Identification of hub salt-responsive genes in Cucumis sativus using a long non-coding RNA and mRNA interaction network

Cucumber is a commercially important vegetable crop whose growth and productivity are significantly influenced by salinity. Currently, there is little information about salt-related genes and the associated biological pathways involved in salt stress response and tolerance in this crop. Accordingly, this study aimed to unravel the complex molecular mechanism components underlying salinity in cucumber using long non-coding RNA (lncRNA) identification and weighted gene co-expression network analysis (WGCNA). Here, two previously published high-throughput RNA-seq datasets obtained from control and salt-treated tissues of cucumber roots and leaves were employed. First, the potential lncRNAs were identified based on a bioinformatics pipeline. Subsequently, differentially expressed genes (DEGs) and differentially expressed lncRNAs (DE-lncRNAs) were utilized as the input for the WGCNA to identify the clusters of highly interconnected lncRNAs and mRNAs. According to the results, 17 DE-lncRNAs out of 279 and 7 DE-lncRNAs out of 166 putative lncRNAs were detected between salt-treated and control samples in root and leaf tissues, respectively. Using WGCNA, 2226 unique DEGs and 23 DE-lncRNAs were categorized into 10 distinctive co-expression modules, of which, four modules, including blue, brown, yellow, and turquoise, contained the highest number of salt-related genes. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis identified four significantly enriched pathways, including, “plant hormone signal transduction”, “starch and sucrose metabolism”, “MAPK signaling pathway”, and “phenylpropanoid biosynthesis”, related to salt stress response in cucumber. The novel hub genes identified in this study could be exploited for further functional studies aiming to introduce salt-tolerant cucumber varieties utilizing molecular engineering approaches.