Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)
Abstract
:1. Introduction
2. Results
2.1. Phenotypic and Physiological Analyses of Foxtail Millet under Drought Stress and Rehydration
2.2. Overview of Transcriptome Sequencing and Differential Expression Genes Responding to Drought Stress
2.3. Transcriptomics Analysis Revealed Complex Mechanisms Involved in Drought Response in Foxtail Millet
2.4. Drought-Responsive Genes Are Mainly Related to Photosynthesis, Signal Transduction and TFs
2.5. Some of DEGs after Re-Watering Different in Roots and Leaves
2.6. Changes of SiP5CS Expression Increase Proline Content and Drought Tolerance
3. Discussion
4. Materials and Methods
4.1. Plants and Experimental Design
4.2. Measurement of Relative Water Content
4.3. Assessment of Antioxidant Enzymesactivities, P5CS Activity and Proline and Malondialdehyde Content
4.4. RNA Extraction, cDNA Library Construction and Sequencing
4.5. RNA-seq Data Analysis and Functional Annotation
4.6. RT-qPCR Validation of DEGs
4.7. Subcellular Localization of SiP5CS2
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Data Availability Statement
Abbreviations
ABA | Abscisic acid |
AP2/ERF | APETALA2/Ethylene responsive factor |
bHLH | Basic helix-loop-helix |
bZIP | Basic region leucine zipper |
CAT | Catalase |
CK | Control |
D | Drought |
DEGs | Differentially expressed genes |
DREB | Dehydration responsive element binding protein |
ERF | Ethylene responsive factor |
FDR | False discovery rate |
GFP | Green fluorescent protein |
GO | Gene ontology |
HD-Zip | Homeodomain-leucine zipper |
KEGG | the Kyoto Encyclopedia of Genes and Genomes |
LWC | Leaf water content |
MYB | v-myb avian myeloblastosis viral oncogene homolog |
NAC | NAM/ATAF1/2/CUC1/2 |
POD | Peroxidase |
R | Rehydration |
RPKM | Reads per kb per million reads |
SOD | Superoxide dismutase |
TF | Transcription factor |
WUE | Water use efficiency |
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Leaves | Roots | |||||
---|---|---|---|---|---|---|
Sample Name | LCK | LD | LR | RCK | RD | RR |
Total reads | 60224561 | 57522977 | 66828528 | 43141689 | 44366653 | 48433784 |
Total mapped | 58424526 (97.00%) | 55680409 (96.81%) | 64842416 (97.02%) | 40677294 (94.28%) | 42250499 (95.22%) | 45618663 (94.26%) |
Uniquely mapped | 57107274 (94.82%) | 53658224 (93.28%) | 63175538 (94.54%) | 39536790 (91.64%) | 42587443 (93.09%) | 44445300 (91.84%) |
Multiple mapped | 1317252 (2.19%) | 2022185 (3.53%) | 1666878 (2.49%) | 1140504 (2.64%) | 944568 (2.14%) | 1173363 (2.42%) |
Reads mapped to ‘+’ | 28529557 (47.37%) | 26802873 (46.59%) | 31558786 (47.23%) | 19754833 (45.79%) | 20635877 (46.51%) | 22204397 (45.88%) |
Reads mapped to ‘−’ | 28577717 (47.45%) | 26855350 (46.68%) | 31616752 (47.31%) | 19781957 (45.85%) | 20670055 (46.58%) | 22240903 (45.96%) |
Non-spliced reads | 34533551 (57.33%) | 32164993 (55.92%) | 38000455 (56.85%) | 26139840 (60.56%) | 27001368 (60.84%) | 29114060 (60.25%) |
Spliced reads | 22573723 (37.49%) | 21493230 (37.36%) | 25175083 (37.69%) | 13396950 (31.08%) | 14304564 (32.24%) | 15331240 (31.58%) |
Comparison | DEGs | Upregulated | Downregulated |
---|---|---|---|
LCK-LD | 4202 | 1652 | 2550 |
LCK-LR | 3266 | 2164 | 1102 |
LD-LR | 5049 | 3287 | 1762 |
RCK-RD | 6374 | 2751 | 3623 |
RCK-RR | 4152 | 2050 | 2102 |
RD-RR | 4020 | 2391 | 1629 |
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Qin, L.; Chen, E.; Li, F.; Yu, X.; Liu, Z.; Yang, Y.; Wang, R.; Zhang, H.; Wang, H.; Liu, B.; et al. Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.). Int. J. Mol. Sci. 2020, 21, 8520. https://doi.org/10.3390/ijms21228520
Qin L, Chen E, Li F, Yu X, Liu Z, Yang Y, Wang R, Zhang H, Wang H, Liu B, et al. Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.). International Journal of Molecular Sciences. 2020; 21(22):8520. https://doi.org/10.3390/ijms21228520
Chicago/Turabian StyleQin, Ling, Erying Chen, Feifei Li, Xiao Yu, Zhenyu Liu, Yanbing Yang, Runfeng Wang, Huawen Zhang, Hailian Wang, Bin Liu, and et al. 2020. "Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)" International Journal of Molecular Sciences 21, no. 22: 8520. https://doi.org/10.3390/ijms21228520
APA StyleQin, L., Chen, E., Li, F., Yu, X., Liu, Z., Yang, Y., Wang, R., Zhang, H., Wang, H., Liu, B., Guan, Y., & Ruan, Y. (2020). Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.). International Journal of Molecular Sciences, 21(22), 8520. https://doi.org/10.3390/ijms21228520