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Research article
Shibin Gao
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, 611130, Sichuan, Chengdu, China
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7184-580X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.
Results: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen and low-nitrogen conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability. An association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN resistance-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521.
Conclusions: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize regarding LN-responsive resistance.
Keywords
maize, nitrogen use efficiency, RNA-Seq, genome-wide association study, lncRNA, co-expression
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This is a list of supplementary files associated with this preprint. Click to download.
- FigureS1.pdf
Fig. S1. The volcano plot of differentially expressed mRNAs (a, b), TUCPs (c, d) and miRNAs (e, f) between two nitrogen conditions in leaf and root.
- FigureS1.pdf
Fig. S1. The volcano plot of differentially expressed mRNAs (a, b), TUCPs (c, d) and miRNAs (e, f) between two nitrogen conditions in leaf and root.
- FigureS2.pdf
Fig. S2. The TPM (Transcripts per million) (a) and length distribution of 18- to 30-nt small RNAs (b). The concentrated length distribution with the peak at 24-nt accounting for 19.77%, 17.3%, 21.6%, 8.8%, 10.47%, 11.64%, 20.44%, 16.14%, 16.91%, 16.19%, 17.06% and 15.18% in the 12 libraries respectively.
- FigureS2.pdf
Fig. S2. The TPM (Transcripts per million) (a) and length distribution of 18- to 30-nt small RNAs (b). The concentrated length distribution with the peak at 24-nt accounting for 19.77%, 17.3%, 21.6%, 8.8%, 10.47%, 11.64%, 20.44%, 16.14%, 16.91%, 16.19%, 17.06% and 15.18% in the 12 libraries respectively.
- FigureS3.pdf
Fig. S3. Expression profiles of mRNA and miRNA during seedling under HN and LN conditions. Cluster heat map of all mRNAs (a) and miRNAs (c) expression in leaf and root. VEEN analysis of differentially expressed mRNAs (b) and miRNAs (d).
- FigureS3.pdf
Fig. S3. Expression profiles of mRNA and miRNA during seedling under HN and LN conditions. Cluster heat map of all mRNAs (a) and miRNAs (c) expression in leaf and root. VEEN analysis of differentially expressed mRNAs (b) and miRNAs (d).
- FigureS4.pdf
Fig. S4. Characteristics of lncRNAs identified in maize seedling under LN condition.
- FigureS4.pdf
Fig. S4. Characteristics of lncRNAs identified in maize seedling under LN condition.
- FigureS5.pdf
Fig. S5. Functional analysis of the LN-responsive lncRNAs. The enriched Kyoto Encyclopedia of Genes (KEGG) pathways in leaf (a, c) and root (b, d).
- FigureS5.pdf
Fig. S5. Functional analysis of the LN-responsive lncRNAs. The enriched Kyoto Encyclopedia of Genes (KEGG) pathways in leaf (a, c) and root (b, d).
- FigureS6.pdf
Fig. S6. Combing with RNA-seq and GWAS data, 45 and 232 consistent candidate genes were detected in root and leaf under LN condition (a) and LNTI (b).
- FigureS6.pdf
Fig. S6. Combing with RNA-seq and GWAS data, 45 and 232 consistent candidate genes were detected in root and leaf under LN condition (a) and LNTI (b).
- SupportingTable1.xlsx
Table S1. Known miRNAs and novel miRNAs identified from RNA-Seq.
- SupportingTable1.xlsx
Table S1. Known miRNAs and novel miRNAs identified from RNA-Seq.
- SupportingTable10.xlsx
Table S10. The information of primer sequences used in this study.
- SupportingTable10.xlsx
Table S10. The information of primer sequences used in this study.
- SupportingTable11.xlsx
Table S11. Trait abbreviation and description collected by manually and WinRizo.
- SupportingTable11.xlsx
Table S11. Trait abbreviation and description collected by manually and WinRizo.
- SupportingTable2.xlsx
Table S2. The targets of lncRNAs predicted by co-location and co-expression.
