At Least Two Origins of Fungicide Resistance in Grapevine Downy Mildew Populations

Abstract

Quinone outside inhibiting (QoI) fungicides represent one of the most widely used groups of fungicides used to control agriculturally important fungal pathogens. They inhibit the cytochrome bc 1 complex of mitochondrial respiration. Soon after their introduction onto the market in 1996, QoI fungicide-resistant isolates were detected in field plant pathogen populations of a large range of species. However, there is still little understanding of the processes driving the development of QoI fungicide resistance in plant pathogens. In particular, it is unknown whether fungicide resistance occurs independently in isolated populations or if it appears once and then spreads globally by migration. Here, we provide the first case study of the evolutionary processes that lead to the emergence of QoI fungicide resistance in the plant pathogen Plasmopara viticola. Sequence analysis of the complete cytochrome b gene showed that all resistant isolates carried a mutation resulting in the replacement of glycine by alanine at codon 143 (G143A). Phylogenetic analysis of a large mitochondrial DNA fragment including the cytochrome b gene (2,281 bp) across a wide range of European P. viticola isolates allowed the detection of four major haplotypes belonging to two distinct clades, each of which contains a different QoI fungicide resistance allele. This is the first demonstration that a selected substitution conferring resistance to a fungicide has occurred several times in a plant-pathogen system. Finally, a high population structure was found when the frequency of QoI fungicide resistance haplotypes was assessed in 17 French vineyards, indicating that pathogen populations might be under strong directional selection for local adaptation to fungicide pressure.Preventing and delaying resistance adaptation to fungicides in pathogen populations is a major goal in sustainable plant pathogen management. The development of effective strategies to control pathogen populations requires precise understanding of the conditions under which fungicide resistance alleles appear, spread, and are maintained in natural populations. Among the factors that influence the evolution of resistance, the rate of mutation in fungicide resistance-associated genes plays an important role. It is still uncertain whether fungicide resistance-associated mutations commonly arise independently or whether pest adaptation occurs by convergent evolution through recurrent mutations at selected sites in the genes coding for the fungicide target. In other words, do alleles conferring fungicide resistance arise once before spreading across populations, or do they arise independently in each locality, and are they favored by large local population sizes of the pathogen population?Numerous experimental and phylogenetic studies in extensive geographical contexts have already examined the pattern of the evolution of genes coding for antimicrobial drugs or pesticide targets in animals, plants, and bacteria. For instance, the question of parallel genetic adaptation to drugs and p...

Population genetics of fungal diseases of plants

“…An example of contrasted mating systems in two closely related species is given by Plasmopara viticola and P. halstedii, oomycetes responsible respectively for the downy mildews of grapevine and sunflower. Molecular markers showed that the two species displayed similar levels of genetic diversity (Chen et al, 2007;Delmotte et al, 2006). The homothallic species P. halstedii showed considerable heterozygote deficit (F IS = 0.95), probably due to limited dispersal ability before mating and thus lack of available sexual partners in the field (Giresse et al, 2007), while the populations of P. viticola only slightly deviated from HardyWeinberg proportions (Chen et al, 2007;Delmotte et al, 2006).…”

“…Molecular markers showed that the two species displayed similar levels of genetic diversity (Chen et al, 2007;Delmotte et al, 2006). The homothallic species P. halstedii showed considerable heterozygote deficit (F IS = 0.95), probably due to limited dispersal ability before mating and thus lack of available sexual partners in the field (Giresse et al, 2007), while the populations of P. viticola only slightly deviated from HardyWeinberg proportions (Chen et al, 2007;Delmotte et al, 2006). Fungi exhibit a variety of other ways to recombine genetic information than sexuality, gathered under the terms of parasexuality or somatic recombination (Bos, 1996).…”

Exploring Mechanisms of Resistance to Respiratory Inhibitors in Field Strains of Botrytis cinerea , the Causal Agent of Gray Mold

“…However, the fungicides of this family have been widely used to control downy mildew due to P. viticola and powdery mildew due to E. necator on grapevine, through one to three treatments per year, since their introduction in 2001 in France. As a consequence, the G143A mutation is now widespread in most French populations of P. viticola, within two different cytb haplotypes (15), resulting in poor disease control when strobilurins are used alone. In contrast, resistance associated with the same cytb alteration took longer to be selected in E. necator and was first recorded in France in 2008 (19), highlighting the …”

Emergence and early evolution of fungicide resistance in North American populations of Zymoseptoria tritici

“…In some cases the strength of selection can lead to rapid fixation of resistance alleles in fungal populations after only a single year of fungicide use (reviewed in Grimmer et al, 2014). In this regard, fungicide resistance evolution is a phenomenon similar to antibiotic resistance evolution (Davies & Davies, 2010), but the literature describing the evolutionary processes that generate, spread and maintain novel resistance alleles in fungal plant pathogens is relatively limited (Chen et al, 2007;Brunner et al, 2008).…”