Dissecting the Regulatory Network of Maize Phase Change in ZmEPC1 Mutant by Transcriptome Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Growth Condition
2.2. Total RNA Isolation and Transcriptome Analysis
2.3. Construction of Regulatory Network in Flowering Stage
2.4. Real-Time qPCR Is Used for Gene Expression Validation
2.5. Statistical Analysis
3. Results
3.1. Phenotypic Alterations of ZmEPC1 Mutant
3.2. Identification of Differentially Expressed Genes
3.3. GO Enrichment Analysis
3.4. KEGG Enrichment Analysis
3.5. Regulatory Network Analysis
3.6. Expression Analysis of Key DEGs
3.7. Expression Analysis of Flowering Time, JA Synthesis, JA Signaling Related Genes and miR156-SPLs
4. Discussion
4.1. ZmEPC1 Is Involved in the Regulation of Maize Developmental Phase Transition
4.2. ZmEPC1 Acts on Phytohormones Signaling Pathway
4.3. Potential Regulatory Mechanism of ZmEPC1 in Developmental Phase Changes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene ID | ZmEPC1 | WT | Log2 Fold Change | Padj | Gene Annotation |
---|---|---|---|---|---|
Zm00001d051093 | 22,414.51 | 0.00 | 16.94 | 2.19 × 10−61 | LRR receptor-like serine/threonine-protein kinase EFR |
Zm00001d050775 | 1391.30 | 0.00 | 12.93 | 7.77 × 10−37 | NADPH-dependent pterin aldehyde reductase |
Zm00001d046835 | 3674.84 | 649.25 | 2.50 | 2.54 × 10−25 | rpo2; RNA polymerase2: single copy |
Zm00001d028548 | 7236.83 | 1342.14 | 2.43 | 2.35 × 10−21 | maternal effect embryo arrest 59 |
Zm00001d051121 | 804.76 | 83.37 | 3.27 | 2.48 × 10−21 | RmlC-like cupins superfamily protein |
Zm00001d005189 | 190.04 | 2.14 | 6.33 | 6.24 × 10−21 | Cadmium/zinc-transporting ATPase HMA2 |
Zm00001d021755 | 821.63 | 122.28 | 2.75 | 4.09 × 10−20 | UDP-glycosyltransferase 88A1 |
Zm00001d037609 | 712.52 | 140.90 | 2.34 | 5.18 × 10−19 | GDSL esterase/lipase |
Zm00001d021419 | 1240.23 | 4.16 | 8.20 | 3.93 × 10−17 | Nicotinate-nucleotide pyrophosphorylase [carboxylating] chloroplastic |
Zm00001d008845 | 2557.67 | 34.49 | 6.21 | 4.25 × 10−17 | Pre-mRNA-processing-splicing factor 8A |
Zm00001d039437 | 4271.64 | 727.03 | 2.55 | 2.83 × 10−16 | dbb3; double B-box zinc finger protein3: similar to Arabidopsis light-regulated zinc finger protein 1 |
Zm00001d026190 | 953.45 | 177.84 | 2.42 | 7.27 × 10−16 | DeSI-like protein |
Zm00001d034515 | 1881.73 | 266.75 | 2.82 | 8.41 × 10−16 | Homeobox-DDT domain protein RLT3 |
Zm00001d011183 | 112,478.99 | 18,093.87 | 2.64 | 9.36 × 10−16 | thi1; thiamine biosynthesis1: low copy |
Zm00001d051088 | 184.50 | 0.00 | 10.02 | 1.93 × 10−15 | Putative leucine-rich repeat receptor-like protein kinase family protein |
Zm00001d011643 | 371.05 | 38.84 | 3.25 | 2.00 × 10−15 | Putative leucine-rich repeat receptor-like protein kinase family protein |
