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).

KEY MESSAGE: The dm5.3 major-effect QTL in cucumber encodes a homolog of Arabidopsis sigma factor binding protein 1 (CsSIB1). CsSIB1 positively regulates defense responses against downy mildew in cucumber through the salicylic acid (SA) biosynthesis/signaling pathway. Downy mildew (DM) caused by the oomycete pathogen Pseudoperonospora cubensis is an important disease of cucumber and other cucurbits. Our knowledge on molecular mechanisms of DM resistance is still limited. In this study, we reported identification and functional characterization of the candidate gene for the major-effect QTL, dm5.3 for DM resistance originated from PI 197088. The dm5.3 QTL was Modelized through marker-assisted development of near isogenic lines (NILs). NIL-derived segregating populations were used for fine mapping which narrowed the dm5.3 locus down to a 144 kb region. Based on multiple lines of evidence, we show that CsSIB1 (CsGy5G027140) that encodes the VQ motif-containing sigma factor binding protein 1 as the most likely candidate for dm5.3. Local association analysis identified a haplotype consisting of 7 SNPs inside the coding and promoter region of CsSIB1 that was associated with DM resistance. Expression of CsSIB1 was up-regulated with P. cubensis infection. Transcriptome profiling of NILs in response to P. cubensis inoculation revealed key players and associated gene networks in which increased expression of CsSIB1 antagonistically promoted salicylic acid (SA) but suppressed jasmonic acid (JA) biosynthesis/signaling pathways. Our work provides novel insights into the function of CsSIB1/dm5.3 as a disease resistance (R) gene. The roles of sigma factor binding protein genes in pathogen defense in cucumber were also discussed.

Quantitative trait loci for horticulturally important traits defining the Sikkim cucumber, Cucumis sativus var. sikkimensis.

KEY MESSAGE: QTL mapping identified simply inherited genes and quantitative trait loci underlying morphologically characteristic traits of the Sikkim cucumber, which reveals their genetic basis during crop evolution. The data suggest the Sikkim cucumber as an ecotype of cultivated cucumber not worthy of formal taxonomic recognition. The Sikkim cucumber, Cucumis sativus var. sikkimensis, is featured with some morphological traits like black spine, brown fruit with fine and heavy netting, as well as large hollow in mature fruit. Despite its establishment as a botanical variety ~ 150 years ago, and its wide use as an important source of disease resistances in cucumber breeding, little is known about its taxonomic status and genetic basis of those characteristic traits. Here we reported QTL mapping with segregating populations derived from two Sikkim-type inbred lines, WI7088D and WI7120, and identification of 48 QTL underlying phenotypic variation for 18 horticulturally important traits. We found that the fruit spine and skin colors in the two populations were controlled by the previously cloned pleiotropic B (black spine) locus. The fruit netting in WI7088D and WI7120 was controlled by the well-known H (Heavy netting) and a novel Rs (Russet skin) locus, which was delimited to a 271-kb region on Chr5 and ~ 736-kb region on Chr1, respectively. A single major-effect QTL was detected for flowering time in each population (ft1.1 for WI7088D and ft6.2 for WI7120). Fifteen, six and five QTL were identified for fruit size, hollow size and flesh thickness variation in the two populations, respectively. No major structural changes were found between the Sikkim and cultivated cucumbers. Except for the rare allele at the Rs locus, there seem no private QTL/alleles identified from this study supporting the Sikkim cucumber as an ecotype of C. sativus, not worthy of formal taxonomic recognition.