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

Abstract

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.

Genome-wide characterization and identification of Trihelix transcription factors and expression profiling in response to abiotic stresses in Chinese Willow (Salix matsudana Koidz)

“…Transcriptome and qRT-PCR data showed that SmTTF30 responded significantly to a variety of abiotic stresses. Our previous study showed that SmTTF30 of the S. matsudana Trihelix gene family was identified as a flooding tolerance hub gene, and analysis of transcriptomic data revealed that the gene was significantly induced at 4 h of flooding (Chen et al, 2022b). Evolutionary tree analysis revealed that this gene is closely related to Arabidopsis HRA1 (At3g10040), and the study demonstrated that HRA1 can be involved in Arabidopsis in response to flooding stress (Giuntoli et al, 2014).…”

“…In previous studies, SmTTF30 was selected as one of the S. matsudana flooding tolerance hub genes by WGCNA (Chen et al, 2022b). We compared the expression of SmTTFs in S. matsudana, and the SmTTF30 gene showed higher gene expression after stress.…”

Molecular responses to salinity stress in Salix matsudana (Koidz) females and males

“…The transcriptome reads were processed into clean, full-length reads by removing the low-quality and adapter reads (Chen et al, 2022). The assembled Salix matsudana Koidz.…”