Transcriptome Analysis Reveals Genes of Flooding-Tolerant and Flooding-Sensitive Rapeseeds Differentially Respond to Flooding at the Germination Stage.

Jijun Li,Liang Guo,Zengdong Tan,Sidra Iqbal,Usman Ali,Yuting Zhang,Yahui Chen

doi:10.3390/plants10040693

Jijun Li, Liang Guo + Show 5 more

Open Access

https://doi.org/10.3390/plants10040693

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Abstract

Flooding results in significant crop yield losses due to exposure of plants to hypoxic stress. Various studies have reported the effect of flooding stress at seedling establishment or later stages. However, the molecular mechanism prevailing at the germination stage under flooding stress remains enigmatic. The present study highlights the comparative transcriptome analysis in two rapeseed lines, i.e., flooding-tolerant (Santana) and -sensitive (23651) lines under control and 6-h flooding treatments at the germination stage. A total of 1840 up-regulated and 1301 down-regulated genes were shared by both lines in response to flooding. There were 4410 differentially expressed genes (DEGs) with increased expression and 4271 DEGs with reduced expression shared in both control and flooding conditions. Gene ontology (GO) enrichment analysis revealed that “transcription regulation”, “structural constituent of cell wall”, “reactive oxygen species metabolic”, “peroxidase”, oxidoreductase”, and “antioxidant activity” were the common processes in rapeseed flooding response. In addition, the processes such as “hormone-mediated signaling pathway”, “response to organic substance response”, “motor activity”, and “microtubule-based process” are likely to confer rapeseed flooding resistance. Mclust analysis clustered DEGs into nine modules; genes in each module shared similar expression patterns and many of these genes overlapped with the top 20 DEGs in some groups. This work provides a comprehensive insight into gene responses and the regulatory network in rapeseed flooding stress and provides guidelines for probing the underlying molecular mechanisms in flooding resistance.

Highlights

Of all the environmental challenges that a plant has to face during its growth period, flooding is considered to be of great concern, especially in areas having excessive rainfall or irrigation with poor drainage
Many studies have been conducted on plant response to hypoxia, one such study conducted in Arabidopsis identified 49 hypoxia-induced genes encoding transcription factors and regulating anerobic respiration through the glycolytic pathway [6]
The suppression trend of neither root nor shoot length of tolerant line (Santana) was statistically significant compared to the control, but the opposite was true in the sensitive line (23651) (Figure 1B,C)

Summary

Introduction

Of all the environmental challenges that a plant has to face during its growth period, flooding is considered to be of great concern, especially in areas having excessive rainfall or irrigation with poor drainage. Global warming has resulted in sea level rise, which is predicted to increase the frequency of oceanic storm surges, heavy precipitation, and flooding events. All these factors are likely to cause significant risk to global agriculture, posing a challenge for researchers in developing crop varieties capable of growing under such conditions [1,2,3]. Flooding affects the plant’s ability to absorb oxygen by hindering respiration and replacing gas spaces with excess water leading to low oxygen conditions (hypoxia), which causes a dramatic change in metabolism in order to provide alternate sources of ATP, jeopardizing plant growth and development [4,5]. Many studies have been conducted on plant response to hypoxia, one such study conducted in Arabidopsis identified 49 hypoxia-induced genes encoding transcription factors and regulating anerobic respiration through the glycolytic pathway [6]

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