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Research article
Jianmin Bian
Jiangxi Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-3703-379X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: In general, the Cd content in indica rice is higher than that in japonica. However, the mechanism underlying this discrepancy has not been elucidated. Thus, understanding the genetic and molecular basis of Cd stress between indica and japonica is highly important for rice improvement programs.
Results: In this study, two varieties of rice, japonica 02428 and indica CH891, were continuously exposed to Cd, and seedlings of the two varieties at two critical stages (the 3rd and 5th day) were selected for dynamic gene analysis by the transcriptome method. The results showed that CH891 was more sensitive to Cd than 02428, and a total of 7,204 and 6,670 differentially expressed genes (DEGs) associated with Cd stress were detected on the 3rd day and 5th day, respectively. Furthermore, we divided these DEGs into three categories: SCR (sensitive variety with Cd-responsive), RCR (resistant variety with Cd-responsive) and CCR (common Cd-responsive). The enriched metabolic pathway analysis of DEGs preferentially expressed in a stage-specific and cultivar-specific manner showed that secondary metabolic processes were enriched in SCR, while protein metabolism and plant hormones were enriched in RCR. The diverted metabolic pathways might be the major reason for the different response mechanisms of Cd in indica and japonica rice.
Conclusion: These results provide novel insights regarding the Cd response mechanism in rice seedlings between different varieties, and these important Cd-responsive DEGs were frequently involved in specific biological processes and metabolic pathways that might help to elucidate the mechanisms of the indica and japonica rice Cd response differences.
Keywords
rice, Cd stress, seedling, transcriptome analysis, indica, japonica
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This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryTableS1S3.xlsx
Supplementary Table S1. FPKM expression of all detected genes. Supplementary Table S2. Quality evaluation of RNA-seq data. Supplementary Table S3. Primer sequences of qRT-PCR and the values of qRT-PCR and RNA-Seq.
- SupplementaryTableS1S3.xlsx
Supplementary Table S1. FPKM expression of all detected genes. Supplementary Table S2. Quality evaluation of RNA-seq data. Supplementary Table S3. Primer sequences of qRT-PCR and the values of qRT-PCR and RNA-Seq.
- SupplementaryTableS4.xlsx
Supplementary Table S4. The classification of three categories of DEGs at 3rd and 5th day and the ICR genes and the key DEGs enriched in the major pathways which were detected in the SCR3, RCR3, CCR3, SCR5, RCR5 and CCR5.And the common genes expressed at two stages in SCR, RCR and CCR
- SupplementaryTableS4.xlsx
Supplementary Table S4. The classification of three categories of DEGs at 3rd and 5th day and the ICR genes and the key DEGs enriched in the major pathways which were detected in the SCR3, RCR3, CCR3, SCR5, RCR5 and CCR5.And the common genes expressed at two stages in SCR, RCR and CCR
- SupplementaryFiguresS1S2.pdf
Supplementary Fig. S1. The KEGG term of DEGs in eight comparison group. (A) Cd3_CH891 vs Cd3_02428 (B) CK3_CH891 vs CK3_02428 (C) Cd3_CH891 vs CK3_CH891 (D) Cd3_02428 vs CK3_02428 (E) Cd5_CH891 vs Cd5_02428 (F) CK5_CH891 vs CK5_02428 (G) Cd5_CH891 vs CK5_CH891 (H) Cd5_02428 vs CK5_02428. Supplementary Fig. S2. The GO terms of ICR genes from SCR, RCR and CCR. (A) SCR3, (B) SCR5, (C) RCR3, (D) RCR5, (E) CCR3, (F) CCR5.
- SupplementaryFiguresS1S2.pdf
Supplementary Fig. S1. The KEGG term of DEGs in eight comparison group. (A) Cd3_CH891 vs Cd3_02428 (B) CK3_CH891 vs CK3_02428 (C) Cd3_CH891 vs CK3_CH891 (D) Cd3_02428 vs CK3_02428 (E) Cd5_CH891 vs Cd5_02428 (F) CK5_CH891 vs CK5_02428 (G) Cd5_CH891 vs CK5_CH891 (H) Cd5_02428 vs CK5_02428. Supplementary Fig. S2. The GO terms of ICR genes from SCR, RCR and CCR. (A) SCR3, (B) SCR5, (C) RCR3, (D) RCR5, (E) CCR3, (F) CCR5.
