Characterization of lncRNAs and mRNAs Involved in Powdery Mildew Resistance in Cucumber
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Updated: Nov 19, 2025
Screening and Identification of RNA Silencing Suppressors from Secreted Effectors of Plant Pathogens
Published on: February 3, 2020
Jingtao Nie1, Huasen Wang1, Wanlu Zhang1
1The Laboratory of Plant Molecular and Developmental Biology, College of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China.
Abstract:
Powdery mildew (PM) is a severe fungal disease of cucumber worldwide. Identification of genetic factors resistant to PM is of great importance for marker-assisted breeding to ensure cucumber production. Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) have been shown to play important roles in plant development and immunity; however, whether they have a role in PM response in cucurbit crops remains unknown. We performed strand-specific RNA sequencing and miRNA sequencing using RNA from cucumber leaves of two near-isogenic lines (NILs), S1003 and NIL (Pm5.1) infected with PM, and systematically characterized the profiles of cucumber lncRNAs and messenger RNA (mRNAs) responsive to PM. In total, we identified 12,903 lncRNAs and 25,598 mRNAs responsive to PM. Differential expression (DE) analysis showed that 119 lncRNAs and 136 mRNAs correlated with PM resistance. Functional analysis of these DE lncRNAs and DE mRNAs revealed that they are significantly associated with phenylpropanoid biosynthesis, phenylalanine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and endocytosis. Particularly, two lncRNAs, LNC_006805 and LNC_012667, might play important roles in PM resistance. In addition, we also predicted mature miRNAs and competing endogenous RNA (ceRNA) networks of lncRNA-miRNA-mRNA involved in PM resistance. A total of 49 DE lncRNAs could potentially act as target mimics for 106 miRNAs. Taken together, our results provide an abundant resource for further exploration of cucumber lncRNAs, mRNAs, miRNAs, and ceRNAs in PM resistance, and will facilitate the molecular breeding for PM-resistant varieties to control this severe disease in cucumber.
Insights
This study identifies long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) involved in cucumber powdery mildew (PM) resistance. These findings offer valuable genetic resources for developing disease-resistant cucumber varieties through molecular breeding.
Area of Science:
- Plant Science
- Genetics
- Molecular Biology
Background:
- Powdery mildew (PM) significantly impacts global cucumber production.
- Understanding genetic resistance factors is crucial for breeding disease-resistant cucumber varieties.
- The roles of long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in cucurbit PM response are largely unknown.
Purpose of the Study:
- To characterize lncRNAs and messenger RNAs (mRNAs) responsive to PM in cucumber.
- To identify genetic factors, including lncRNAs and mRNAs, associated with PM resistance.
- To explore the potential roles of lncRNAs, miRNAs, and competing endogenous RNA (ceRNA) networks in cucumber's defense against PM.
Main Methods:
- Strand-specific RNA sequencing and miRNA sequencing were performed on cucumber leaves from resistant and susceptible near-isogenic lines (NILs) infected with PM.
- Differential expression analysis was used to identify PM-responsive and PM-resistance-correlated lncRNAs and mRNAs.
- Bioinformatic tools were employed to predict mature miRNAs, ceRNA networks, and functional associations of identified genes.
Main Results:
- Over 12,900 lncRNAs and 25,500 mRNAs responsive to PM were identified.
- 119 lncRNAs and 136 mRNAs were found to be significantly correlated with PM resistance.
- DE lncRNAs and mRNAs were notably associated with phenylpropanoid biosynthesis, phenylalanine metabolism, and endocytosis pathways.
- Two specific lncRNAs (LNC_006805 and LNC_012667) showed potential key roles in PM resistance.
- 49 DE lncRNAs were predicted to function as target mimics for 106 miRNAs, forming potential ceRNA networks.
Conclusions:
- This study provides a comprehensive resource of PM-responsive lncRNAs, mRNAs, and miRNAs in cucumber.
- Identified lncRNAs and their associated ceRNA networks offer novel targets for enhancing PM resistance.
- These findings will facilitate marker-assisted and molecular breeding strategies for developing PM-resistant cucumber cultivars.
