The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet
Abstract
:1. Introduction
2. Results
2.1. DNA Methylation Pattern of Sugar Beet
2.2. DNA Methylation Level Analysis of DY5CMS and DY5O
2.3. Verification of WGBS Sequencing Data by Bisulfite Conversion Method
2.4. Differential Methylation Genes (DMGs) Identification of DY5CMS and DY5O
2.5. GO Annotation and KEGG Enrichment Analysis of Sugar Beet DMGs
2.6. Analysis of the Relationship between DMGs’ Methylation and Expression Level’
3. Discussion
3.1. Related DMGs Involved in Carbohydrate and Energy Metabolism
3.2. Related DMGs Involved in Pollen Wall Development
3.3. Related DMGs with Transcriptional Regulation
3.4. DMGs Associated with Endogenous Hormones
4. Materials and Methods
4.1. Plant Materials
4.2. DNA Extraction and WGBS
4.3. WGBS Data Validation
4.4. Evaluation of Methylation Level at Site C
4.5. Differential Methylation Regions (DMRS) and Differential Methylation Genes (DMGS) Were Identified
4.6. GO and KEGG Enrichment Analysis of Differential Methylated Genes
4.7. qRT-PCR Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Clean Bases | Mapped Reads | Mapping Rate (%) | Average Depth (X) | Bisulfite Conversion Rate (%) |
---|---|---|---|---|---|
DY5O | 248,189,440 | 213,850,619 | 86.16 | 29.58 | 99.14 |
DY5CMS | 301,409,704 | 262,053,058 | 86.94 | 36.00 | 99.33 |
Background | Sample | Number of Methylated Cytosine | Mean Methylation Level (%) |
---|---|---|---|
C | DY5CMS | 53,612,497 | 27.32 |
DY5O | 51,332,141 | 27.18 | |
CG | DY5CMS | 14,155,733 | 80.43 |
DY5O | 14,101,006 | 79.96 | |
CHG | DY5CMS | 12,223,221 | 58.72 |
DY5O | 12,149,595 | 58.69 | |
CHH | DY5CMS | 27,233,543 | 12.42 |
DY5O | 25,081,540 | 12.28 |
Target Area | Sample | DNA Total Methylation Level (%) | mCG (%) | mCHG (%) | mCHH (%) |
---|---|---|---|---|---|
Chr7: 1,633,239–1,633,426 | CMS | 12 | 57.94 | 4.5 | 1 |
O | 13 | 62.05 | 36.46 | 20.45 | |
Chr3: 51,195,686–51,195,932 | CMS | 14 | 85.08 | 37.21 | 1.98 |
O | 10 | 69.42 | 0 | 2.02 | |
Chr1: 7,437,126–7,437,376 | CMS | 9 | 16.23 | 66.57 | 6.7 |
O | 5 | 3.05 | 6.27 | 6.23 |
Gene Name | Location | Methylation Status | Gene Annotation |
---|---|---|---|
BVRB_3g061680 | gene | Hypo | MADS-box transcription factor family protein |
BVRB_6g133580 | gene, prompter | Hypo | WRKY transcription factor family protein |
BVRB_2g032900 | promoter | Hyper | AP2/ERF and B3 domain-containing transcription factor family protein |
BVRB_2g047050 | gene | Hyper | NADH dehydrogenase |
BVRB_6g137940 | gene | Hyper | galacturonosyltransferase |
BVRB_003480 | gene | Hypo | UDP-Glycosyltransferase superfamily protein |
BVRB_004020 | gene, prompter | Hyper | pyruvate dehydrogenase E1 component subunit beta-3 |
BVRB_9g208010 | gene | Hyper | ABC transporter A family protein |
BVRB_4g073090 | gene | Hypo | ABC transporter G family protein |
BVRB_2g036570 | gene | Hypo | PPR superfamily protein |
BVRB_3g049380 | gene | Hypo | ACO family protein |
BVRB_7g172330 | promoter | Hypo | TDR transcription factor family protein |
Primer | Primer Sequence | Location | Length (bp) |
---|---|---|---|
Primer1 | F:TATTATTTTAAGGGATGGATGTTTTG | Chr7 | 228 |
R:ACTCCAAATTCACAACTATAACCTTCT | 1,633,303–1,633,462 | ||
Primer2 | F:TGGGTTGATTTAGGTTTATTTGAAT | Chr5 | 249 |
R:ACAAAAAATACATACCCCCTCAAT | 51,195,686–51,195,932 | ||
Primer3 | F:TGGGGTTAATAATTGTTAGTTTTAT | Chr1 | 249 |
R:TCACCACCCCATCTAAAATATATAC | 7,437,126–7,437,376 |
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Weng, J.; Wang, H.; Cheng, D.; Liu, T.; Zeng, D.; Dai, C.; Luo, C. The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet. Int. J. Mol. Sci. 2024, 25, 1118. https://doi.org/10.3390/ijms25021118
Weng J, Wang H, Cheng D, Liu T, Zeng D, Dai C, Luo C. The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet. International Journal of Molecular Sciences. 2024; 25(2):1118. https://doi.org/10.3390/ijms25021118
Chicago/Turabian StyleWeng, Jiamin, Hui Wang, Dayou Cheng, Tianjiao Liu, Deyong Zeng, Cuihong Dai, and Chengfei Luo. 2024. "The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet" International Journal of Molecular Sciences 25, no. 2: 1118. https://doi.org/10.3390/ijms25021118