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I alternate therefore I generalize: how the intrinsic resistance risk of fungicides counterbalances their durability

Citation

Ballu, Agathe et al. (2021), I alternate therefore I generalize: how the intrinsic resistance risk of fungicides counterbalances their durability, Dryad, Dataset, https://doi.org/10.5061/dryad.63xsj3v2r

Abstract

The evolution of resistance to pesticides is a major burden in agriculture. Resistance management involves maximizing selection pressure heterogeneity, particularly by combining active ingredients with different modes of action. We tested the hypothesis that alternation may delay the build-up of resistance not only by spreading selection pressure over longer periods, but also by decreasing the rate of evolution of resistance to alternated fungicides, by applying an experimental evolution approach to the economically important crop pathogen Zymoseptoria tritici. Our results show that alternation is either neutral or slows the evolution of resistance, relative to continuous fungicide use, but results in higher levels of generalism in evolved lines. We demonstrate that the relative risk of resistance intrinsic to fungicide alternation probably underlies a trade-off between the number of fungicides and the frequency of alternation. This trade-off is also dynamic over the course of resistance evolution. These findings open up new possibilities for tailoring resistance management effectively while optimizing interplay between alternation components.

Methods

This date were collected throughout an experimental evolution carried out with the pathogenic fungus Zymoseptoria tritici submitted to various selection regimes including three agricultural fungicides.

The dataset includes:

- Optical density measurement at 405 nm achieved for each line at the end of the twelve cycles of the experiment.

- Scores established in droplet tests aiming at testing the sensitivty of strains isolated in straight lines throughout the experiment and for all lines at the end of the experiments. This data included resistance description to fungicides used in the experiment but also to unused fungicides.

Usage Notes

No missing values in the dataset.

Sheet “Alternation_OD_data”:

Referred as "Alternation_OD_data.txt" in the script

Raw data of DO405 measurement, samples description and statistical estimates

  • Column “DO405” : raw data of optical density at 405 nm
  • Column “Plate_repetition”: experimental repeat of DO405 measurement (1 or 2)
  • Column “Lines”: names of selection regimes
  • Column “Erlen_repetition”: biological repeat of each selection regime (I, II, III or IV)
  • Colum “Acyclical_name”: unique identifier for each line
  • Column “DO405norm”: optical density at 405 nm normalized with the one of the control
  • Column “Concentration”: spore concentration estimated from the DO405norm
  • Column “Malthusian_growth”: Malthusian growth calculated from spore concentration
  • Column “Fungicide”: fungicide used to treat a given cycle (Benzo=benzovindiflupyr; Carb=carbendazim; ProDo=prothioconazole-desthio)
  • Column “Cycle”: cycle of the experimental evolution (1 to 12)
  • Column “Conc_rel_ctrl”: Spore concentration divided by the spore concentration of the control lines
  • Column “ConcYPD_limit_rel_ctrl”: limit of detection of spore concentration, expressed as a fraction of the sporeconcentration of the control lines
  • Column “Malthusian_growth_norm”: Malthusian growth of the line divided by the Malthusian growth of the control line
  • Column “Malth_grw_YPD_limit_rel_ctrl”: limit of detection of the Malthusian growth, expressed as a fraction of the Malthusian growth of the control line
  • Column “sum_carb”: number of cycles treated with carbendazim
  • Column “sum_benzo”: number of cycles treated with benzovindiflupyr
  • Column “sum_prodo”: number of cycles treated with prothioconazole-desthio

Sheet “Alternation_mean_data_cycles”:

Referred as "Alternation_data_mean_normalized_malt_growth_cycles.txt" in the script

Mean Malthusian growth summarized for each line of each selection regime over the course of the experiment (12 cycles)

  • Column “Acyclical_name”: unique identifier for each line
  • Column “Lines”: names of selection regimes
  • Column “Mean_malth_growth”: mean of normalized Malthusian growth calculated for each repeated line of each selection regimes and the twelve cycles of the experimental evolution
  • Column “Rhythm”: rhythm of alternation (0, 1, 2 or 3)
  • Column “AIs_number”: number of AIs used in a given selection regime (1, 2 or 3)

Sheet “Alternation_mean_data_sum_carb”:

Referred as "Alternation_data_mean_normalized_malt_growth_sumcarb.txt" in the script

Mean Malthusian growth summarized for each line of each selection regime over the maximum number of carbendazim exposition cycles

