DOI: 10.5061/dryad.vp8n9
title: Data from: Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew

description: 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.
description: Genetic data (gene
 haplotypes and microsatellite genotypes) and geographic sampling locations
 for each isolateGenetic 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.txtQuantitative traits of pathogenicity of Plasmopara viticolaQuantitative 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.txtDNA sequences (cytb gene)QoI.fastaDNA sequences (CesA3 gene, short fragment)CAA_short.fastaDNA sequences (CesA3 gene; long fragment)Note that North-American isolates have IDs beginning with MSUCesA3_long.fasta