Transcriptome Analysis Reveals the Different Response to Toxic Stress in Rootstock Grafted and Non-Grafted Cucumber Seedlings
Abstract
:1. Introduction
2. Results
2.1. Plant Morphology and Biomass
2.2. Chlorophyll Contents and Gas Exchange Parameters
2.3. Summary Analysis of mRNA Sequencing
2.4. Identification of Differentially Expressed Genes (DEGs)
2.5. Functional Classifications of DEGs Response to Grafting
2.6. Functional Classifications of DEGs Response to CA Stress
2.7. DEGs Involved in Photosynthesis and Carbon Metabolism
2.8. Transcription Factors Encoded by DEGs
2.9. Validation of mRNA-Seq by qRT-PCR
3. Discussion
3.1. Overall Analysis of Gene Expression Based on RNA-seq
3.2. Discrepancy of Morphology and Photosynthesis between NG and RG Cucumber Seedlings
3.3. Carbon and Nitrogen Metabolism Analysis
3.4. Transcription Factor Analysis
4. Materials and Methods
4.1. Plant Materials and Cinnamic acid Treatments
4.2. Plant Morphology and Biomass
4.3. Leaf Photosynthesis
4.4. RNA-Seq Library Construction and Sequencing
4.5. Transcriptomic Analysis
4.6. Validation of mRNA-Seq by Quantitative Real-Time PCR (qRT-PCR)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Treatment | Plant Height (cm) | Stem Diameter (mm) | Leaves Area (cm2) | Shoot | Root | ||
---|---|---|---|---|---|---|---|
Fresh Weight (g) | Dry Weight (g) | Fresh Weight (g) | Dry Weight (g) | ||||
RG-CK | 14.67 ± 1.76 a | 7.96 ± 0.13 a | 432.81 ± 2.61 a | 12.13 ± 0.09 a | 1.11 ± 0.010 a | 2.54 ± 0.23 a | 0.13 ± 0.010 a |
RG-CA | 15.17 ± 1.04 a | 7.86 ± 0.25 a | 427.86 ± 10.44 a | 12.02 ± 0.17 a | 1.10 ± 0.021 a | 2.12 ± 0.16 a | 0.12 ± 0.012 a |
NG-CK | 14.17 ± 2.08 a | 7.75 ± 0.46 a | 420.68 ± 3.28 a | 9.83 ± 0.20 a | 0.73 ± 0.026 a | 1.82 ± 0.06 a | 0.07 ± 0.006 a |
NG-CA | 9.50 ± 0.50 b | 7.37 ± 0.25 a | 380.15 ± 5.72 b | 8.16 ± 0.22 b | 0.69 ± 0.017 a | 1.45 ± 0.07 b | 0.04 ± 0.006 b |
Sample Name | Raw Reads | Clean Reads | Total Mapped Ratio (%) | Unique Mapped Ratio (%) | Q30 Percentage (%) | Expressed Genes | Expressed Genes Ratio (% of Annotated Genes) |
---|---|---|---|---|---|---|---|
RG-CK-1 | 60065280 | 58347004 | 93.64% | 91.81% | 89.84 | 17434 | 74.99 |
RG-CK-2 | 52976972 | 51443526 | 93.71% | 91.92% | 90.03 | 17386 | 74.78 |
RG-CK-3 | 52288760 | 51039256 | 94.32% | 92.45% | 90.83 | 17453 | 75.07 |
RG-CA-1 | 46296420 | 45246686 | 93.23% | 91.53% | 88.34 | 17629 | 75.83 |
RG-CA-2 | 49512360 | 48120914 | 93.17% | 91.27% | 89.82 | 17564 | 75.55 |
RG-CA-3 | 48778530 | 47442262 | 92.92% | 90.96% | 90.11 | 17279 | 74.32 |
NG-CK-1 | 50039680 | 48367266 | 93.51% | 91.83% | 89.96 | 17686 | 76.08 |
NG-CK-2 | 59498560 | 58473188 | 94.13% | 92.32% | 90.53 | 17484 | 75.21 |
NG-CK-3 | 44090680 | 43071056 | 94.1% | 92.35% | 90.56 | 17430 | 74.97 |
NG-CA-1 | 48323566 | 47469736 | 93.98% | 92.28% | 90.43 | 17467 | 75.13 |
NG-CA-2 | 54922480 | 53952812 | 94.08% | 92.27% | 90.81 | 17626 | 75.82 |
NG-CA-3 | 50581658 | 49314228 | 94.35% | 92.58% | 90.72 | 17417 | 74.92 |
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Xiao, X.; Lv, J.; Xie, J.; Feng, Z.; Ma, N.; Li, J.; Yu, J.; Calderón-Urrea, A. Transcriptome Analysis Reveals the Different Response to Toxic Stress in Rootstock Grafted and Non-Grafted Cucumber Seedlings. Int. J. Mol. Sci. 2020, 21, 774. https://doi.org/10.3390/ijms21030774
Xiao X, Lv J, Xie J, Feng Z, Ma N, Li J, Yu J, Calderón-Urrea A. Transcriptome Analysis Reveals the Different Response to Toxic Stress in Rootstock Grafted and Non-Grafted Cucumber Seedlings. International Journal of Molecular Sciences. 2020; 21(3):774. https://doi.org/10.3390/ijms21030774
Chicago/Turabian StyleXiao, Xuemei, Jian Lv, Jianming Xie, Zhi Feng, Ning Ma, Ju Li, Jihua Yu, and Alejandro Calderón-Urrea. 2020. "Transcriptome Analysis Reveals the Different Response to Toxic Stress in Rootstock Grafted and Non-Grafted Cucumber Seedlings" International Journal of Molecular Sciences 21, no. 3: 774. https://doi.org/10.3390/ijms21030774