Variation in Zymoseptoria tritici virulence genes in field isolates

The fungus Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), oneof the most economically devastating diseases of wheat (Triticum aestivum)particularly in the humid countries of Northern-Western Europe, including Ireland. Themanagement of STB is a problem due to the ability of the pathogen to adapt toenvironmental changes, to overcome resistant varieties and fungicide insensitivity .Little is known about the molecular and cellular strategies used by the pathogen tocause disease. This study aimed to identify candidate virulence genes and search fordifferences in gene expression and polymorphic variants between two Irish isolates(IPO553 and IPO560), and the Dutch isolate IPO323, that may impact on theprogression of STB. We sequenced the transcriptome of the Z. tritici isolates IPO323,IPO553 and IPO560 obtained from infected wheat seedlings at 7 dpi. The RNAsequencing allowed the identification of 9556 genes expressed in all the fungal isolates.This includes 820 genes encode proteins predicted to be secreted during wheatpathogenesis, while 363 of them are Small Secreted Peptides (SSPs), some of whichare highly expressed at 7 days post infection (dpi), suggesting that these genes mayplay a role in wheat pathogenesis. Twelve genes encoding SSPs were significantlydifferentially expressed between Z. tritici isolates, which may be involved inintraspecific variation in STB. This includes several genes encoding SSPs, interestingly,with no functional annotation. We also performed a genomic approach to search forSingle Nucleotide Polymorphisms (SNPs) in the Irish isolates IPO553 and IPO560,compared to the reference genome isolate IPO323. Focusing on SSPs exhibitingsignificant differences in gene expression, eleven of these exhibit Single NucleotidePolymorphisms (SNPs) in the Irish isolates IPO553 and IPO560, in comparison to thereference genome isolate IPO323. We also evaluated variations in disease severity andprogression in the Z. tritici isolates IPO323, IPO553, IPO560. The Irish isolate IPO553was found to be the most virulent, exhibiting a higher percentage of pycnidia coverageat 21 dpi and causing early disease symptoms compared to the isolates IPO323 andIPO560. Six candidate virulence genes were cloned and their expression profile wasanalysed during the progression of disease. All six genes were expressed in all Z. triticiisolates at 7 dpi, but most of them were highly expressed in the Irish isolate IPO553compared to the other isolates.