Zm00001d019269 | 731.46 | 77.18 | 3.25 | 2.59 × 10−15 | Pentatricopeptide repeat-containing protein |
Zm00001d011927 | 688.27 | 151.24 | 2.19 | 4.50 × 10−15 | Phospholipid/glycerol acyltransferase family protein |
Zm00001d009180 | 2249.54 | 34.74 | 6.02 | 5.03 × 10−15 | Folate-biopterin transporter 1 chloroplastic |
Zm00001d002181 | 8050.18 | 43.95 | 7.52 | 1.52 × 10−14 | G-type lectin S-receptor-like serine/threonine-protein kinase B120 |
Zm00001d003811 | 217.64 | 1.86 | 6.84 | 2.13 × 10−14 | Two-component response regulator-like APRR1 |
Zm00001d006081 | 1093.69 | 38.92 | 4.81 | 2.80 × 10−14 | Pleckstrin homology (PH) domain superfamily protein |
Zm00001d016674 | 3864.89 | 662.37 | 2.54 | 5.21 × 10−14 | Heat shock factor protein 2 |
Zm00001d047256 | 1355.16 | 28.39 | 5.58 | 5.22 × 10−14 | Protein kinase domain superfamily protein |
Zm00001d007340 | 105.04 | 9.27 | 3.51 | 6.62 × 10−14 | ADP-ribosylation factor GTPase-activating protein AGD12 |
Zm00001d010200 | 475.70 | 73.10 | 2.70 | 9.45 × 10−14 | ATP binding protein |
Zm00001d019668 | 543.90 | 19.24 | 4.83 | 2.58 × 10−13 | P-loop containing nucleoside triphosphate hydrolases superfamily protein |
Zm00001d043050 | 1292.41 | 233.74 | 2.47 | 2.70 × 10−13 | RING-H2 finger protein ATL74 |
Zm00001d045276 | 233.19 | 54.10 | 2.11 | 4.34 × 10−13 | Lactoylglutathione lyase/glyoxalase I family protein |
Zm00001d020915 | 5139.10 | 596.47 | 3.11 | 4.45 × 10−13 | Pirin-like protein 2 |
Zm00001d004573 | 19.69 | 1264.00 | −5.98 | 1.70 × 10−113 | 60 kDa jasmonate-induced protein |
Zm00001d015327 | 1181.74 | 91,543.55 | −6.28 | 6.72 × 10−69 | ubi1; ubiquitin1: genomic sequence |
Zm00001d035570 | 185.35 | 5360.00 | −4.85 | 1.00 × 10−66 | α/β-Hydrolases superfamily protein |
Zm00001d050837 | 338.61 | 18,172.00 | −5.75 | 1.63 × 10−66 | Gibberellin receptor GID1L2 |
Zm00001d010627 | 18.94 | 1873.88 | −6.62 | 5.24 × 10−66 | Protein LURP-one-related 8 |
Zm00001d004248 | 1.81 | 5168.05 | −11.55 | 4.66 × 10−40 | UDP-glycosyltransferase 85A7 |
Zm00001d021961 | 265.56 | 1601.37 | −2.59 | 6.62 × 10−40 | α-L-fucosidase 3 |
Zm00001d026271 | 806.06 | 20,462.16 | −4.67 | 4.35 × 10−39 | Putative AP2/EREBP transcription factor superfamily protein |
Zm00001d009808 | 2.72 | 479.37 | −7.56 | 3.00 × 10−38 | Probable galacturonosyltransferase 7 |
Zm00001d021881 | 2069.86 | 15,095.67 | −2.87 | 9.70 × 10−36 | Root border cell-specific protein |
Zm00001d033139 | 17.39 | 803.40 | −5.53 | 7.63 × 10−35 | Cytochrome P450 71D7 |
Zm00001d011923 | 244.42 | 1037.29 | −2.08 | 8.32 × 10−33 | BTB/POZ domain-containing protein |
Zm00001d007079 | 558.49 | 4887.17 | −3.13 | 8.37 × 10−33 | Phospholipase A2 family protein |
