Adaptation produces hard or soft selective sweeps depending on the supply of adaptive genetic polymorphism. The evolution of pesticide resistance in parasites is a striking example of rapid adaptation that can shed light on selection processes. Plasmopara viticola, which causes grapevine downy mildew, forms large populations, in which resistance has rapidly evolved due to excessive fungicide use. We investigated the pathways by which fungicide resistance has evolved in this plant pathogen, to determine whether hard or soft selective sweeps were involved. An analysis of nucleotide polymorphism in 108 field isolates from the Bordeaux region revealed recurrent mutations of cytb and CesA3 conferring resistance to quinone outside inhibiting (QoI) and carboxylic acid amide (CAA) fungicides, respectively. Higher levels of genetic differentiation were observed for nucleotide positions involved in resistance than for neutral microsatellites, consistent with local adaptation of the pathogen to fungicide treatments. No hitchhiking was found between selected sites and neighbouring polymorphisms in cytb and CesA3, confirming multiple origins of resistance alleles. We assessed resistance costs, by evaluating the fitness of the 108 isolates through measurements of multiple quantitative pathogenicity traits under controlled conditions. No significant differences were found between sensitive and resistant isolates, suggesting that fitness costs may be absent or negligible. Our results indicate that the rapid evolution of fungicide resistance in P. viticola has involved a soft sweep.
Genetic data (gene haplotypes and microsatellite genotypes) and geographic sampling locations for each isolate
Genetic data (gene haplotypes and microsatellite genotypes) and geographic sampling locations for the 108 Plasmopara viticola isolates.
Column description:
Isolate_ID: unique isolate identifier
Lat: latitude in decimal degrees
Long: longitude in decimal degrees
Wine_region: region of origin
Trait_data: indicates whether quantitative traits were recorded for this isolate (see the « PV_trait_data.txt » file)
Fungicide_category: resistance to CAA and QoI fungicides
cytb_hap: cytochrome b haplotype. Names follow Chen et al. 2007
CesA3_short_hap1 & 2: CesA3 (short fragment) haplotypes
CesA3_long_hap1 & 2: CesA3 (long fragment) haplotypes
The last 23 columns give the allele sizes for the amplified microsatellite loci (1 column per locus, each allele is coded by a 3 digit number).
Missing data are encoded by "999".
PV_genetic_data.txt
Quantitative traits of pathogenicity of Plasmopara viticola
Quantitative traits of pathogenicity of Plasmopara viticola when inoculated on two different hosts (susceptible: Vitis vinifera cv. Cabernet sauvignon, CS and partially resistant: Cabernet carbon, CC).
108 isolates from the Bordeaux wine region were used and 8 (on CS) and 6 (on CC) leaf discs were inoculated for each isolate (i.e. repetition). The final sample analysed consisted of 1357 leaf discs corresponding to 214 plant-pathogen interactions.
Details for each isolate (geographic locations and genetic data) are described in the « PV_genetic_data » file of this package. Cells left blank indicate missing data.
The « Latency_Ndays » column indicates the latency period (number of days between inoculation and the first recorded sporangia). The « Sporangium_prod_per_mm2 » column indicates the number of sporangia per mm2 of leaf disc counted at seven days post inoculation (cumulative, over seven days of infection). The « Sporangium_size_µm » column indicates the weighted average of sporangium size. The « nbzoo_per_sporangium » column indicates the number of zoospores contained by each sporangium (on two leaf discs per isolate). The « T50 » column indicates the time at which the pathogen reached 50% of its maximal sporulation at 7 dpi. The « slope_at_T50 » column indicates the slope of the curve (sporulation vs. time) at T50. The « phenotype_CAA » column indicates whether the isolate is resistant or sensitive to CAA fungicides (see the « PV_genetic_data » file of this package). The « phenotype_QOI » column indicates whether the isolate is resistant or sensitive to QoI fungicides (see the « PV_genetic_data » file of this package). The « Fungicide category » column indicates whether the isolate is resistant and/or sensitive to CAA and QoI fungicides.
PV_trait_data.txt
DNA sequences (cytb gene)
QoI.fasta
DNA sequences (CesA3 gene, short fragment)
CAA_short.fasta
DNA sequences (CesA3 gene; long fragment)
Note that North-American isolates have IDs beginning with MSU
CesA3_long.fasta
