Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Comparison of Seedlings, Young Grafts and Adult Trees
2.2. Transcriptional Profiles of Seedlings, Young Grafts and Adult Trees
2.3. Global DNA Methylation Analysis of Seedlings, Young Grafts and Adult Trees
2.4. Classes of Genes Enriched with Differentially Methylated Regions (DMRs)
2.5. Relationship between DNA Methylation and Transcription
3. Discussion
3.1. Newly Grafted Plants Are at an Intermediate State between Adult Tree and Juvenile Seedling
3.2. DMRs Correlate with Neighboring Gene Transcription
4. Materials and Methods
4.1. Plant Material
4.2. Phenotyping
4.3. DNA and RNA Extraction
4.4. Bisulfite Sequencing and DMRs Calling
4.5. Microarray
4.6. Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) Microarray Validation
4.7. Differentially Expressed Transcript (DET) Analysis
4.8. Association between DMR and Differentially Transcribed Gene (DTG) or Differentially Transcribed Transposable Element (DTTE)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Old Graft vs. Seedling | Old Graft vs. Young Graft | |||||
---|---|---|---|---|---|---|
Context | Hypomethylated | Hypermethylated | ∑ | Hypomethylated | Hypermethylated | ∑ |
Number (%) | Number (%) | Number (%) | Number (%) | Number (%) | Number (%) | |
CHH | 93.784 (94,9) | 4998 (5,1) | 98.782 (99,3) | 27.945 (65,5) | 14.749 (34,5) | 42.694 (97,0) |
CHG | 22 (12,3) | 157 (87,7) | 179 (0,2) | 19 (4,9) | 370 (95,1) | 389 (0,9) |
CG | 78 (16,4) | 398 (83,6) | 476 (0,5) | 68 (7,4) | 850 (92,6) | 918 (2,1) |
∑ | 93.884 (94,4) | 5553 (5,6) | 99.437 | 28.032 (63,7) | 15.969 (36,3) | 44.001 |
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Perrin, A.; Daccord, N.; Roquis, D.; Celton, J.-M.; Vergne, E.; Bucher, E. Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees. Epigenomes 2020, 4, 4. https://doi.org/10.3390/epigenomes4010004
Perrin A, Daccord N, Roquis D, Celton J-M, Vergne E, Bucher E. Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees. Epigenomes. 2020; 4(1):4. https://doi.org/10.3390/epigenomes4010004
Chicago/Turabian StylePerrin, Adrien, Nicolas Daccord, David Roquis, Jean-Marc Celton, Emilie Vergne, and Etienne Bucher. 2020. "Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees" Epigenomes 4, no. 1: 4. https://doi.org/10.3390/epigenomes4010004