Lettuce is one of the most important leafy vegetable crops world-wide. Salt stress adversely affects lettuce production, leading to considerable yield losses. Understanding the molecular mechanisms underlying the salt stress response is essential for breeding and development of lettuce cultivars with improved salt tolerance. Thus, the objective of this research was to identify differentially expressed genes (DEGs) in lettuce root and leaf tissues under salt stress and non-salt stress conditions. We have compared two salt-stress tolerant and two salt-sensitive accessions from crisphead and leaf horticultural types. Differential gene expression was compared between salt-tolerant and salt-sensitive accessions from the same horticultural type to minimize the effect of horticultural types on the comparison. In the root samples of the salt-tolerant accessions, we identified 3,789 and 4,022 DEGs, while for the salt-sensitive accessions 9,030 and 9,945 DEGs were identified, for the crisphead and leaf types, respectively. In leaf tissues, we observed 5,683 and 9,445 DEGs in the salt-tolerant accessions and 5,836 and 10,172 DEGs in the sensitive accessions, respectively, for the crisphead and leaf types. Thus, the number of DEGs was higher in sensitive accessions of both root and leaf tissues, with a notably greater disparity in root tissues. Functional annotations of the DEGs indicated stress response as a common biological process in both root and leaf tissues. Protein phosphatase inhibitor and peroxidase were the most significantly enriched molecular function terms in roots, while chaperone and glycosyltranferase molecular function terms were most significantly enriched in leaves. Gene Ontology (GO) enrichment analysis determined that genes related to the organic substance biosynthetic process were most significantly enriched in roots, while genes related to photosynthesis, response to light stimulus, chlorophyll binding and regulation of the jasmonic acid-mediated signaling pathway were significantly enriched in leaves. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that plant hormone signal transduction, biosynthesis of secondary metabolites, and the MAPK signaling pathway were significantly enriched terms in both root and leaf tissues, while cysteine and methionine metabolism terms were most significantly enriched in roots and photosynthesis was most significantly enriched in leaves. Identification of the salt-stress responsive genes and the results on their expression patterns in salt-tolerant vs salt-sensitive cultivars obtained in the present study open the door for further functional analysis of these genes and their utilization in improving salt-stress tolerance in lettuce.
