Comparative Transcriptome Analysis Reveals Key Genes and Pathways Associated with Phosphate-Sensitive Behaviors in Cunninghamia lanceolata (Lamb.) Hook.
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Materials and Pi Treatment
2.2. Morphology Traits and Nutrient Analyses
2.3. Total RNA Extraction, Library Construction, and RNA-Seq
2.4. Construction of Module Genes Network and HUB Genes Identification
2.5. Quantitative Real-Time-PCR Analysis
3. Results
3.1. Evaluation of Clones with Different Phosphorus Efficiency Based on Morphological Changes during Pi-Deficiency Stress
3.2. Global Profiling and Functional Annotation of the Pi-Responsive Genes in Pi-Sensitive Clones
3.3. Analysis of the Gene Co-Expression Network and Selection of Hub Genes in Pi-Sensitive Clones
3.4. Gene-Specific Expression Analysis of Pi-Sensitive Clones
3.5. qRT-PCR Analysis of Chinese Fir Clone Genes
4. Discussion
4.1. Ethylene Played an Important Role in the Early Response to Pi-Deficiency Stress of Pi-Sensitive Clone
4.2. Pi-Deficiency Stress Suppressed the More Pi-Deficiency Response Genes Expression in Pi-Sensitive Clones than That in Pi-Tolerant Clones, Especially the Genes Involving in Plant Endogenous Hormone and ATP Synthase
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Trait | Source of Variation | ||
---|---|---|---|
Genotype | Pi Concentration | Genotype × Pi Concentration | |
Plantlets height increment | 8.76 ** | 9.77 ** | 0.32 |
Plantlets ground-diameter increment | 7.41 ** | 5.50 * | 0.11 |
Root dry mass | 6.63 ** | 8.34 ** | 1.59 |
Stem dry mass | 9.59 ** | 11.65 ** | 2.86 * |
Leaf dry mass | 9.12 ** | 8.88 ** | 1.64 |
Total dry mass | 10.19 ** | 13.82 ** | 2.08 |
Root-shoot ratio | 6.85 ** | 1.33 | 1.55 |
Total root length | 61.31 ** | 12.83 ** | 1.12 |
Total root surface area | 23.85 ** | 5.24 * | 0.42 |
Total root volume | 17.27 ** | 8.03 ** | 0.48 |
Average root diameter | 6.71 ** | 24.66 ** | 1.41 |
Leaf thickness | 11.24 ** | 2.68 | 3.40 * |
Leaf length | 9.96 ** | 6.25 * | 0.87 |
Leaf surface area | 8.84 ** | 8.26 ** | 3.01 * |
Leaf volume | 7.94 ** | 8.31 ** | 3.20 * |
Leaf mass per area | 5.90 ** | 8.15 ** | 0.41 |
Root P content | 2.52 * | 10.97 ** | 1.26 |
Total P content | 6.63 ** | 15.57 ** | 1.51 |
Total N content | 13.54 ** | 20.20 ** | 0.85 |
Total K content | 19.11 ** | 22.74 ** | 1.32 |
Total Ca content | 7.63 ** | 16.11 ** | 1.79 |
Total Mg content | 7.30 ** | 16.43 ** | 0.77 |
Root P utilization efficiency | 5.40 ** | 17.90 ** | 4.47 ** |
Total P utilization efficiency | 2.59 * | 4.69 * | 0.86 |
Gene Set | Total Number of DEGs | Up-Regulated | Down-Regulated |
---|---|---|---|
+Pc5 _vs._ −Pc5 | 8128 | 4048 | 4080 |
+Pc4 _vs._ −Pc4 | 48 | 22 | 26 |
+Pc5 _vs._+Pc4 | 4981 | 2692 | 2289 |
−Pc5 _vs._ −Pc4 | 8371 | 4114 | 4257 |
Gene Set | KEGG Category | Pathway ID | UP | Down | p-Value |
---|---|---|---|---|---|
+Pc4 _vs._ −Pc4 | Oxidative phosphorylation | ko00190 | 4 | 0.00013 | |
Photosynthesis | ko00195 | 2 | 0.00743 | ||
Diterpenoid biosynthesis | ko00904 | 1 | 0.04714 | ||
Zeatin biosynthesis | ko00908 | 1 | 0.01785 | ||
+Pc5 _vs._ −Pc5 | Endocytosis | ko04144 | 39 | 3.30 × 10−5 | |
Plant-pathogen interaction | ko04626 | 29 | 0.00024 | ||
Glycerophospholipid metabolism | ko00564 | 21 | 0.00041 | ||
alpha-Linolenic acid metabolism | ko00592 | 17 | 0.00043 | ||
Terpenoid backbone biosynthesis | ko00900 | 15 | 0.00049 | ||
Plant hormone signal transduction | ko04075 | 52 | 0.00018 | ||
Cutin, suberine and wax biosynthesis | ko00073 | 11 | 0.00031 | ||
Other glycan degradation | ko00511 | 10 | 0.00034 | ||
Starch and sucrose metabolism | ko00500 | 51 | 0.00067 | ||
Carotenoid biosynthesis | ko00906 | 14 | 0.00084 |
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Wei, R.; Hu, D.; Chen, J.; Zheng, H.; Shi, J. Comparative Transcriptome Analysis Reveals Key Genes and Pathways Associated with Phosphate-Sensitive Behaviors in Cunninghamia lanceolata (Lamb.) Hook. Forests 2023, 14, 1203. https://doi.org/10.3390/f14061203
Wei R, Hu D, Chen J, Zheng H, Shi J. Comparative Transcriptome Analysis Reveals Key Genes and Pathways Associated with Phosphate-Sensitive Behaviors in Cunninghamia lanceolata (Lamb.) Hook. Forests. 2023; 14(6):1203. https://doi.org/10.3390/f14061203
Chicago/Turabian StyleWei, Ruping, Dehuo Hu, Jinhui Chen, Huiquan Zheng, and Jisen Shi. 2023. "Comparative Transcriptome Analysis Reveals Key Genes and Pathways Associated with Phosphate-Sensitive Behaviors in Cunninghamia lanceolata (Lamb.) Hook." Forests 14, no. 6: 1203. https://doi.org/10.3390/f14061203
APA StyleWei, R., Hu, D., Chen, J., Zheng, H., & Shi, J. (2023). Comparative Transcriptome Analysis Reveals Key Genes and Pathways Associated with Phosphate-Sensitive Behaviors in Cunninghamia lanceolata (Lamb.) Hook. Forests, 14(6), 1203. https://doi.org/10.3390/f14061203