Elucidation of the molecular responses of a cucumber segment substitution line carrying Pm5.1 and its recurrent parent triggered by powdery mildew by comparative transcriptome profiling

Abstract

BackgroundPowdery mildew (PM) is one of the most severe fungal diseases of cucurbits, but the molecular mechanisms underlying PM resistance in cucumber remain elusive. In this study, we developed a PM resistant segment substitution line SSL508-28 that carried a segment on chromosome five representing the Pm5.1 locus from PM resistant donor Jin5-508 using marker-assisted backcrossing of an elite PM susceptible cucumber inbred line D8.ResultsWhole-genome resequencing of SSL508-28, Jin5-508 and D8 was performed to identify the exact boundaries of the breakpoints for this introgression because of the low density of available single sequence repeat markers. This led to the identification of a ~6.8 Mb substituted segment predicted to contain 856 genes. RNA-seq was used to study gene expression differences in PM treated (plants harvested 48 h after inoculation) and untreated (control) SSL508-28 and D8 lines. Exactly 1,248 and 1,325 differentially expressed genes (DEGs) were identified in SSL508-28 and D8, respectively. Of those, 88 DEGs were located in the ~6.8 Mb segment interval. Based on expression data and annotation, we identified 8 potential candidate genes that may participate in PM resistance afforded by Pm5.1, including two tandemly arrayed genes encoding receptor protein kinases, two transcription factors, two genes encoding remorin proteins, one gene encoding a P-type ATPase and one gene encoding a 70 kDa heat shock protein. The transcriptome data also revealed a complex regulatory network for Pm5.1-mediated PM resistance that may involve multiple signal regulators and transducers, cell wall modifications and the salicylic acid signaling pathway.ConclusionThese findings shed light on the cucumber PM defense mechanisms mediated by Pm5.1 and provided valuable information for the fine mapping of Pm5.1 and breeding of cucumber with enhanced resistance to PM.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3438-z) contains supplementary material, which is available to authorized users.

Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing

“…Cucumber seedlings of D8 and SSSL508-28 were grown in a growth chamber under controlled conditions (65% relative humidity, 28 • C/16 h light and 20 • C/8 h dark). At 21 days (threeleaf stage), homogeneous plants were selected for inoculation by spraying with a P. xanthii conidia (harvested from naturally infected D8 leaves) spore suspension of 1 × 10 6 conidia/mL containing 0.01% Tween-20 or sterile distilled water until runoff (Xu et al, 2017). The leaves sprayed with the sterile water served as mock controls.…”

“…The remaining targets either showed no significant change in their expression levels or had similar expression patterns as the corresponding miRNAs. Among the 92 miRNA-mRNA interaction pairs in D8, two were located on the substituted segment (Chr5:16,676,542-23,484,079 bp;Xu et al, 2017) that includes Csa-miR172c-3p and Csa-miR395a-3p. Eight targets of Csa-miR172c-3p that were negatively regulated upon PM inoculation were classified as TFs, namely, two Dofs (Csa1G009790 and Csa1G033250), one TALE (Csa6G426360), one AP2 (Csa2G279250), one LBD (Csa5G219380), one Trihelix (Csa2G350410), one bHLH (Csa1G612950), and one CO-like (Csa7G031530) (Supplementary Table 7).…”

“…Genetic mapping, RNA sequencing-based transcriptomic, and iTRAQ-based proteomic studies have revealed candidate genes and pathways associated with the genetic control and molecular responses of host immunity against cucumber PM. They include genes that encode cysteine-rich receptor-like protein kinases (Csa1G064780 and Csa1G064790) and mildew locus O (Csa5M623470), as well as molecular events involving cell wall modifications, salicylic acid metabolism, and signal transduction pathways (Berg et al, 2015;Xu et al, 2016;Xu et al, 2017). However, little is known about the coordination and regulation of host genes that affect these biological processes.…”

Genome-wide analysis of the WRKY gene family in the cucumber genome and transcriptome‑wide identification of WRKY transcription factors that respond to biotic and abiotic stresses

“…These results suggested that CsWRKYs may play crucial roles in the response to various stresses. To further confirm whether CsWRKYs are involved in the response to various stresses, we analysed the comprehensive expression patterns of CsWRKY genes under different abiotic and biotic stresses, including salt, heat, downy mildew (DM, Pseudoperonospora cubensis) and powdery mildew (PM, Podosphaera fusca), based on public transcriptome information [54,60,61] and transcriptomic data that we generated.…”

“…To explore the potential functions of CsWRKYs in resistance to biotic stresses, we performed a CsWRKY expression analysis of the susceptible and resistant cucumber lines inoculated with PM for 48 h (Fig. 9A) based on published RNA-seq data [61]. Eleven and 12 CsWRKY genes that were differentially expressed were identified in the susceptible and resistant cucumber lines, respectively, compared with the controls.…”