Comparative Transcriptome Analysis Reveals the Molecular Mechanism of Salt Combined with Flooding Tolerance in Hybrid Willow (Salix matsudana × alba)

Plants in coastal areas often face the combined stress of salt and flooding, which can cause severe damage. The impact of multiple stresses on plant growth and survival is greater than that of individual stresses. However, the molecular responses of hybrid willow (Salix matsudana × alba) to the combination of salt and flooding have not been well understood. In this study, we conducted a comparative transcriptome analysis to investigate the molecular mechanism underlying the tolerance of hybrid willow to salt-flooding. Seedings were, respectively, treated with 200 mM NaCl and flooded with water or 200 mM NaCl solution for 3 d, 10 d, and 17 d. We identified 1842, 3350, and 2259 differentially expressed genes (DEGs) regulated by hybrid willow under single salt stress, single flooding stress, and combined salt and flooding stress, respectively. Many DEGs detected in single salt- and flooding-treated plants were expressed differentially after the combined salt and flooding. Most of the shared transcripts exhibited similar fold changes in common molecular responses such as detoxification of reactive oxygen species (ROS) and signaling pathways related to calcium, phytohormones, and protein kinases, which were also observed in plants exposed to each stress individually. Additionally, a large number of specific DEGs were identified under salt-flooding stress, primarily associated with cell wall remodeling, osmotic adjustments, stress signaling, primary metabolism, and ROS scavenging. KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation indicated that hybrid willow leaves responded to salt-flooding stress mainly through phytohormone signaling and MAPK signaling pathways. Overall, this study provides new insights into the molecular mechanisms underlying the response of Salix species to multiple stresses and identifies potential candidate genes for enhancing the performance of hybrid willows.