Genome-Wide Analysis of a TaLEA-Introduced Transgenic Populus simonii × Populus nigra Dwarf Mutant
Abstract
:1. Introduction
2. Results and Discussion
2.1. Characterization of the Dwf1 Mutant
2.2. Analyses of T-DNA Flanking Sequences
2.3. Genome-Wide mRNA Expression Analysis in the Dwf1 Mutant
2.4. Functional Classification of Differentially Expressed Genes
2.5. Biological Pathway Analyses According to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
2.6. Genes Related to Plant Hormones
2.7. Transcription Factors with Differential Expression Patterns
2.8. Transcript Profile Analysis of the Plant Hormones Related Genes and Transcript Factors in Other Transgenic Lines by Using Digital Gene Expression Method
3. Experimental Section
3.1. Plant Materials and Transgene
3.2. RNA Isolation and cDNA Synthesis
3.3. Quantitative Real-Time PCR
3.4. DNA Isolation and Identification of T-DNA Insertion Site
3.5. Affymetrix Microarray Analysis Experiment and Microarrays Data Analysis
3.6. DGE Analysis
3.7. Chlorophyll Content
4. Conclusions
Supplementary Information
ijms-13-02744-s001.pdfAcknowledgments
References
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Transgenic Line | Chlorophyll Content (SPAD) | Leaf Area (cm2) | Length/Width | Root Length (cm) |
---|---|---|---|---|
WT | 32.14 ± 4.04 a | 43.79 ± 13.21 a | 1.11 ± 0.14 a | 4.08 ± 0.35 a |
XL-5 | 32.66 ± 3.71 a | 42.27 ± 9.22 a | 1.05 ± 0.13 a | 4.10 ± 0.47 a |
XL-6 | 31.53 ± 5.74 a | 29.85 ± 5.71 b | 1.04 ± 0.13 a | 4.17 ± 0.41 a |
dwf1 | 37.15 ± 4.24 b | 39.54 ± 10.49 a | 0.90 ± 0.08 b | 1.95 ± 0.51 b |
Border Sequence | Start | Stop | Description | |
---|---|---|---|---|
Right border | T-DNA insertion sit | 10,569,359 bp | 10,570,141 bp | Chr IV |
region displayed | 10,566,600 bp | 10,573,600 bp | no putative genes | |
Left border | T-DNA insertion sit | 7,459,761 bp | 7,460,314 bp | Chr VIII |
region displayed | 7,456,200 bp | 7,463,200 bp | putative AP2 transcription factor |
Probe Set ID | Description | Fold Change (dwf1/WT) |
---|---|---|
Receptors Related | ||
PtpAffx.225074.1.S1_at | Receptor-related protein kinase-like | 13.8804 |
PtpAffx.75698.1.A1_at | Receptor-like serine/threonine kinase | 10.9634 |
PtpAffx.35408.1.S1_at | BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, putative | 7.4219 |
PtpAffx.224953.1.S1_x_at | Leucine-rich repeat receptor-like protein kinase 1 | 5.951 |
PtpAffx.18756.1.S1_a_at | Receptor serine/threonine kinase, putative | 5.1724 |
Ptp.1239.2.S1_at | Vacuolar sorting receptor, putative | 4.4382 |
PtpAffx.223006.1.S1_s_at | leucine-rich repeat receptor-like protein kinase | 4.2346 |
PtpAffx.225656.1.S1_at | Receptor-like protein kinase homolog RK20-1 | 3.9744 |
PtpAffx.225480.1.S1_at | (Receptor Like Protein 19); kinase/ protein binding | 3.9717 |
PtpAffx.26522.1.S1_at | Stress-induced receptor-like kinase | 3.329 |
PtpAffx.48409.1.S1_at | BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor | 2.8082 |
