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Integrated Transcriptome and Proteome Analysis Reveals Complex Regulatory Mechanism of Cotton in Response to Salt Stress
Xiyan Yang
Huazhong Agricultural University: Huazhong Agriculture University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Soil salt stress seriously restricts the yield and quality of cotton worldwide. To investigate the molecular mechanism of cotton response to salt stress, a main cultivated variety Gossypium hirsutum L. acc. Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.
Results
Through transcriptome analysis of cotton treated with salt stress for 0 h (T0), 3 h (T3) and 12 h (T12), we identified 8,436, 11,628 and 6,311 differentially expressed genes (DEGs) inT3 / T0, T12 / T0 and T12 / T3, respectively. A total of 459 differentially expressed proteins (DEPs) were identified by proteomic analysis, of which 273, 99 and 260 DEPs were identified in T3 / T0, T12 / T0 and T12 / T3, respectively. Metabolic pathways, biosynthesis of secondary metabolites, photosynthesis and plant hormone signal transduction were the main enrichment pathways by annotation of DEGs or DEPs. Detail analysis of the DEGs or DEPs revealed that complex signal pathways, such as ABA and JA signal, calcium signal, MAPK signal cascade, transcription factors, followed by activation of antioxidant and ion transporters, were identified to participate in regulating salt response in cotton.
Conclusions
Our results not only contribute to understand the mechanism of cotton response to salt stress, but also provide nine candidate genes, which might be used for molecular breeding to improve salt-tolerance in cotton.
Keywords
Association analysis, Cotton, Proteome, Salt stress, Transcriptome
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- Additionalfile1.rar
Fig. S1 Description of Xinluzhong 54. a Cultivation area of Xinluzhong 54. b-c Plant phenotype of Xinluzhong 54 under 150mM and 250mM NaCl treatment, respectively. Fig. S2 Identification of differentially expressed genes (DEGs) in response to salt stress. a The number of DEGs on each chromosome. b qRT-PCR validation of transcript levels evaluated by RNA-Seq. Fig. S3 Functional enrichment analysis of DEGs. a Expression patterns and enrichment pathways of 1136 common DEGs. b KEGG analysis of up-regulated DEGs. c KEGG analysis of down-regulated DEGs. Fig. S4 Functional enrichment analysis of DEGs. a KEGG analysis of up-regulated DEPs. b KEGG analysis of down-regulated DEPs. Fig. S5 Expression patterns of differentially expressed proteins involved in photosynthesis and carbon catabolism. a-c stand for the expression patterns of DEPs involved in photosynthesis, glycolysis/ gluconeogenesis and TCA cycle, respectively. Fig. S6 Plant hormone signal pathways analysis. The expression changes of key node genes involved in different hormone signal pathway under salt stress treatment. Fig. S7 Transcription factors response to salt stress in cotton. a and b stand for the statistics of up-regulated and down-regulated transcription factors induced by salt stress, respectively. c The expression patterns of different transcription factors under salt stress treatment. Fig. S8 Potential protein interaction models through the STRING database. a Predicted CBL-CIPK protein interaction patterns. b Predicted MAPK signal cascade protein interaction patterns. Table S1 Primers used for qRT-PCR. Table S2 Transcriptome data statistics. Table S3 Statistics on the correlation between DEGs and DEPs. Table S4 Information of associated genes.
- Additionalfile1.rar
Fig. S1 Description of Xinluzhong 54. a Cultivation area of Xinluzhong 54. b-c Plant phenotype of Xinluzhong 54 under 150mM and 250mM NaCl treatment, respectively. Fig. S2 Identification of differentially expressed genes (DEGs) in response to salt stress. a The number of DEGs on each chromosome. b qRT-PCR validation of transcript levels evaluated by RNA-Seq. Fig. S3 Functional enrichment analysis of DEGs. a Expression patterns and enrichment pathways of 1136 common DEGs. b KEGG analysis of up-regulated DEGs. c KEGG analysis of down-regulated DEGs. Fig. S4 Functional enrichment analysis of DEGs. a KEGG analysis of up-regulated DEPs. b KEGG analysis of down-regulated DEPs. Fig. S5 Expression patterns of differentially expressed proteins involved in photosynthesis and carbon catabolism. a-c stand for the expression patterns of DEPs involved in photosynthesis, glycolysis/ gluconeogenesis and TCA cycle, respectively. Fig. S6 Plant hormone signal pathways analysis. The expression changes of key node genes involved in different hormone signal pathway under salt stress treatment. Fig. S7 Transcription factors response to salt stress in cotton. a and b stand for the statistics of up-regulated and down-regulated transcription factors induced by salt stress, respectively. c The expression patterns of different transcription factors under salt stress treatment. Fig. S8 Potential protein interaction models through the STRING database. a Predicted CBL-CIPK protein interaction patterns. b Predicted MAPK signal cascade protein interaction patterns. Table S1 Primers used for qRT-PCR. Table S2 Transcriptome data statistics. Table S3 Statistics on the correlation between DEGs and DEPs. Table S4 Information of associated genes.
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CURRENT STATUS: Under Review
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Posted 19 Nov, 2020
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Review #2 received
Received 17 Jan, 2021
Review #1 received
Received 13 Jan, 2021
Reviewer #2 agreed
On 03 Jan, 2021
Reviewer #1 agreed
On 31 Dec, 2020
Reviewers invited
Invitations sent on 09 Dec, 2020
Submission checks complete
On 17 Nov, 2020
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On 16 Nov, 2020
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Subject Areas
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This preprint is under consideration at Journal of Cotton Research. 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
Integrated Transcriptome and Proteome Analysis Reveals Complex Regulatory Mechanism of Cotton in Response to Salt Stress
Xiyan Yang
Huazhong Agricultural University: Huazhong Agriculture University
Corresponding Author
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 Review
Version 1
Posted 19 Nov, 2020
No community comments so far
Review #2 received
Received 17 Jan, 2021
Review #1 received
Received 13 Jan, 2021
Reviewer #2 agreed
On 03 Jan, 2021
Reviewer #1 agreed
On 31 Dec, 2020
Reviewers invited
Invitations sent on 09 Dec, 2020
Submission checks complete
On 17 Nov, 2020
Editor assigned
On 16 Nov, 2020
Editor invited
On 16 Nov, 2020
First submitted
On 12 Nov, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Agricultural Economics & Policy
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Soil salt stress seriously restricts the yield and quality of cotton worldwide. To investigate the molecular mechanism of cotton response to salt stress, a main cultivated variety Gossypium hirsutum L. acc. Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.
Results
Through transcriptome analysis of cotton treated with salt stress for 0 h (T0), 3 h (T3) and 12 h (T12), we identified 8,436, 11,628 and 6,311 differentially expressed genes (DEGs) inT3 / T0, T12 / T0 and T12 / T3, respectively. A total of 459 differentially expressed proteins (DEPs) were identified by proteomic analysis, of which 273, 99 and 260 DEPs were identified in T3 / T0, T12 / T0 and T12 / T3, respectively. Metabolic pathways, biosynthesis of secondary metabolites, photosynthesis and plant hormone signal transduction were the main enrichment pathways by annotation of DEGs or DEPs. Detail analysis of the DEGs or DEPs revealed that complex signal pathways, such as ABA and JA signal, calcium signal, MAPK signal cascade, transcription factors, followed by activation of antioxidant and ion transporters, were identified to participate in regulating salt response in cotton.
Conclusions
Our results not only contribute to understand the mechanism of cotton response to salt stress, but also provide nine candidate genes, which might be used for molecular breeding to improve salt-tolerance in cotton.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6