Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots
Abstract
:1. Introduction
2. Results
2.1. Identification of lncRNAs in Maize Roots at Seedling Stage
2.2. Drought Induced lncRNAs in Maize Roots Showed Strong Specificity in Expression
2.3. LncRNAs in Maize Roots Respond to Drought Stress
2.4. Differences in Epigenetic Modifications between lncRNA Genes and Coding Genes
2.5. Regulatory Networks of the lncRNA–mRNA and lncRNA-miRNA-circRNA/mRNA
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. Libraries Construction and RNA Sequencing
5.2. Identification of LncRNAs
5.3. Transcriptome Annotation and Expression Calculation
5.4. qRT-PCR
5.5. Differential Expression Analysis
5.6. LncRNA Expression Pattern Analysis
5.7. MeDIP-seq
5.8. M6A-seq
5.9. ChIP-seq
5.10. Phenotypic Data Collection
5.11. Construction of the lncRNA Based Maize Root Co-Expression Network in Response to Drought Stress
5.12. Construction of the lncRNA/circRNA-miRNA-mRNA Network
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Total * | Sign (α = 0.05) | Coding Genes | LncRNA Genes | χ2 Test (cd–ncd) | |
---|---|---|---|---|---|
Up | 107,350 | 63,005 | 60,196 (21.4%) | 2809 (38.9%) | p < 0.001 |
Down | 139,224 | 87,181 | 83,537 (29.8%) | 3644 (50.5%) | p < 0.001 |
Equal | 432,610 | 137,687 | 136,920 (48.8%) | 767 (10.6%) | p < 0.001 |
Total * | 679,184 | 287,873 | 280,653 | 7220 | |
χ2-test (Up–Down) | p < 0.001 | p < 0.001 |
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Tang, X.; Li, Q.; Feng, X.; Yang, B.; Zhong, X.; Zhou, Y.; Wang, Q.; Mao, Y.; Xie, W.; Liu, T.; et al. Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots. Int. J. Mol. Sci. 2023, 24, 15039. https://doi.org/10.3390/ijms242015039
Tang X, Li Q, Feng X, Yang B, Zhong X, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, et al. Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots. International Journal of Molecular Sciences. 2023; 24(20):15039. https://doi.org/10.3390/ijms242015039
Chicago/Turabian StyleTang, Xin, Qimeng Li, Xiaoju Feng, Bo Yang, Xiu Zhong, Yang Zhou, Qi Wang, Yan Mao, Wubin Xie, Tianhong Liu, and et al. 2023. "Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots" International Journal of Molecular Sciences 24, no. 20: 15039. https://doi.org/10.3390/ijms242015039