. Only crosses between individuals from the same species were successful. Moreover, population genetics analysis revealed a high level of diversity within each species and a lack of gene flow between them. Finally, a population survey over time showed that B. cinerea was the predominant species but that B. pseudocinerea was more abundant in spring, on floral debris. This observation could not be explained by temperature adaptation in tests carried out in vitro or by aggressiveness on tomato or bean leaves. This study clearly establishes that B. cinerea and B. pseudocinerea constitute a complex of two cryptic species living in sympatry on several hosts, including grapevine and blackberry. We propose several biological or molecular tools for unambiguous differentiation between the two species. B. pseudocinerea probably makes a negligible contribution to gray mold epidemics on grapevine. This new species has been deposited in the MycoBank international database.

This study aimed to determine whether powdery mildew caused by Blumeria graminis is an endemic pathogen of triticale (·Triticosecale: Triticum · Secale), emerging as a result of recent changes in its pathogenicity, or whether it is a new pathogen, possibly resulting from hybridization between ff. spp. tritici and secalis. A secondary aim was to consider breeding practices that may have favoured this emergence. Phylogenetic analyses based upon six genes revealed the close relatedness of the novel entity and the ff. spp. tritici and secalis, but the IGS marker finally grouped together the isolates collected on triticale and on wheat, supporting the scenario of a recent host-range expansion from wheat to triticale. Pathotype analyses concluded that virulence spectra of B. graminis infecting triticale were new in comparison to those observed for other reference formae speciales, and lack of fungicide resistance in triticale isolates strengthens the hypothesis of no or little genetic exchange between wheat and triticale populations of powdery mildew. This adaptation may follow the breakdown of plant resistance genes, which are probably not very diverse in current triticale cultivars since this criterion was not considered as a major one until recent years. Moreover, the complex selection and genetics of this hybrid cereal makes it difficult to predict the transmission of powdery mildew resistance genes.