PtpAffx.225585.1.S1_at | Receptor-like protein kinase 4, putative (RLK4) | 2.3771 |
PtpAffx.50721.1.A1_s_at | Receptor serine-threonine protein kinase, putative | 0.3798 |
PtpAffx.222905.1.S1_s_at | Leucine-rich repeat receptor-like protein kinase | 0.3393 |
PtpAffx.200885.1.S1_x_at | F-box family protein | 0.4794 |
PtpAffx.200885.1.S1_at | F-box family protein | 0.4765 |
PtpAffx.45694.1.S1_at | F-box family protein | 0.3875 |
PtpAffx.125908.1.A1_at | F-box protein family | 2.2595 |
Cytochrome P450 genes | ||
PtpAffx.225317.1.S1_at | Cytochrome P450-like | 7.2083 |
PtpAffx.224780.1.S1_s_at | Putative cytochrome P450 | 3.1479 |
PtpAffx.225200.1.S1_at | Cytochrome P450 family protein | 2.6336 |
PtpAffx.124621.1.S1_s_at | Cytochrome P450 | 2.3608 |
Ptp.2894.1.A1_at | Cytochrome P450 | 2.1906 |
PtpAffx.203255.1.S1_s_at | Cytochrome P450, putative | 0.4878 |
PtpAffx.220980.1.S1_s_at | Cytochrome P450 82C1-soybean | 0.4874 |
Ptp.962.1.S1_s_at | Cytochrome P450 monooxygenase CYP77A3v2 | 0.4822 |
PtpAffx.209025.1.S1_at | Putative cytochrome P450 | 0.4497 |
PtpAffx.224872.1.S1_s_at | Cytochrome P450 | 0.3524 |
PtpAffx.158051.1.A1_at | Cytochrome P450 | 0.2578 |
Ubiquitins | ||
PtpAffx.20179.1.A1_at | Ubiquitin | 2.3644 |
PtpAffx.20179.3.A1_at | Ubiquitin | 2.3096 |
PtpAffx.20179.2.S1_at | Ubiquitin | 2.0378 |
Ptp.7320.1.S1_a_at | Ubiquitin, putative | 2.0015 |
PtpAffx.2814.1.A1_at | Ubiquitin-protein ligase, putative | 0.4885 |
Ptp.3476.1.S1_s_at | Ubiquitin | 0.4401 |
PtpAffx.113991.1.A1_at | E2 ubiquitin-conjugating enzyme UBC10 | 0.4293 |
Plant hormone response genes | ||
PtpAffx.113518.1.S1_at | Dormancy/auxin associated protein-related | 3.2637 |
PtpAffx.218532.1.S1_s_at | Auxin-responsive GH3 family protein | 2.3382 |
PtpAffx.72392.1.A1_at | GH3 family protein | 2.2979 |
Ptp.128.1.S1_at | Aux/IAA protein | 0.4928 |
PtpAffx.123395.1.S1_at | Auxin-induced protein | 0.4888 |
PtpAffx.204268.1.S1_at | Auxin-induced protein 15A | 0.4348 |
PtpAffx.39778.1.A1_at | Aux/IAA protein | 0.4174 |
Ptp.127.1.S1_s_at | Aux/IAA protein | 0.4027 |
Probe Set ID | Description | Fold Change (dwf1/WT) |
---|---|---|
PtpAffx.37401.1.A1_s_at | Basic-leucine zipper (bZIP) transcription factor | 18.4804 |
PtpAffx.107622.1.A1_at | WRKY transcription factor, putative | 17.1165 |
PtpAffx.205219.1.S1_at | WRKY family transcription factor | 11.0952 |
PtpAffx.211278.1.S1_at | WRKY family transcription factor | 10.6904 |
Ptp.5995.1.S1_at | WRKY transcription factor, putative | 5.4609 |
PtpAffx.101694.1.A1_at | WRKY transcription factor, putative | 2.6628 |
PtpAffx.5224.1.A1_at | WRKY transcription factor 2 | 2.551 |
PtpAffx.22176.1.A1_at | Transcriptional factor B3 | 2.4954 |
PtpAffx.26228.1.S1_at | AP2/ERF domain-containing transcription factor | 2.4415 |
PtpAffx.37783.1.A1_s_at | WRKY transcription factor, putative | 2.4322 |
PtpAffx.10330.2.S1_a_at | putative zinc finger (B-box type) family protein | 2.4221 |
