Tissue-Specific RNA-Seq Analysis of Cotton Roots’ Response to Compound Saline-Alkali Stress and the Functional Validation of the Key Gene GhERF2
Abstract
:1. Introduction
2. Results
2.1. Transcriptome Sequencing and Data Quality Assessment
2.2. Identification and Functional Enrichment Analysis of DEGs
2.3. Key DEG Screening and Functional Enrichment Investigation
2.4. Analysis of Key Pathways Related to Compound Salinze-Alkali Stress
2.5. Validation of RNA-Seq Data Using qRT-PCR Experiment
2.6. Expression Pattern Analysis of GhERF2 Under Compound Saline-Alkali Stress
2.7. Silencing of GhERF2 Reduces Cotton Tolerance to Saline-Alkali Stress
2.8. Physiological Characteristics of GhERF2-Silenced Cotton Plants
3. Discussion
3.1. Transcriptome Sequencing and Analysis
3.2. Role of Candidate Gene GhERF2 in Cotton’s Response to Compound Saline-Alkali Stress
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. RNA Extraction and Library Sequencing
4.3. Transcriptome Sequencing and Data Analysis
4.4. qRT-PCR Analyses of Gene Expression
4.5. Cloning of GhERF2 and Transient Transformation in Tobacco
4.6. Virus-Induced Gene Silencing (VIGS) Experiment
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Sample Name | Clean Reads | Clean Base | Read Length | Q20 (%) | GC (%) |
---|---|---|---|---|---|
NRCK1 | 24,013,230 | 7,203,969,000 | PE150 | 96.30 | 43.93 |
NRCK2 | 24,069,156 | 7,220,746,800 | PE150 | 96.56 | 43.98 |
NRCK3 | 24,102,895 | 7,230,868,500 | PE150 | 96.01 | 43.94 |
RCK1 | 23,546,010 | 7,063,803,000 | PE150 | 96.19 | 44.27 |
RCK2 | 24,006,143 | 7,201,842,900 | PE150 | 96.45 | 44.18 |
RCK3 | 24,115,835 | 7,234,750,500 | PE150 | 96.30 | 44.07 |
RS1 | 24,097,237 | 7,229,171,100 | PE150 | 96.53 | 44.43 |
RS2 | 24,130,131 | 7,239,039,300 | PE150 | 96.54 | 44.41 |
RS3 | 24,044,474 | 7,213,342,200 | PE150 | 96.59 | 44.49 |
NRS1 | 24,073,680 | 7,222,104,000 | PE150 | 96.58 | 44.70 |
NRS2 | 24,138,006 | 7,241,401,800 | PE150 | 96.72 | 44.73 |
NRS3 | 24,114,157 | 7,234,247,100 | PE150 | 96.62 | 44.67 |
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Zhang, A.; Liu, Q.; Du, X.; Xing, B.; Zhang, S.; Li, Y.; Hao, L.; Wei, Y.; Liu, Y.; Li, P.; et al. Tissue-Specific RNA-Seq Analysis of Cotton Roots’ Response to Compound Saline-Alkali Stress and the Functional Validation of the Key Gene GhERF2. Plants 2025, 14, 756. https://doi.org/10.3390/plants14050756
Zhang A, Liu Q, Du X, Xing B, Zhang S, Li Y, Hao L, Wei Y, Liu Y, Li P, et al. Tissue-Specific RNA-Seq Analysis of Cotton Roots’ Response to Compound Saline-Alkali Stress and the Functional Validation of the Key Gene GhERF2. Plants. 2025; 14(5):756. https://doi.org/10.3390/plants14050756
Chicago/Turabian StyleZhang, Aiming, Qiankun Liu, Xue Du, Baoguang Xing, Shaoliang Zhang, Yanfang Li, Liuan Hao, Yangyang Wei, Yuling Liu, Pengtao Li, and et al. 2025. "Tissue-Specific RNA-Seq Analysis of Cotton Roots’ Response to Compound Saline-Alkali Stress and the Functional Validation of the Key Gene GhERF2" Plants 14, no. 5: 756. https://doi.org/10.3390/plants14050756
APA StyleZhang, A., Liu, Q., Du, X., Xing, B., Zhang, S., Li, Y., Hao, L., Wei, Y., Liu, Y., Li, P., Hu, S., & Peng, R. (2025). Tissue-Specific RNA-Seq Analysis of Cotton Roots’ Response to Compound Saline-Alkali Stress and the Functional Validation of the Key Gene GhERF2. Plants, 14(5), 756. https://doi.org/10.3390/plants14050756