- SupportingTable2.xlsx
Table S2. The targets of lncRNAs predicted by co-location and co-expression.
- SupportingTable3.xlsx
Table S3. LncRNA-mRNA pairs of cis-acting.
- SupportingTable3.xlsx
Table S3. LncRNA-mRNA pairs of cis-acting.
- SupportingTable4.xlsx
Table S4. LncRNA-mRNA pairs of trans-acting.
- SupportingTable4.xlsx
Table S4. LncRNA-mRNA pairs of trans-acting.
- SupportingTable5.xlsx
Table S5. The GO analysis of lncRNAs.
- SupportingTable5.xlsx
Table S5. The GO analysis of lncRNAs.
- SupportingTable6.xlsx
Table S6. The KEGG analysis of lncRNAs.
- SupportingTable6.xlsx
Table S6. The KEGG analysis of lncRNAs.
- SupportingTable7.xlsx
Table S7. The candidate genes identified by GWAS and RNA-Seq.
- SupportingTable7.xlsx
Table S7. The candidate genes identified by GWAS and RNA-Seq.
- SupportingTable8.xlsx
Table S8. Pearson (r) correlations between all 17 traits.
- SupportingTable8.xlsx
Table S8. Pearson (r) correlations between all 17 traits.
- SupportingTable9.xlsx
Table S9. The targets of lncRNAs contained significant SNPs for multiple root traits.
- SupportingTable9.xlsx
Table S9. The targets of lncRNAs contained significant SNPs for multiple root traits.
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View the published article at BMC Plant Biology.
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On 20 Nov, 2020
Reviewer #1 agreed
On 18 Nov, 2020
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
See the published version of this preprint at BMC Plant Biology.
This is a preprint, 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
Shibin Gao
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, 611130, Sichuan, Chengdu, China
Corresponding Author
ORCiD: https://orcid.org/0000-0001-7184-580X
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
View the published article at BMC Plant Biology.
Version 1
Posted 13 Nov, 2020
No community comments so far
Editorial decision: Major revision
On 24 Dec, 2020
Review #4 received
Received 20 Dec, 2020
Review #2 received
Received 20 Dec, 2020
Reviewer #4 agreed
On 03 Dec, 2020
Review #3 received
Received 02 Dec, 2020
Review #1 received
Received 02 Dec, 2020
Reviewer #3 agreed
On 26 Nov, 2020
Reviewer #2 agreed
On 20 Nov, 2020
Reviewer #1 agreed
On 18 Nov, 2020
Reviewers invited
Invitations sent on 09 Nov, 2020
Editor assigned
On 04 Nov, 2020
Submission checks complete
On 04 Nov, 2020
Editor invited
On 04 Nov, 2020
First submitted
On 18 Oct, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Plant Biology.
Background: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.
Results: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen and low-nitrogen conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability. An association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN resistance-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521.
Conclusions: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize regarding LN-responsive resistance.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
Figure 7
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- FigureS1.pdf
Fig. S1. The volcano plot of differentially expressed mRNAs (a, b), TUCPs (c, d) and miRNAs (e, f) between two nitrogen conditions in leaf and root.
- FigureS1.pdf
Fig. S1. The volcano plot of differentially expressed mRNAs (a, b), TUCPs (c, d) and miRNAs (e, f) between two nitrogen conditions in leaf and root.
- FigureS2.pdf
Fig. S2. The TPM (Transcripts per million) (a) and length distribution of 18- to 30-nt small RNAs (b). The concentrated length distribution with the peak at 24-nt accounting for 19.77%, 17.3%, 21.6%, 8.8%, 10.47%, 11.64%, 20.44%, 16.14%, 16.91%, 16.19%, 17.06% and 15.18% in the 12 libraries respectively.
- FigureS2.pdf
Fig. S2. The TPM (Transcripts per million) (a) and length distribution of 18- to 30-nt small RNAs (b). The concentrated length distribution with the peak at 24-nt accounting for 19.77%, 17.3%, 21.6%, 8.8%, 10.47%, 11.64%, 20.44%, 16.14%, 16.91%, 16.19%, 17.06% and 15.18% in the 12 libraries respectively.
