Loop-mediated isothermal amplification assays for rapid detection of Ralstonia solanacearum species complex and phylotype I in solanaceous crops

Robène Isabelle, Maillot-Lebon Véronique, Pecrix Yann, Ravelomanantsoa Santatra, Massé Delphine, Jouen Emmanuel, Rasoamanana Hasina, Fenelon Babbitha, Javegny Stéphanie, Seguin Marc, Lebon Sylvain, Poussier Stéphane, Pruvost Olivier. 2023. Loop-mediated isothermal amplification assays for rapid detection of Ralstonia solanacearum species complex and phylotype I in solanaceous crops. PhytoFrontiers, 3 (3) : 582-593.

https://doi.org/10.1094/phytofr-08-22-0089-r

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Résumé : The Ralstonia solanacearum species complex (RSSC) causes bacterial wilt diseases, which affect a wide range of plant hosts, including Solanaceae, and is of major economic importance. Point-of-care (POC) techniques such as loop-mediated isothermal amplification (LAMP) enable the rapid and sensitive detection of plant pathogens and can be deployed directly in the field. For fast and reliable diagnosis on site, we optimized an RSSC-LAMP assay and developed a real-time LAMP assay targeting the phylotype I. Both LAMPs were highly specific, yielding negative results for a wide collection of nontarget strains and positive results for all target strains, except for two particular mulberry strains for the phylotype I assay. These results were supported by an extensive in silico analysis performed on 6,105 genomes of Burkholderiaceae. The two LAMP assays displayed high sensitivity on pure suspensions, with a detection limit at 103 and 104 CFU/ml for phylotype I and the RSSC, respectively. These thresholds correspond to theoretical quantities of as low as 5 and 50 CFU per reaction. Two simplified extraction methods were successfully used to detect the pathogen from different Solanaceae samples. We demonstrated that LAMP assays were operable on solanaceous crops during field surveys and varietal evaluation trials as rapid POC diagnostics tools, which can improve the disease management and control of the RSSC.

Mots-clés Agrovoc : Ralstonia solanacearum, Burkholderiaceae, maladie bactérienne, Solanum lycopersicum, identification, diagnostic, phylogénie, maladie des plantes, Ralstonia, plante hôte

Mots-clés géographiques Agrovoc : La Réunion, France, Mayotte

Mots-clés libres : Detection, Diagnosis, Genomes, LAMP, Phylotype I, Point-of-care testing, Ralstonia solanacearum species complex, Simplified extraction method

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Agricultural Fund for Rural Development, European Regional Development Fund

Agences de financement hors UE : Conseil Régional de La Réunion, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Agropolis Fondation

Programme de financement européen : INTERREG V Océan Indien

Projets sur financement : (EU) EPIdémiosurveillance et BIOcontrôle dans le Sud-Ouest de l’Océan Indien

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