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Editorial decision: Major revision
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Reviewer #2 agreed
On 09 Sep, 2020
Reviewers invited
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Jianmin Bian
Jiangxi Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0003-3703-379X
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Revision
Version 2
Posted 10 Nov, 2020
No community comments so far
Editorial decision: Major revision
On 26 Dec, 2020
Review #2 received
Received 17 Nov, 2020
Review #1 received
Received 10 Nov, 2020
Reviewer #2 agreed
On 09 Nov, 2020
Reviewers invited
Invitations sent on 06 Nov, 2020
Reviewer #1 agreed
On 06 Nov, 2020
Editor assigned
On 31 Oct, 2020
Submission checks complete
On 31 Oct, 2020
Editor invited
On 31 Oct, 2020
No comments provided
Editorial decision: Major revision
On 29 Sep, 2020
Review #2 received
Received 26 Sep, 2020
Review #1 received
Received 13 Sep, 2020
Reviewer #1 agreed
On 09 Sep, 2020
Reviewer #2 agreed
On 09 Sep, 2020
Reviewers invited
Invitations sent on 08 Sep, 2020
Editor assigned
On 01 Sep, 2020
Submission checks complete
On 31 Aug, 2020
Editor invited
On 31 Aug, 2020
First submitted
On 29 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: In general, the Cd content in indica rice is higher than that in japonica. However, the mechanism underlying this discrepancy has not been elucidated. Thus, understanding the genetic and molecular basis of Cd stress between indica and japonica is highly important for rice improvement programs.
Results: In this study, two varieties of rice, japonica 02428 and indica CH891, were continuously exposed to Cd, and seedlings of the two varieties at two critical stages (the 3rd and 5th day) were selected for dynamic gene analysis by the transcriptome method. The results showed that CH891 was more sensitive to Cd than 02428, and a total of 7,204 and 6,670 differentially expressed genes (DEGs) associated with Cd stress were detected on the 3rd day and 5th day, respectively. Furthermore, we divided these DEGs into three categories: SCR (sensitive variety with Cd-responsive), RCR (resistant variety with Cd-responsive) and CCR (common Cd-responsive). The enriched metabolic pathway analysis of DEGs preferentially expressed in a stage-specific and cultivar-specific manner showed that secondary metabolic processes were enriched in SCR, while protein metabolism and plant hormones were enriched in RCR. The diverted metabolic pathways might be the major reason for the different response mechanisms of Cd in indica and japonica rice.
Conclusion: These results provide novel insights regarding the Cd response mechanism in rice seedlings between different varieties, and these important Cd-responsive DEGs were frequently involved in specific biological processes and metabolic pathways that might help to elucidate the mechanisms of the indica and japonica rice Cd response differences.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryTableS1S3.xlsx
Supplementary Table S1. FPKM expression of all detected genes. Supplementary Table S2. Quality evaluation of RNA-seq data. Supplementary Table S3. Primer sequences of qRT-PCR and the values of qRT-PCR and RNA-Seq.
- SupplementaryTableS1S3.xlsx
Supplementary Table S1. FPKM expression of all detected genes. Supplementary Table S2. Quality evaluation of RNA-seq data. Supplementary Table S3. Primer sequences of qRT-PCR and the values of qRT-PCR and RNA-Seq.
- SupplementaryTableS4.xlsx
Supplementary Table S4. The classification of three categories of DEGs at 3rd and 5th day and the ICR genes and the key DEGs enriched in the major pathways which were detected in the SCR3, RCR3, CCR3, SCR5, RCR5 and CCR5.And the common genes expressed at two stages in SCR, RCR and CCR
- SupplementaryTableS4.xlsx
Supplementary Table S4. The classification of three categories of DEGs at 3rd and 5th day and the ICR genes and the key DEGs enriched in the major pathways which were detected in the SCR3, RCR3, CCR3, SCR5, RCR5 and CCR5.And the common genes expressed at two stages in SCR, RCR and CCR
- SupplementaryFiguresS1S2.pdf
Supplementary Fig. S1. The KEGG term of DEGs in eight comparison group. (A) Cd3_CH891 vs Cd3_02428 (B) CK3_CH891 vs CK3_02428 (C) Cd3_CH891 vs CK3_CH891 (D) Cd3_02428 vs CK3_02428 (E) Cd5_CH891 vs Cd5_02428 (F) CK5_CH891 vs CK5_02428 (G) Cd5_CH891 vs CK5_CH891 (H) Cd5_02428 vs CK5_02428. Supplementary Fig. S2. The GO terms of ICR genes from SCR, RCR and CCR. (A) SCR3, (B) SCR5, (C) RCR3, (D) RCR5, (E) CCR3, (F) CCR5.
- SupplementaryFiguresS1S2.pdf
Supplementary Fig. S1. The KEGG term of DEGs in eight comparison group. (A) Cd3_CH891 vs Cd3_02428 (B) CK3_CH891 vs CK3_02428 (C) Cd3_CH891 vs CK3_CH891 (D) Cd3_02428 vs CK3_02428 (E) Cd5_CH891 vs Cd5_02428 (F) CK5_CH891 vs CK5_02428 (G) Cd5_CH891 vs CK5_CH891 (H) Cd5_02428 vs CK5_02428. Supplementary Fig. S2. The GO terms of ICR genes from SCR, RCR and CCR. (A) SCR3, (B) SCR5, (C) RCR3, (D) RCR5, (E) CCR3, (F) CCR5.
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