Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

• Main Authors: Kinga Kęska, Michał Wojciech Szcześniak, Izabela Makałowska, Małgorzata Czernicka
• Format: Article
• Language: English
• Published: MDPI AG 2021-01-01
• Series: Genes
• Subjects: <i>Cucumis sativus</i> L.; DEGs; gene expression; hypoxia; priming; RNA-Seq
• Online Access: https://www.mdpi.com/2073-4425/12/2/189

Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., <i>alcohol dehydrogenase</i> (<i>adh</i>), <i>1-aminocyclopropane-1-carboxylate oxidase</i> (<i>aco</i>) and <i>long chain acyl-CoA synthetase 6</i> (<i>lacs6</i>) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.