  • Column “Acyclical_name”: unique identifier for each line
  • Column “Lines”: names of selection regimes
  • Column “Mean_malth_growth_6_sumcarb”: mean of normalized Malthusian growth calculated for each repeated line of each selection regimes that received carbendazim applications, except BCP, over the 6 applications of carbendazim
  • Column “Mean_malth_growth_4_sumcarb”: mean of normalized Malthusian growth calculated for each repeated line of each selection regimes that received carbendazim applications, over 4 applications of carbendazim
  • Column “Rhythm”: rhythm of alternation (0, 1, 2 or 3)
  • Column “AIs_number”: number of AIs used in a given selection regime (1, 2 or 3)

Sheet “Alternation_mean_data_sum_prodo”:

Referred as "Alternation_data_mean_normalized_malt_growth_sumprodo.txt" in the script

Mean Malthusian growth summarized for each line of each selection regime over the maximum number of prothioconazole-desthio exposition cycles

  • Column “Acyclical_name”: unique identifier for each line
  • Column “Lines”: names of selection regimes
  • Column “Mean_malth_growth_6_sumprodo”: mean of normalized Malthusian growth calculated for each repeated line of each selection regimes that received prothioconazole-desthio applications, except BCP, over the 6 applications of prothioconazole-desthio
  • Column “Mean_malth_growth_4_sumprodo”: mean of normalized Malthusian growth calculated for each repeated line of each selection regimes that received prothioconazole-desthio applications, over 4 applications of prothioconazole-desthio
  • Column “Rhythm”: rhythm of alternation (0, 1, 2 or 3)
  • Column “AIs_number”: number of AIs used in a given selection regime (1, 2 or 3)

Sheet “Alternation_mean_data_sum_benzo”:

Referred as "Alternation_data_mean_normalized_malt_growth_sumbenzo.txt" in the script

Mean Malthusian growth summarized for each line of each selection regime over the maximum number of benzovindiflupyr exposition cycles

  • Column “Acyclical_name”: unique identifier for each line
  • Column “Lines”: names of selection regimes
  • Column “Mean_malth_growth_6_sumbenzo”: mean of normalized Malthusian growth calculated for each repeated line of each selection regimes that received benzovindiflupyr applications, except BCP, over the 6 applications of benzovindiflupyr
  • Column “Mean_malth_growth_4_sumbenzo”: mean of normalized Malthusian growth calculated for each repeated line of each selection regimes that received benzovindiflupyr applications, over 4 applications of benzovindiflupyr
  • Column “Rhythm”: rhythm of alternation (0, 1, 2 or 3)
  • Column “AIs_number”: number of AIs used in a given selection regime (1, 2 or 3)

Sheet “Alternation_droplet_test_scores”:

(Referred as "Alternation_droplet_test_scores.txt” in the script)

Scores of susceptibility to multiple fungicides established for each isolate in droplet tests

  • Column “Isolate”: unique identifier for each isolate (3 isolates per repetitions per line per cycle)
  • Column “Lines”: names of selection regimes
  • Column “Cycle”: cycle of the experimental evolution (1 to 12)
  • Column “Azo”: score of sensitivity to azoxystrobin
  • Column “B”: score of sensitivity to benzovindiflupyr
  • Column “Bx2”: score of sensitivity to benzovindiflupyr, two times the dose of column “B”
  • Column “B+C”: score of sensitivity to benzovindiflupyr and carbendazim (mixture)
  • Column “B+P”: score of sensitivity to benzovindiflupyr and prothioconazole-desthio (mixture)
  • Column “Bosc”: score of sensitivity to boscalid
  • Column “C”: score of sensitivity to carbendazim
  • Column “Cx2”: score of sensitivity to carbendazim, two times the dose of column “C”
  • Column “C+P”: score of sensitivity to carbendazim and prothioconazole-desthio (mixture)
  • Column “Solvent”: score of growth on medium amended only with ethanol 80%
  • Column “P”: score of sensitivity to prothioconazole-desthio
  • Column “Px2”: score of sensitivity to prothioconazole-desthio, two times the dose of column “P”
  • Column “Tol”: score of sensitivity to tolnaftate

Funding

Institut National de la Recherche Agronomique, Award: STRATAGEME

French Ministry of Higher Education, Research and Innovation, Award: CIFRE Program

Syngenta International, Award: CIFRE Program

French Ministry of Higher Education, Research and Innovation, Award: CIFRE Program