- FigureS3.pdf
Fig. S3. Expression profiles of mRNA and miRNA during seedling under HN and LN conditions. Cluster heat map of all mRNAs (a) and miRNAs (c) expression in leaf and root. VEEN analysis of differentially expressed mRNAs (b) and miRNAs (d).
- FigureS3.pdf
Fig. S3. Expression profiles of mRNA and miRNA during seedling under HN and LN conditions. Cluster heat map of all mRNAs (a) and miRNAs (c) expression in leaf and root. VEEN analysis of differentially expressed mRNAs (b) and miRNAs (d).
- FigureS4.pdf
Fig. S4. Characteristics of lncRNAs identified in maize seedling under LN condition.
- FigureS4.pdf
Fig. S4. Characteristics of lncRNAs identified in maize seedling under LN condition.
- FigureS5.pdf
Fig. S5. Functional analysis of the LN-responsive lncRNAs. The enriched Kyoto Encyclopedia of Genes (KEGG) pathways in leaf (a, c) and root (b, d).
- FigureS5.pdf
Fig. S5. Functional analysis of the LN-responsive lncRNAs. The enriched Kyoto Encyclopedia of Genes (KEGG) pathways in leaf (a, c) and root (b, d).
- FigureS6.pdf
Fig. S6. Combing with RNA-seq and GWAS data, 45 and 232 consistent candidate genes were detected in root and leaf under LN condition (a) and LNTI (b).
- FigureS6.pdf
Fig. S6. Combing with RNA-seq and GWAS data, 45 and 232 consistent candidate genes were detected in root and leaf under LN condition (a) and LNTI (b).
- SupportingTable1.xlsx
Table S1. Known miRNAs and novel miRNAs identified from RNA-Seq.
- SupportingTable1.xlsx
Table S1. Known miRNAs and novel miRNAs identified from RNA-Seq.
- SupportingTable10.xlsx
Table S10. The information of primer sequences used in this study.
- SupportingTable10.xlsx
Table S10. The information of primer sequences used in this study.
- SupportingTable11.xlsx
Table S11. Trait abbreviation and description collected by manually and WinRizo.
- SupportingTable11.xlsx
Table S11. Trait abbreviation and description collected by manually and WinRizo.
- SupportingTable2.xlsx
Table S2. The targets of lncRNAs predicted by co-location and co-expression.
- SupportingTable2.xlsx
Table S2. The targets of lncRNAs predicted by co-location and co-expression.
- SupportingTable3.xlsx
Table S3. LncRNA-mRNA pairs of cis-acting.
- SupportingTable3.xlsx
Table S3. LncRNA-mRNA pairs of cis-acting.
- SupportingTable4.xlsx
Table S4. LncRNA-mRNA pairs of trans-acting.
- SupportingTable4.xlsx
Table S4. LncRNA-mRNA pairs of trans-acting.
- SupportingTable5.xlsx
Table S5. The GO analysis of lncRNAs.
- SupportingTable5.xlsx
Table S5. The GO analysis of lncRNAs.
- SupportingTable6.xlsx
Table S6. The KEGG analysis of lncRNAs.
- SupportingTable6.xlsx
Table S6. The KEGG analysis of lncRNAs.
- SupportingTable7.xlsx
Table S7. The candidate genes identified by GWAS and RNA-Seq.
- SupportingTable7.xlsx
Table S7. The candidate genes identified by GWAS and RNA-Seq.
- SupportingTable8.xlsx
Table S8. Pearson (r) correlations between all 17 traits.
- SupportingTable8.xlsx
Table S8. Pearson (r) correlations between all 17 traits.
- SupportingTable9.xlsx
Table S9. The targets of lncRNAs contained significant SNPs for multiple root traits.
- SupportingTable9.xlsx
Table S9. The targets of lncRNAs contained significant SNPs for multiple root traits.
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