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Risk assessment of Aphanomyces euteiches root rot disease: quantification of low inoculum densities in field soils using droplet digital PCR

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Abstract

Aphanomyces euteiches Drechs is a pathogenic soil-borne oomycete that causes root rot of legumes, one of the most serious diseases affecting legume production worldwide. There is currently no registered pesticide and no available resistant pea cultivar. Avoidance of infested fields based on disease risk assessment prior to pea sowing remains the main method available to manage the disease, but time-consuming bioassays are required to assess disease severity on susceptible plants grown in field soil samples. Direct quantification of A. euteiches inoculum in the soil by targeting multicopy genomic sequences of the internal transcribed spacer 1 with a qPCR-based method has been proposed as a rapid alternative for disease prediction. However, the method lacks sensitivity to accurately quantify low inoculum levels from naturally infested fields. We developed a suitable methodology based on droplet digital PCR (ddPCR) to quantify low A. euteiches inoculum levels in naturally infested soils. The methodology was validated on 200 soil samples taken from four naturally infested fields in the main pea cropping area in the north of France. The comparative analysis of inoculum density and disease severity of the 50 samples within each of the four fields revealed a non-homogeneous distribution of the A. euteiches population; this explains why the disease is visible in the form of foci. A significant relationship between pea root rot disease severity determined by bioassays and A. euteiches inoculum density was highlighted, and a linear mixed model is proposed to predict disease severity from inoculum density.

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Acknowledgments

Simon Gibert was financially supported by a PhD funding from Bonduelle SAS (59653 Villeneuve d’Ascq, France) and the National Association of Technical Research (ANRT) (CIFRE n°2017/0852).

The authors would like to thank Guillaume Fourrier of Bio-Rad laboratories for his technical assistance at the beginning of the project and for his help for the design of a ddPCR probe. The authors thank Cécile Jacot-des-Combes for the expertise and facilities of the DTAMB platform (University Lyon 1).

This work, through the involvement of the technical facilities of the GenoSol platform of the infrastructure ANAEE-Services, indirectly benefited from a grant from the French state through the National Agency for Research under the program “Investments for the Future” (reference ANR-11-INBS-0001), as well as from a grant from the Regional Council of Bourgogne Franche Comté. The BRC GenoSol is a part of BRC4Env, the pillar “Environmental Resources” of the Research Infrastructure AgroBRC-RARe.

Code availability

R scripts developed in this study are available in a supplementary information file.

Funding

Simon Gibert was financially supported by a PhD funding from Bonduelle SAS (59653 Villeneuve d’Ascq, France) and the National Association of Technical Research (ANRT) (CIFRE n°2017/0852).

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Authors and Affiliations

  1. Agroécologie, AgroSup Dijon, INRAE, University Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France

    Simon Gibert, Véronique Edel-Hermann, Rayanti Moussa Mcolo, Elodie Gautheron, Joël Michel, Eric Bernaud, Nadine Gautheron & Christian Steinberg

  2. Société BONDUELLE SAS, Rue Nicolas Appert – BP 17, 59653, Villeneuve d’Ascq, Cedex, France

    Simon Gibert, Jean-Marie Sol, Gery Capelle, Rachel Galland, Arnaud Bardon-Debats & Claudine Lambert

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  1. Simon Gibert
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  2. Véronique Edel-Hermann
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Correspondence to Véronique Edel-Hermann.

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Gibert, ., Edel-Hermann, V., Moussa Mcolo, R. et al. Risk assessment of Aphanomyces euteiches root rot disease: quantification of low inoculum densities in field soils using droplet digital PCR. Eur J Plant Pathol 161, 503–528 (2021). https://doi.org/10.1007/s10658-021-02325-5

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