PtpAffx.202579.1.S1_x_at | myb family transcription factor (MYB114) | 2.4031 |
PtpAffx.16157.1.S1_s_at | Transcription factor GT-3b | 2.3955 |
Ptp.4550.1.S1_at | Transcription factor LHY | 2.3908 |
PtpAffx.132628.1.S1_s_at | Putative WRKY transcription factor 30 | 2.2339 |
PtpAffx.34370.1.S1_at | Transcription factor, putative | 2.1851 |
PtpAffx.221169.1.S1_at | Transcriptional factor B3 family protein | 2.1293 |
PtpAffx.214377.1.S1_s_at | AP2-like ethylene-responsive transcription factor | 2.1219 |
PtpAffx.219808.1.S1_at | Homeodomain transcription factor ATHB-51 | 2.1169 |
PtpAffx.152367.1.S1_s_at | WRKY transcription factor, putative | 2.0796 |
PtpAffx.34524.3.A1_a_at | AP2 domain-containing transcription factor | 2.0643 |
PtpAffx.200385.1.S1_at | Ethylene-responsive transcription factor CRF2 | 2.0245 |
PtpAffx.1802.2.S1_at | Heat shock transcription factor (HSF) | 2.0112 |
PtpAffx.147430.1.A1_at | AP2/ERF domain-containing transcription factor | 0.4931 |
PtpAffx.200077.1.S1_s_at | AP2-like ethylene-responsive transcription factor | 0.4527 |
PtpAffx.68429.2.S1_at | WRKY transcription factor, putative | 0.4489 |
Probe Set ID | Fold Change (microarrays) dwf1/WT | Fold Change (DGE) | ||
---|---|---|---|---|
XL-5/WT | XL-6/WT | dwf1/WT | ||
Hormones related | ||||
PtpAffx.35408.1.S1_at | 7.4219 | 1.02 | 1.07 | 13.81 |
PtpAffx.223006.1.S1_s_at | 4.2346 | 1.34 | 1.76 | 3.49 |
PtpAffx.222905.1.S1_s_at | 0.3393 | 1.34 | 1.06 | 0.66 |
PtpAffx.200885.1.S1_x_at | 0.4794 | 1.02 | 0.98 | 0.87 |
PtpAffx.200885.1.S1_at | 0.4765 | 0.81 | 0.78 | 0.32 |
PtpAffx.45694.1.S1_at | 0.3875 | 1.21 | 1.34 | 0.65 |
PtpAffx.224780.1.S1_s_at | 3.1479 | 0.82 | 1.21 | 4.51 |
PtpAffx.225317.1.S1_at | 7.2083 | 0.91 | 0.75 | 5.55 |
PtpAffx.20179.1.A1_at | 2.3644 | 1.71 | 1.52 | 3.12 |
Ptp.127.1.S1_s_at | 0.4027 | 1.02 | 1.31 | 0.22 |
PtpAffx.34524.3.A1_a_at | 2.0643 | 1.77 | 0.95 | 3.09 |
PtpAffx.5224.1.A1_at | 2.551 | 1.55 | 1.78 | 1.87 |
PtpAffx.200077.1.S1_s_at | 0.4527 | 1.57 | 1.88 | 0.58 |
PtpAffx.214377.1.S1_s_at | 2.1219 | 0.53 | 0.78 | 4.59 |
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Yuan, H.-M.; Chen, S.; Lin, L.; Wei, R.; Li, H.-Y.; Liu, G.-F.; Jiang, J. Genome-Wide Analysis of a TaLEA-Introduced Transgenic Populus simonii × Populus nigra Dwarf Mutant. Int. J. Mol. Sci. 2012, 13, 2744-2762. https://doi.org/10.3390/ijms13032744
Yuan H-M, Chen S, Lin L, Wei R, Li H-Y, Liu G-F, Jiang J. Genome-Wide Analysis of a TaLEA-Introduced Transgenic Populus simonii × Populus nigra Dwarf Mutant. International Journal of Molecular Sciences. 2012; 13(3):2744-2762. https://doi.org/10.3390/ijms13032744
Chicago/Turabian StyleYuan, Hong-Mei, Su Chen, Lin Lin, Rui Wei, Hui-Yu Li, Gui-Feng Liu, and Jing Jiang. 2012. "Genome-Wide Analysis of a TaLEA-Introduced Transgenic Populus simonii × Populus nigra Dwarf Mutant" International Journal of Molecular Sciences 13, no. 3: 2744-2762. https://doi.org/10.3390/ijms13032744