PREPRINT | New powdery mildew resistance QTL found on chromosome 9 in Solanum cheesmaniae

This article is a preprint and has not been certified by peer review

Sangaré, A., Bourgeay, J.F, Massire, A., Berard, A., Hinsinger, D., Caromel, B., Bardin, M. (2026) New powdery mildew resistance QTL found on chromosome 9 in Solanum cheesmaniae. RESEARCH SQUARE.

 https://doi.org/10.21203/rs.3.rs-10443568

abstract: Powdery mildew, caused by Oidium neolycopersici, is one of the major fungal diseases affecting tomato production, particularly in greenhouse systems. Although several resistance genes have been identified in wild tomato relatives, their use in breeding programs remains limited due to genetic barriers and linkage drag. This study aimed to identify new resistance loci in the wild species Solanum cheesmaniae closely related to the cultivated tomato S. lycopersicum. An F2 mapping population was developed from a cross between the susceptible accession S. lycopersicum cv. Rose de Berne and the resistant accession S. cheesmaniae LA0421 to identify quantitative trait loci (QTLs) associated with resistance to O. neolycopersici. A QTL-seq analysis was performed using deep sequencing of DNA bulks from individuals with extreme phenotypes, resulting in the identification of one resistance QTL located on chromosome 9. In addition, linkage QTL mapping was performed on 143 F2 individuals to validate the QTL location identified by QTL-seq, designed On-q9lche. The QTL was confirmed on the long arm of chromosome 9, explaining 14.60% of the phenotypic variance. Furthermore, we identified several candidate genes potentially involved in powdery mildew resistance conferred by S. cheesmaniae, including genes encoding an ETO1-like protein, a serine/threonine-protein kinase, a NIMA-related kinase 2, a kinase-interacting protein, a 3-ketoacyl-CoA synthase, and the transcription factors UNE12/bHLH59. Overall, this study identified a novel source of resistance to powdery mildew in S. cheesmaniae, providing promising perspectives for tomato resistance breeding.