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Comparative Study
. 2018 Mar 21;8(1):4931.
doi: 10.1038/s41598-018-23094-y.

Comparative transcriptome analysis reveals phytohormone signalings, heat shock module and ROS scavenger mediate the cold-tolerance of rubber tree

Xiaomin Deng  1 , Jianxiao Wang  2 , Yan Li  1 , Shaohua Wu  1 , Shuguang Yang  1 , Jinquan Chao  1 , Yueyi Chen  1 , Shixin Zhang  1 , Minjing Shi  1 , Weimin Tian  3
Affiliations
Comparative Study

Comparative transcriptome analysis reveals phytohormone signalings, heat shock module and ROS scavenger mediate the cold-tolerance of rubber tree

Xiaomin Deng et al. Sci Rep. .

Abstract

Two contrasting cold response rubber tree clones, the cold-resistant '93-114' and cold-sensitive 'Reken501', were subject to a global transcriptome response assessing via high-throughput RNA-seq technique and comprehensive bioinformatics analysis using the referenced rubber tree genome with the purpose of exploring the potential molecular cues underlying the tolerance of rubber trees to cold stress. As a result, a total of 1919 genes had significantly higher expression, while 2929 genes had significantly lower expression in '93-114' than in 'Reken501' without cold stress. Upon cold stress, the numbers of genes with significantly higher expression decreased to 1501 at 1 h treatment and to 1285 at 24 h treatment in '93-114' than that of 'Reken501', conversely, the numbers of genes with significantly lower expression increased to 7567 at 1 h treatment and to 5482 at 24 h treatment. Functional annotation of the differentially expressed genes between '93-114' and 'Reken501' suggests that down-regulation of auxin and ethylene signaling and activation of heat shock module and ROS scavengers is a primary strategy for H. brasiliensis to cope with cold stress. Our identified vital differentially expressed genes may be beneficial for elucidation of the molecular mechanisms underlying cold tolerance and for genetic improvement of H. brasiliensis clones.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Statistical analysis of differentially expressed genes. (a) Numbers of differentially expressed genes between ‘93–114’ and ‘Reken501’ before cold treatment (0 h, A0 vs B0) and after cold treatment for 1 h (A1 vs B1) and 24 h (A2 vs B2). The number of up-regulated (red) and down-regulated (green) genes is shown between ‘93–114’ (B0 for control, B1 for 1 h cold treatment, B2 for 24 h cold treatment) and ‘Reken501’ (A0 for control, A1 for 1 h cold treatment, A2 for 24 h cold treatment). (b,c) Distribution of differentially expressed genes (FDR ≤ 0.001 and |log2 ratio| ≥ 1).
Figure 2
Figure 2
Functional GO annotation of DGEs compared between ‘93–114’ and ‘Reken501’. GO classification analysis of the differentially expressed genes after 0 h (a, A0 vs B0), 1 h (b, A1 vs B1) and 24 h (c, A2 vs B2) of cold treatment. GO categories of ‘biological process,’ ‘cellular component’ and ‘molecular function’ are shown. The up-regulated and down-regulated genes are represented by red and green colors, respectively.
Figure 3
Figure 3
Functional KEGG classification of the DGEs in the pathway analysis between ‘93-114’ and ‘Reken501’. The functional KEGG classification and enrichment assays of the differentially expressed genes with a hypergeometric test (Bonferroni correction P ≤ 0.05) after 0 h, 1 h and 24 h of cold treatment.
Figure 4
Figure 4
Heatmap of the genes associated with the JA signaling pathway between ‘93–114’ and ‘Reken501’.
Figure 5
Figure 5
Heatmap of the genes associated with the heat shock module between ‘93–114’ and ‘Reken501’.
Figure 6
Figure 6
Heatmap of the ROS scavenging enzyme genes between ‘93–114’ and ‘Reken501’.
Figure 7
Figure 7
The qRT-PCR analysis of stress-related genes in the upstream analysis at different time intervals before and after cold treatment. The relative expression of each gene was calculated as the 2−ΔΔCT value and normalized to the endogenous reference genes. The standard deviation of three biological replicates is indicated by 1 or 2 asterisks depending on the P value for the significant difference (P < 0.05, P < 0.01, respectively) after t-test analysis (two group comparisons).
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