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. 2019 Sep 5;20(18):4358.
doi: 10.3390/ijms20184358.

Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation

Xiaoxiang Zhang  1   2 , Niansheng Huang  2 , Lanjing Mo  1 , Minjia Lv  1 , Yingbo Gao  1 , Junpeng Wang  1 , Chang Liu  1 , Shuangyi Yin  1 , Juan Zhou  1 , Ning Xiao  2 , Cunhong Pan  2 , Yabin Xu  3 , Guichun Dong  1 , Zefeng Yang  1 , Aihong Li  2 , Jianye Huang  1 , Yulong Wang  4 , Youli Yao  5
Affiliations

Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation

Xiaoxiang Zhang et al. Int J Mol Sci. .

Abstract

Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.

Keywords: gamma irradiation; gene network; morphology; rice (Oryza sativa L.); transcriptomic analysis.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Germination profiles of japonica and indica rice at different irradiation dose. (A) Seedling survival rate of different japonica rice under different irradiation dose; (B) Seedling survival rate of different indica rice under different irradiation dose; (C) Seed germination potential of japonica rice Nipponbare (NPB) and indica rice Yangdao6 (YD6) under different irradiation doses; (D) Seed germination rate of NPB and YD6 under different irradiation dose; (E) Seedling emergence rate of NPB and YD6 under different irradiation dose; (F) Seedling survival rate of NPB and YD6 under different irradiation doses. There are three biological replicates and each biological replicate contains one hundred seeds. LD50, 50% lethal dose; Bars are mean ± SD of three independent biological replicates, and asterisks indicate significant difference (*, p ≤ 0.05; **, p ≤ 0.01) compared to control (0 Gy).
Figure 2
Figure 2
Correlation between four indices of shoot and root at different irradiation dose (0 Gy, 50 Gy, 100 Gy, 150 Gy, 250 Gy, 300 Gy, 400 Gy and 500 Gy) in japonica rice NPB and indica rice YD6. Three biological replicates and each biological replicate contains one hundred seeds. * (p ≤ 0.05), ** (p ≤ 0.01) represent significance level.
Figure 3
Figure 3
Comet assay of shoot and root cells. (A) Morphological characteristics of seedlings of NPB and YD6. Bar = 1 cm; (B) nuclei collected from shoot and root of NPB and YD6 treated with 0 Gy and 50 Gy; (C) the tail moment values of NPB. NG0R and NG0S, the control (0 Gy) of root and shoot in NPB, respectively. NG5R and NG5S, the irradiation treatment (50 Gy) of root and shoot in NPB, respectively; (D) the tail moment values of YD6. YG0R and YG0S, the control of root and shoot in YD6, respectively. YG5R and YG5S, the irradiation treatment of root and shoot in YD6, respectively. ** (p ≤ 0.01) indicates significant difference compared to control.
Figure 4
Figure 4
Correlation of RNA-seq results and qRT-PCR validation in 50 representative genes. * (p ≤ 0.05) and ** (p ≤ 0.01) represents significant difference.
Figure 5
Figure 5
Differences of global gene expression profiling in shoot and root of NPB and YD6 under irradiation. (A,B) Venn diagrams of differentially expressed genes (DEGs) between irradiation response (A) and varietal effect (B); (C,D) Numbers of DEGs in each comparison between irradiation response (C) and varietal effect (D); (E–M) Changes of some DEGs associated with core histone (E), cyclin (F), MCM (G), DNA-repair (H), glutathione S-transferase (I), heavy metal associated/transport/detoxification (J), glycosyl hydrolase (K), oxidoreductase (L) and universal stress protein (M) in response to irradiation.
Figure 6
Figure 6
MapMan analysis of DEGs in irradiation response (A,C,E,G) and cultivar effect (B,D,F,H). Results of mapping 552 and 2350 genes to metabolism (A,B), large enzyme families (C,D), cellular response (E,F) and transcriptions (G,H). Red boxes, up-regulated genes; blue boxes, down-regulated genes.
Figure 7
Figure 7
Weighted gene co-expression network analysis (WGCNA) of gene expressions and traits. (A) Hierarchical cluster tree showing 37 co-expression modules based on WGCNA. Each branch in the tree represents an individual gene; (B) Module—trait relationships and corresponding p-value. The panel on the left shows 37 modules and the panel on the right is the relevant color scale from −1 to 1. The numbers above the parentheses represent the correlation coefficient (r), and the numbers in parentheses represent the significance (p). (C) Top half is heatmap showing the FPKM and lower part is the eigengene expression profile in magenta module; (D) Top half is heatmap showing the FPKM of each gene and lower part is the eigengene expression profile in royal blue module.
Figure 8
Figure 8
Co-expression network analysis of length and surface area related modules. (A,B) Gene co-expression networks of positive correlation magenta module (A) and negative correlation royal blue module (B) visualized using Cytoscape software platform. The size of the circle and the depth of the color indicate the degree of connectivity of the gene; (C,D) The correlation networks of top 20 nodes in magenta module (C) and royal blue module (D). The depth of the color represents the number of associated nodes, respectively.
Figure 9
Figure 9
Gene expressions of top ten node genes of six related modules. (A) Heatmap comparison showing the expression profiles of top ten node genes in each module; (B) Changes in the expression levels of hub genes in top ten node genes of magenta module and royal blue module.
Figure 10
Figure 10
Schematic model for the regulation mechanism in rice plant cells’ response to gamma radiation.
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