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Research article
Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain
Guanghui Chen
Hunan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1743-138X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
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 4,535 DEGs and 70 miRNAs between the two cultivars. Most genes related 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
RNA-seq, Cadmium, Panicle node, Node I, Low cadmium accumulation
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Published
On 06 Feb, 2020
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On 25 Dec, 2019
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Editorial decision: Major revision
On 25 Oct, 2019
Review #1 received
Received 19 Oct, 2019
Review #2 received
Received 15 Oct, 2019
Reviewer #2 agreed
On 08 Oct, 2019
Reviewer #1 agreed
On 06 Oct, 2019
Reviewers invited
Invitations sent on 03 Oct, 2019
Submission checks complete
On 03 Sep, 2019
Editor assigned
On 28 Aug, 2019
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On 27 Aug, 2019
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Subject Areas
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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
Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain
Guanghui Chen
Hunan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1743-138X
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: Published
Version 4
Posted 14 Jan, 2020
Published
On 06 Feb, 2020
No community comments so far
Submission checks complete
On 10 Jan, 2020
Editorial decision: Accept
On 09 Jan, 2020
No comments provided
Editorial decision: Minor revision
On 03 Jan, 2020
Editor assigned
On 26 Dec, 2019
Submission checks complete
On 25 Dec, 2019
Editor invited
On 25 Dec, 2019
No comments provided
Editorial decision: Major revision
On 18 Dec, 2019
Review #2 received
Received 16 Dec, 2019
Reviewer #2 agreed
On 05 Dec, 2019
Review #1 received
Received 05 Dec, 2019
Reviewers invited
Invitations sent on 04 Dec, 2019
Reviewer #1 agreed
On 04 Dec, 2019
Editor assigned
On 01 Dec, 2019
Submission checks complete
On 30 Nov, 2019
Editor invited
On 30 Nov, 2019
No comments provided
Editorial decision: Major revision
On 25 Oct, 2019
Review #1 received
Received 19 Oct, 2019
Review #2 received
Received 15 Oct, 2019
Reviewer #2 agreed
On 08 Oct, 2019
Reviewer #1 agreed
On 06 Oct, 2019
Reviewers invited
Invitations sent on 03 Oct, 2019
Submission checks complete
On 03 Sep, 2019
Editor assigned
On 28 Aug, 2019
First submitted
On 27 Aug, 2019
Editor invited
On 27 Aug, 2019
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
View the published version at BMC Genomics.
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 4,535 DEGs and 70 miRNAs between the two cultivars. Most genes related 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.
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