Comparative transcriptomic analysis reveals potential mechanisms for high tolerance to submergence in arbor willows

BACKGROUND: Submergence threatens plant growth and survival by decreasing or eliminating oxygen supply. Uncovering the complex regulatory network underlying the tolerance of Salix to submergence and identifying the key regulators are important for molecular-assisted breeding of Salix. METHODS: In this study, we screened germplasm resources of arbor willows and discovered both submergence-tolerant and submergence-sensitive varieties. Then, by performing RNA-seq, we compared the differences between the transcriptomes of two varieties, i.e., the submergence-tolerant variety “Suliu 795” and the submergence-sensitive variety “Yanliu No. 1,” and the different submergence treatment time points to identify the potential mechanisms of submergence in Salix and the unique approaches by which the variety “Suliu 795” possessed a higher tolerance compared to “Yanliu No. 1”. RESULTS: A total of 22,790 differentially expressed genes were identified from 25 comparisons. Using gene ontology annotation and pathway enrichment analysis, the expression pattern of transcriptional factors, important players in hormone signaling, carbohydrate metabolism, and the anaerobic respiration pathway were found to differ significantly between the two varieties. The principal component analysis and qRT-PCR results verified the reliability of the RNA sequencing data. The results of further analysis indicated that “Suliu 795” had higher submergence tolerant activity than “Yanliu No. 1” because of three characteristics: (1) high sensitivity to the probable low oxygen stress and initiation of appropriate responding mechanisms in advance; (2) maintenance of energy homeostasis to prevent energy depletion under hypoxic stress; and (3) keep “quiescence” through fine-tuning the equilibrium between phytohormones GA, SA and ethylene.