Fine mapping of cucumber downy mildew resistance loci identifies candidate genes linked to ethylene-associated stomatal defence.

Authors

Mahdi Badri Anarjan, Saeed Omrani, Chunying Zhang, Shahida Begum, Khin Thanda Win, Haisu Li, Chunhua Wang, Tao Wu, Sanghyeob Lee

Published in

Journal of the science of food and agriculture. Oct 12, 2026. Epub Oct 12, 2026.

Abstract

Downy mildew, caused by Pseudoperonospora cubensis, is one of the most destructive diseases affecting cucumber and remains difficult to manage sustainably through fungicide-dependent control strategies. Although several resistance loci have been reported, many previously mapped regions remain too broad for efficient marker-assisted selection or reliable candidate-gene prioritisation. This study aimed to refine three TH118FLM-derived downy mildew resistance loci and to identify biologically plausible candidate genes associated with resistance by integrating advanced recombinant populations, QTL-seq, parent-bulk concordance analysis, and candidate-gene evaluation.
Two recombinant inbred line populations, dm2.1-F₇ and dm2.2-F₇, and one near-isogenic/backcross-derived population, dm5.1-BC₄F₂, were developed from a cross between TH118FLM and WMEJ. Phenotypic distributions in all three populations showed a higher frequency of susceptible disease-index classes, supporting the involvement of multiple resistance-associated quantitative loci rather than a single dominant resistance factor. QTL-seq reduced the dm2.1, dm2.2, and dm5.1 regions to 333, 296, and 694 kb, respectively. Subsequent parent-bulk concordance analysis of SNPs and INDELs further refined these loci to 61.7, 84.7, and 80.0 kb, containing seven, ten, and five annotated genes, respectively. By integrating positional, sequence, transcriptional, and predicted structural evidence, CsACO, CsCA, and CsSTPK were prioritised as the candidate genes for dm2.1, dm2.2, and dm5.1, respectively. Expression and physiological analyses further showed that these candidates responded to pathogen infection and ethephon treatment, while the resistant background exhibited reduced stomatal aperture and altered stomatal conductance following ethephon application, supporting a testable ethylene-associated stomatal-defence hypothesis.
This study refined three cucumber downy mildew resistance loci into compact, marker-ready intervals and identified CsACO, CsCA, and CsSTPK as biologically credible candidate genes. The findings provide practical genomic resources for marker-assisted cucumber resistance breeding and a testable biological framework, suggesting that TH118FLM-derived resistance may involve ethylene-associated stomatal defence. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

PMID:
42864848
Bibliographic data and abstract were imported from PubMed on 13 Oct 2026.

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