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, 21 (1), 127

Transcriptome Analysis Reveals the Roles of Stem Nodes in Cadmium Transport to Rice Grain

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Transcriptome Analysis Reveals the Roles of Stem Nodes in Cadmium Transport to Rice Grain

Ailing Liu et al. BMC Genomics.

Abstract

Background: Node is the central organ of transferring nutrients and ions in plants. Cadmium (Cd) induced crop pollution threatens the food safety. Breeding of low Cd accumulation cultivar is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 (low Cd accumulation cultivar) and Yuzhenxiang (high Cd accumulation cultivar). RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs.

Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang, and node I had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4535 DEGs and 70 miRNAs between the two cultivars. Most genesrelated to the "transporter activity", such as OsIRT1, OsNramp5, OsVIT2, OsNRT1.5A, and OsABCC1, play roles in blocking the upward transport of Cd. Among the genes related to "response to stimulus", we identified OsHSP70 and OsHSFA2d/B2c in Xiangwanxian No. 12, but not in Yuzhenxiang, were all down-regulated by Cd stimulus. The up-regulation of miRNAs (osa-miR528 and osa-miR408) in Xiangwanxian No. 12 played a potent role in lowering Cd accumulation via down regulating the expression of candidate genes, such as bZIP, ERF, MYB, SnRK1 and HSPs.

Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang. Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar. MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs, to play a role in Cd stress response.

Keywords: Cadmium; Low cadmium accumulation; Node I; Panicle node; RNA-seq.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Cd contents and regulator expression profiles in these two rice varieties. a shows the Cd contents in different stem nodes and grain. DW, dry weight (kg); XP, panicle node of Xiangwanxian No.12; XN, node I of Xiangwanxian No.12; yP, panicle node of Yuzhenxiang; yN, node I of Yuzhenxiang; XG, grain of Xiangwanxian No.12; yG, grain of Yuzhenxiang. # p < 0.05, ## p < 0.01 Cd treatment vs. control; * p < 0.01, ** p < 0.05 y (Yuzhenxiang) vs. X (Xiangwanxian No.12). b to e show the interleaved violin plot of the expression of OsMAPK, OsHMA3, OsZIP4 and OsPCS, respectively
Fig. 2
Fig. 2
Sample clustering and correlation analysis. a and c the principal component analysis (PCA) of the samples sequenced using the mRNA and miRNA expression level, respectively. b and d the sample-to-sample clustering analysis based on the mRNA and miRNA expression level, respectively. The color depth notes the similarity between samples (0~1). The deeper the color, the higher the similarity
Fig. 3
Fig. 3
Summary of differentially expressed genes (DEGs). a The Venn figures of the DEGs in pairwise comparison of Cd-treated (T) vs. untreated control (C) of node I (N) and panicle node (P) in “X” and “y” cultivar, respectively. b the statistics of the up- and down-regulated DEGs. The number on the column indicates the percent of the up and down-regulated DEGs by each comparison
Fig. 4
Fig. 4
Differentially expressed genes (DEGs) between high and low Cd accumulation cultivars. a Gene Ontology (GO) and KEGG pathway enrichment analyses of down-regulated DEGs in pairwise comparison of Cd-treated (T) vs. untreated control (C) of node I (N) and panicle node (P) in “X” and “y” cultivar, respectively. The redder the color, the more significantly enriched DEGs there were, the greener the color, the less; b and c Hierarchical clustering analysis of the DEGs involved in “transporter activity” (B) and “response to stimulus” (C), respectively
Fig. 5
Fig. 5
Heatmap of known 52 Cd-responsive genes. These Cd-responsive genes were collected from previous literatures. The change of color from blue to red indicated that gene expression level was low to high
Fig. 6
Fig. 6
Differentially expressed miRNAs (DEmiRNAs) responsible for low Cd accumulation. a The statistics of the up- and down-regulated DEmiRNAs. The number on the column indicates the number of the up and down-regulated DEGs by each comparison; b The Venn figures of the of DEmiRNAs in Node I DEGs in pairwise comparison. The common DEmiRNAs were pointed out by the arrow; c Expression of the common DEmiRNAs in Cd-treated (T) vs. untreated control (C) of node I (N) and panicle node (P) in “X” and “y” cultivar, respectively; d Heatmap of the candidate miRNAs and their differentially expressed family members. The change of color from blue to red indicated that gene expression level was low to high
Fig. 7
Fig. 7
Regulatory network of candidate miRNAs and target genes. formula image represented down-regulated differentially expressed miRNAs (DEmiRNAs) after Cd teratment; formula image represented up-regulated DEmiRNAs after Cd treatment; formula image represented the target genes. Different p values are expressed in different colors, as shown in the figure. formula image indicated that the target gene was a transcription factor. Different p values are expressed in different colors, as shown in the figure
Fig. 8
Fig. 8
Consistency results of qRT-PCR and RNA-seq. a Expression of mRNAs in different group. b Expression of miRNAs in different group. c Consistency results of qRT-PCR and RNA-seq (including mRNAs and miRNAs). The figure was based on the fold change of qRT-PCR and log2 fold change of RNA-seq. R2 represented the correlation coefficient between qRT-PCR and RNA-seq
Fig. 9
Fig. 9
Schematic maps of upward transport mechanism of blocking Cd in different rice varieties. Panicle node (P) and node I (N) were marked in blue on the rice sketch. The schematic map (the right of the figure) showed the upward transport mechanism of blocking Cd in Xiangwanxian No.12 (pale green) and Yuzhenxiang (pale pink). The ellipse at top and bottom represented panicle node and node I, respectively. The expression of key genes was showed by heatmap (box on left and right represented control and Cd treatment, respectively), the redder the color, the higher the expression. The direction of Cd transportation was indicated by arrows and the content of Cd was expressed by the number of “Cd2+

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References

    1. Wang C, Mo Z, Wang H, Wang Z, Cao Z. The transportation, time-dependent distribution of heavy metals in paddy crops. Chemosphere. 2003;50(6):717–723. - PubMed
    1. Wang M, Chen A, Wong MH, Qiu R, Cheng H, Ye Z. Cadmium accumulation in and tolerance of rice (Oryza sativa L.) varieties with different rates of radial oxygen loss. Environ Pollut. 2011;159(6):1730–1736. - PubMed
    1. Afzal J, Hu C, Imtiaz M, Elyamine A, Rana M, Imran M, Farag M. Cadmium tolerance in rice cultivars associated with antioxidant enzymes activities and Fe/Zn concentrations. Int J Environ Sci Technol. 2018:1–12. https://www.researchgate.net/publication/328433396_Cadmium_tolerance_in_rice_cultivars_associated_with_antioxidant_enzymes_activities_and_FeZn_concentrations
    1. Luo JS, Yang Y, Gu T, Wu Z, Zhang Z. The Arabidopsis defensin gene AtPDF2. 5 mediates cadmium tolerance and accumulation. Plant Cell Environ. 2019. 10.1111/pce.13592. - PubMed
    1. Zhang ZH, Zhou T, Tang TL, Song HX, Guan CY, Huang JY, Hua YP. Multiomics landscapes uncover the pivotal role of subcellular reallocation of cadmium in regulating rapeseed resistance to cadmium toxicity. J Exp Bot. 2019:erz295. - PMC - PubMed

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