A dispensable paralog of succinate dehydrogenase subunit C mediates standing resistance towards a subclass of SDHI fungicides in Zymoseptoria tritici

Succinate dehydrogenase inhibitor (SDHI) fungicides are widely used for the control of a broad range of fungal diseases. This has been the most rapidly expanding fungicide group in terms of new molecules discovered and introduced for agricultural use over the past fifteen years. A particular pattern of differential sensitivity (resistance) to a subclass of chemically-related SDHIs (SHA-SDHIs) was observed in naive Zymoseptoria tritici populations. Class specific SHA-SDHI resistance was confirmed at the enzyme level but did not correlate with the genotypes of the succinate dehydrogenase (SDH) encoding genes. Mapping and characterization of the genetic factor responsible for standing SHA-SDHI resistance in natural field isolates identified a gene (alt-SDHC) encoding a paralog of the C subunit of succinate dehydrogenase. This paralog was not present within our sensitive reference isolates and found at variable frequencies within Z. tritici populations. Using reverse genetics, we showed that alt-SDHC associates with the three other SDH subunits leading to a fully functional enzyme and that a unique Qp-site residue within the alt-SDHC protein confers SHA-SDHI resistance. Enzymatic assays, computational modelling and docking simulations for the two types of SQR enzymes (alt-SDHC, SDHC) enabled us to describe protein-inhibitor interactions at an atomistic level and to propose rational explanations for differential potency and resistance across SHA-SDHIs. European Z. tritici populations displayed a presence (20-30%) / absence polymorphism of alt-SDHC, as well as differences in alt-SDHC expression levels and splicing efficiency. These polymorphisms have a strong impact on SHA-SDHI resistance phenotypes. Characterization of the alt-SDHC promoter in European Z. tritici populations suggest that transposon insertions are associated with the strongest resistance phenotypes. These results establish that a dispensable paralogous gene determines SHA-SDHIs fungicide resistance in natural populations of Z. tritici. This study paves the way to an increased awareness of the role of fungicidal target paralogs in resistance to fungicides and demonstrates the paramount importance of population genomics in fungicide discovery.