Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars
Abstract
:1. Introduction
2. Results
2.1. Total ATPase Activity and Total Amino Acid and Soluble Sugar Contents
2.2. MicroRNAs Profiling Response to Salinity Stress
2.3. Identification of Known and Novel miRNAs
2.4. Evolutionary Conservation Analysis of Known miRNAs Families
2.5. Identification of miRNAs Related to Salt Stress
2.6. Validation of Targets mRNA and miRNA with qRT-PCR
2.7. Prediction of Target Genes and Their Associated Regulatory Pathways
3. Discussion
3.1. Effect of Salinity on Total ATPase Activity, Total Amino Acids and Soluble Sugar Contents
3.2. tae-miR156, tae-miR160 and tae-miR171a/b May Confer Salt Tolerance in Roots of Suntop
3.3. miR319/PCF5 Module May Regulate Salt Tolerance in Suntop
3.4. miR159a-b, and miR9657 May Regulate Salt Tolerance in Suntop
3.5. Novel miRNAs Exclusively Expressed in Suntop
4. Materials and Methods
4.1. Plant Materials and Experimental Design
4.2. Determination of Total Soluble Sugars
4.3. Determination of Total Amino Acids Contents and ATPase Activity
4.4. Small RNA Library Construction and High Throughput Sequencing
4.5. Data Pre-Processing and De Novo Assembly
4.6. Differential Expression of Salinity-Responsive miRNAs
4.7. Target Gene Prediction and GO and KEGG Enrichment Analysis
4.8. mRNAs and miRNAs Validation by qRT-PCR
4.9. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Library Type | Suntop | Suntop | Sunmate | Sunmate |
---|---|---|---|---|
Control | NaCl | Control | NaCl | |
Total raw reads | 29,114,838.5 | 28,580,752.5 | 28,973,938.5 | 29,753,197 |
Total clean reads | 27,175,593.5 | 26,292,555 | 25,900,067 | 25,819,464 |
Clean tag (%) | 95.08 | 90.31 | 89.39 | 86.77 |
Q20 of clean tag (%) | 99.20 | 99 | 99.30 | 99.30 |
Mapped reads | 24,908,414 (91.66%) | 24,352,075.5 (92.62%) | 24,230,503.5 (93.55%) | 22,175,264 (85.89%) |
Total miRNAs reads | 4,180,023 | 5,014,878.5 | 5,127,462.5 | 5,644,374.5 |
Known miRNAs reads | 529,287 | 452,384.5 | 627,551 | 242,607 |
Novel miRNAs reads | 3,650,736 | 4,562,494 | 4,499,911.5 | 5,401,767.5 |
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Zeeshan, M.; Qiu, C.-W.; Naz, S.; Cao, F.; Wu, F. Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars. Int. J. Mol. Sci. 2021, 22, 12556. https://doi.org/10.3390/ijms222212556
Zeeshan M, Qiu C-W, Naz S, Cao F, Wu F. Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars. International Journal of Molecular Sciences. 2021; 22(22):12556. https://doi.org/10.3390/ijms222212556
Chicago/Turabian StyleZeeshan, Muhammad, Cheng-Wei Qiu, Shama Naz, Fangbin Cao, and Feibo Wu. 2021. "Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars" International Journal of Molecular Sciences 22, no. 22: 12556. https://doi.org/10.3390/ijms222212556