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. 2022 Feb 3:10:e12881.
doi: 10.7717/peerj.12881. eCollection 2022.

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

Yanhong Chen #  1   2 , Jie Yang #  1   2 , Hongyi Guo  1   2 , Yawen Du  1   2 , Guoyuan Liu  1   2 , Chunmei Yu  1   2 , Fei Zhong  1   2 , Bolin Lian  1   2 , Jian Zhang  1   2
Affiliations

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

Yanhong Chen et al. PeerJ. .

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.

Keywords: Anaerobic respiration pathway; Hormone; Hypoxia; Salix; Submergence stress; Transcription factors; Transcriptomic analysis.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Four growth indicators of the arbor willow germplasm under submergence stress, and the phenotypes of the submergence-tolerant and submergence-sensitive varieties.
Thirteen varieties selected for the submergence stress experiments and four indicators, including total root number, total root length, shoot number, and shoot length, are listed: (A) total root number; (B) total root length; (C) total shoot number; (D) total shoot length; (E) growth phenotype under control condition (hydroponics culture) and submergence stress of “Suliu 795” (66 days); (F) growth phenotype under control condition (hydroponics culture) and submergence stress of “Yanliu No. 1” (66 days) (F).
Figure 2
Figure 2. Statistical analysis on RNA sequencing results.
(A) PCA analysis. (B) Statistical analysis of differentially expressed genes (DEGs) from 25 comparisons (5 categories). (C) Venn diagrams of upregulated and downregulated DEGs from the comparisons of categories A, B, and C.
Figure 3
Figure 3. Biological processes in gene ontology (GO) enrichment analysis of DEGs during submergence stress in the submergence-tolerant and submergence-sensitive varieties of Salix.
GO enrichment analysis was performed using Blast2GO. Only significantly enriched terms (top 20) with corrected P < 0.05 were indicated. The color and size of each point represents the ‒log10 (FDR) values and enrichment scores. A higher ‒log10 (FDR) value and enrichment score indicate a greater degree of enrichment. Red and blue labeled-terms represent the different and identical terms in different comparisons, respectively.
Figure 4
Figure 4. Statistical analysis and heatmap illustration on TF DEGs.
(A) Statistical analysis of transcription factor (TF) differentially expressed genes (DEGs). (B) Heatmap illustration on the expression profiles of some TF DEGs from seven families. (C) Heatmap illustration of the expression profiles of 14 members from the AP2/ERF Group VII subfamily.
Figure 5
Figure 5. Heatmap analysis of differentially expressed genes (DEGs) encoding for important players in submergence response.
(A) Heatmap analysis of differentially expressed genes (DEGs) encoding for important factors in carbohydrate metabolism and anaerobic respiration. (B) ROS signaling pathway and N-end rule pathway. (C) Ethylene, GA, and SA synthesis and signaling.
Figure 6
Figure 6. Identification of hub genes in co-expression network under submergence stress.
(A) Eleven hub genes were identified from the red module. (B) Five hub genes were identified from the green module. The co-expression network was analyzed using WGCNA software and the graphic network was created by Cytoscape.
Figure 7
Figure 7. Verification of the DEGs with differentially expressed patterns under submergence stress by quantitative real-time PCR.
The gene expression profiles were evaluated using the 2−∆∆Ct method, and the control values were normalized to 1. Three biological replicates were performed for each sample. Bars represent the standard deviation of the mean.
Figure 8
Figure 8. The potential mechanisms for Submergence-tolerant willow “Suliu 795” gaining a higher tolerance.
See this image and copyright information in PMC

References

    1. Akman M, Bhikharie AV, McLean EH, Boonman A, Visser EJ, Schranz ME, van Tienderen PH. Wait or escape? Contrasting submergence tolerance strategies of Rorippa amphibia, Rorippa sylvestris and their hybrid. Annals of Botany. 2012;109(7):1263–1276. doi: 10.1093/aob/mcs059. - DOI - PMC - PubMed
    1. Arora K, Panda KK, Mittal S, Mallikarjuna MG, Rao AR, Dash PK, Thirunavukkarasu N. RNAseq revealed the important gene pathways controlling adaptive mechanisms under waterlogged stress in maize. Scientific Report. 2017;7:10950. doi: 10.1038/s41598-017-10561-1. - DOI - PMC - PubMed
    1. Ayano M, Kani T, Kojima M, Sakakibara H, Kitaoka T, Kuroha T, Angeles-Shim RB, Kitano H, Nagai K, Ashikari M. Gibberellin biosynthesis and signal transduction is essential for internode elongation in deepwater rice. Plant Cell and Environment. 2014;37:2313–2324. doi: 10.1111/pce.12377. - DOI - PMC - PubMed
    1. Barding GA, Jr, Fukao T, Béni S, Bailey-Serres J, Larive CK. Differential metabolic regulation governed by the rice SUB1A gene during submergence stress and identification of alanylglycine by 1H NMR spectroscopy. Journal of Proteome Research. 2012;11:320–330. doi: 10.1021/pr200919b. - DOI - PubMed
    1. Butsayawarapat P, Juntawong P, Khamsuk O, Somta P. Comparative transcriptome analysis of waterlogging-sensitive and tolerant zombi pea (Vigna Vexillata) reveals energy conservation and root plasticity controlling waterlogging tolerance. Plants. 2019;8(8):264. doi: 10.3390/plants8080264. - DOI - PMC - PubMed

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