Zm00001d029940 | 14.07 | 1216.41 | −6.43 | 1.30 × 10−30 | Ethylene-responsive transcription factor ERF105 |
Zm00001d022395 | 8199.81 | 47,204.65 | −2.53 | 1.09 × 10−29 | Rhythmically expressed protein |
Zm00001d051056 | 22,281.59 | 105,340.39 | −2.24 | 1.41 × 10−29 | S-adenosylmethionine decarboxylase proenzyme |
Zm00001d039524 | 121.19 | 26,122.74 | −7.75 | 1.85 × 10−29 | Transposon protein CACTA%2C En/Spm sub-class |
Zm00001d014007 | 234.22 | 8122.34 | −5.12 | 2.19 × 10−29 | senescence regulator |
Zm00001d040289 | 14.74 | 220.77 | −3.88 | 3.27 × 10−28 | DUF4378 domain protein |
Zm00001d021665 | 195.07 | 10,587.20 | −5.76 | 5.32 × 10−28 | PRAS-rich protein |
Zm00001d010676 | 30.35 | 1108.32 | −5.19 | 6.00 × 10−28 | Ethylene-responsive transcription factor 12 |
Zm00001d040784 | 2035.80 | 11,391.05 | −2.48 | 6.40 × 10−28 | Glycine-rich domain-containing protein 1 |
Zm00001d000339 | 423.35 | 13,472.84 | −4.99 | 1.46 × 10−27 | Putative AP2/EREBP transcription factor superfamily protein ereb92 |
Zm00001d035587 | 0.00 | 2416.06 | −13.94 | 2.15 × 10−27 | Putative S-locus receptor-like protein kinase family protein |
Zm00001d051018 | 2320.48 | 10,694.66 | −2.20 | 2.46 × 10−27 | dbb4; double B-box zinc finger protein4: |
Zm00001d016017 | 0.00 | 201.76 | −24.66 | 4.42 × 10−27 | Protein disulfide isomerase-like 1–2 |
Zm00001d004334 | 2.70 | 207.13 | −6.23 | 7.24 × 10−27 | ATG8-interacting protein 1 |
Zm00001d013208 | 272.99 | 3432.28 | −3.65 | 3.45 × 10−26 | Zinc finger protein AZF2 |
Zm00001d049364 | 85.17 | 4635.09 | −5.77 | 7.57 × 10−26 | Ethylene-responsive transcription factor |
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Li, X.; Li, W.; Li, N.; Tian, R.; Qi, F.; Meng, J.; Jiang, Y.; Wang, C.; Chen, Y.; Guo, Z.; et al. Dissecting the Regulatory Network of Maize Phase Change in ZmEPC1 Mutant by Transcriptome Analysis. Genes 2022, 13, 1713. https://doi.org/10.3390/genes13101713
Li X, Li W, Li N, Tian R, Qi F, Meng J, Jiang Y, Wang C, Chen Y, Guo Z, et al. Dissecting the Regulatory Network of Maize Phase Change in ZmEPC1 Mutant by Transcriptome Analysis. Genes. 2022; 13(10):1713. https://doi.org/10.3390/genes13101713
Chicago/Turabian StyleLi, Xiaoqi, Weiya Li, Na Li, Runmiao Tian, Feiyan Qi, Juan Meng, Yajuan Jiang, Chenhui Wang, Yongqiang Chen, Zhanyong Guo, and et al. 2022. "Dissecting the Regulatory Network of Maize Phase Change in ZmEPC1 Mutant by Transcriptome Analysis" Genes 13, no. 10: 1713. https://doi.org/10.3390/genes13101713
APA StyleLi, X., Li, W., Li, N., Tian, R., Qi, F., Meng, J., Jiang, Y., Wang, C., Chen, Y., Guo, Z., Tang, J., & Zhang, Z. (2022). Dissecting the Regulatory Network of Maize Phase Change in ZmEPC1 Mutant by Transcriptome Analysis. Genes, 13(10), 1713. https://doi.org/10.3390/genes13101713