Sigma factor binding protein 1 (CsSIB1) is a putative candidate of the major-effect QTL dm5.3 for downy mildew resistance in cucumber (Cucumis sativus)

Authors: TAN, JUNYI - University Of Wisconsin; WANG, YUHUI - University Of Wisconsin; DYMERSKI, RONALD - University Of Wisconsin; WU, ZHIMING - University Of Wisconsin; Weng, Yiqun

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/2/2022
Publication Date: 9/12/2022
Citation: Tan, J., Wang, Y., Dymerski, R.D., Wu, Z., Weng, Y. 2022. Sigma factor binding protein 1 (CsSIB1) is a putative candidate of the major-effect QTL dm5.3 for downy mildew resistance in cucumber (Cucumis sativus). Theoretical and Applied Genetics. 135:4197–4215. https://doi.org/10.1007/s00122-022-04212-x.
DOI: https://doi.org/10.1007/s00122-022-04212-x

Interpretive Summary: Background: Downy mildew is an important disease in cucumber production. Our previous study identified 8 quantitative traits loci (QTL) for DM resistance in the cucumber inbred line WI7088D including dm5.3 that has the largest contribution to DM resistance. However, the physical interval of this QTL is still very large, and the mechanisms for DM resistance conferred by dm5.3 are unknown. Findings: In this study, we conducted fine genetic mapping of dm5.3. Two near isogenic lines (NILs) were developed through marker-assisted selection to Mendelize the dm5.3 locus. DM screening in NIL-derived segregating populations revealed that dm5.3 contributed partial resistance to DM with both anti-chlorosis and anti-necrosis effects against DM pathogen infection, and the resistance seems to be dominant over susceptibility. Extensive phenotyping in multiple screening tests and fine mapping delimited the dm5.3 locus into a 144 kb region. Multiple lines of evidence supported CsGy5G027140 as the most possible candidate for dm5.3, which encodes the ‘sigma factor binding protein 1’ (CsSIB1), a member of the VQ motif-containing protein family. A single nucleotide mutation inside the only exon of CsSIB1 was likely the cause of dm5.3-conferred DM resistance. This SNP would result in a non-synonymous amino acid substitution in the CSSIB1 protein. In response to DM pathogen inoculation, CsSIB1 exhibited higher expression in the resistant than in the susceptible NILs. RNA-Seq analysis in the NILs before and after DM pathogen inoculation identified key players in CsSIB1-dependent gene network for DM resistance. Who cares: This work is of theoretical interest for plant pathologists in understanding the molecular mechanisms of DM resistance in cucumber and other crop plants. This work also provides molecular markers that could be used for marker-assisted breeding of DM resistances in cucumber breeding

Technical Abstract: Downy mildew (DM) caused by the oomycete pathogen Pseudoperonospora cubensis is an important disease of cucumber and other cucurbits. Our previous study identified multiple QTL for DM resistance in the cucumber inbred line WI7088D including a major-effect QTL dm5.3 on cucumber chromosome 5. In this study, we conducted fine genetic mapping of dm5.3. Two near isogenic lines (NILs) were developed through marker-assisted selection to Mendelize the dm5.3 locus. DM screening in NILs and a NIL-derived segregating population revealed that dm5.3 contribute partial resistance to DM with both anti-chlorosis and anti-necrosis effects against DM pathogen infection, and the resistance seems to be dominant over susceptibility. Extensive phenotyping in multiple screening tests and fine mapping delimited the dm5.3 locus into a 144 kb region. Allelic diversity and comparative expression analyses of genes in the target region, as well as local genome wide association analysis all supported CsGy5G027140 as the most possible candidate for dm5.3, which encodes the ‘sigma factor binding protein 1’ (CsSIB1), a member of the VQ motif-containing protein family. A single nucleotide mutation inside the only exon of CsSIB1 was likely the cause of dm5.3-conferred DM resistance. This SNP would result in a non-synonymous amino acid substitution (E84K) in the CSSIB1 protein. In response to DM pathogen inoculation, the expression of CsSIB1 exhibited higher expression in the resistant than in the susceptible NILs. Comparative analysis of the transcriptomes in the NILs before and after DM pathogen inoculation with RNA-Seq identified key players in CsSIB1-dependent gene network for DM resistance. Our work provided a novel mechanism for disease resistance against an oomycete pathogen in cucumber.