Physiological, Cytological, and Transcriptomic Analysis of Magnesium Protoporphyrin IX Methyltransferase Mutant Reveal Complex Genetic Regulatory Network Linking Chlorophyll Synthesis and Chloroplast Development in Rice
Abstract
:1. Introduction
2. Results
2.1. Alteration of Pigment Contents and Chloroplast Structure in the Chlm Mutant
2.2. Hormone Changes in the Chlm Mutant
2.3. Transcriptomic Alterations in Chlm Mutant
2.4. Analysis of Differentially Expressed Genes (DEGs)
2.5. Functional Analysis of DEGs
2.6. Functional Interaction Network of DEGs
2.7. Genes Regulating Chlorophyll and Carotenoid Metabolism Were Identified in the Chlm Mutant
2.8. Genes Regulating Chloroplast Development Were Identified in the Chlm Mutant
2.9. Genes Regulating Hormone Regulatory Pathways Were Identified in the Chlm Mutant
2.10. Genes Regulating Signal Pathways Were Identified in the Chlm Mutant
2.11. Transcription Factors Were Identified in the Chlm Mutant
2.12. Verification by qRT-PCR of Some DEGs
3. Discussion
3.1. Chlorophyll Metabolism Were Regulated by the ChlM Gene
3.2. Chloroplast Development Was Regulated by the ChlM Gene
3.3. JA, SA and IAA May Play an Important Role in the Regulation Process of ChlM Gene to Chlorophyll Synthesis and Chloroplast Development
3.4. Signal Pathways May Play an Important Role in the Regulation Process of ChlM Gene to Chlorophyll Synthesis and Chloroplast Development
3.5. Transcription Regulation May Play an Important Role in the Regulation Process of ChlM Gene to Chlorophyll Synthesis and Chloroplast Development
3.6. Possible Patterns for the Involvement of the ChlM Gene in the Retrograde Signaling Pathway
4. Materials and Methods
4.1. Plant Material and Sample Collection
4.2. Determination of Chlorophyll and Hormone Contents
4.3. Transmission Electron Microscopic Observation
4.4. RNA Extraction and Preparation of cDNA Library
4.5. Illumina Deep Sequencing and Data Analysis
4.6. Identification and Functional Enrichment Analysis of Differentially Expressed Genes
4.7. Quantitative Real-Time PCR (qRT-PCR) Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
ChlM | Magnesium protoporphyrin IX methyltransferase |
MgP | Magnesium protoporphyrin IX |
MgPME | Magnesium protoporphyrin IX methyl ester |
WT | Wild type |
JA | Jasmonic acid |
SA | Salicylic acid |
IAA | Indole acetic acid |
ABA | Abscisic acid |
DEGs | Differentially expressed genes |
FPKM | Fragments Per Kilobase of transcript per Million fragments mapped |
FDR | False discovery rate |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
PPI | Protein–protein interaction |
qRT-PCR | Quantitative real-time PCR |
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Samples | WT-1 | WT-2 | WT-3 | chlm-1 | chlm-2 | chlm-3 |
---|---|---|---|---|---|---|
Total reads | 56,640,244 | 44,565,826 | 43,136,908 | 44,053,700 | 40,418,298 | 40,776,152 |
Clean reads | 28,320,122 | 22,282,913 | 21,568,454 | 22,026,850 | 20,209,149 | 20,388,076 |
Clean bases | 8,411,102,720 | 6,636,988,544 | 6,420,743,624 | 6,551,792,242 | 6,010,508,590 | 6,071,105,796 |
Q20 (%) | 93.3 | 93.29 | 93.22 | 93.22 | 93.3 | 93.24 |
Q30 (%) | 85.18 | 85.11 | 85.06 | 85.07 | 85.12 | 85.06 |
GC (%) | 54.56 | 54.59 | 54.85 | 55.14 | 54.67 | 54.74 |
Total mapped | 86.94% | 86.94% | 86.91% | 86.72% | 86.94% | 87.15% |
Uniquely mapped | 83.56% | 83.42% | 83.93% | 82.61% | 83.68% | 83.49% |
Multiple mapped | 3.38% | 3.52% | 2.98% | 4.10% | 3.26% | 3.66% |
MSU-ID | Gene Name | Description | Expression Patterns | Reference |
---|---|---|---|---|
Chlorophyll metabolism | ||||
LOC_Os02g02860 | OsGluRS; Cde1(t) | Glutamyl tRNA synthetase | up | [19] |
LOC_Os04g52130 | RLIN1; LLM1 | Coproporphyrinogen III oxidase | up | [5] |
LOC_Os03g59640 | OsChlD; ygl3 | Magnesium chelatase D subunit | up | [8] |
LOC_Os03g27770 | OsHO2; OsYLC2 | Heme oxygenase | up | [20] |
LOC_Os06g24730 | OsNYC3 | Alpha/beta fold hydrolase family protein | down | [21] |
Chloroplast development | ||||
LOC_Os04g51280 | WSP1; OsMORF2 | Multiple organellar RNA editing factor | up | [22] |
LOC_Os08g29110 | OsTrxZ; wp2 | Subunit of PEP (plastid-encoded RNA polymerase) in chloroplasts | up | [23,24] |
LOC_Os01g63220 | WLP2; OsFLN1 | Plastid-encoded RNA polymerase associated protein | up | [25] |
LOC_Os05g49920 | OsPPR6 | Triangular pentapeptide repeat protein | up | [26] |
LOC_Os08g09270 | CDE4 | A pentapeptide repeat protein | up | [27] |
LOC_Os11g01210 | etl1 | Etiolation gene | up | [28] |
LOC_Os12g01210 | etl2 | Etiolation gene | up | [28] |
LOC_Os10g32540 | WSL3 | Non-core subunit of plastid-encoded RNA polymerase | up | [29] |
LOC_Os03g45400 | OsNUS1 | Plastid protein | up | [30] |
LOC_Os01g54540 | WLP1 | A chloroplast ribosome L13 protein | up | [31] |
LOC_Os02g15900 | ASL2 | A plastid 50S ribosomal protein L21 | up | [32] |
LOC_Os07g06940 | OsValRS2 | Val-tRNA synthetase | up | [33] |
LOC_Os07g47300 | ObgC | A spo0B-associated GTP binding protein | up | [34] |
LOC_Os02g38210 | EF-Tu | Translation elongation factor | up | [35] |
LOC_Os02g05890 | YL1 | A nucleus encoded chloroplast protein | up | [36] |
LOC_Os03g03990 | OscpSRP43 | A chloroplast signal recognition particle 43 | up | [37] |
LOC_Os11g05552 | YGL138(t) | Putative signal recognition particle 54 kDa protein | up | [38] |
LOC_Os03g31150 | AL1 | The sole octotricopeptide repeat protein | up | [39] |
LOC_Os02g01440 | OsNOA1 | Nitric oxide synthesis-related protein | up | [40] |
LOC_Os03g29810 | VYL | A chloroplast protein | up | [41] |
LOC_Os03g45710 | OsFd1 | Ferredoxin | up | [42] |
LOC_Os03g48040 | OsFdC2 | Ferredoxin-like protein | up | [43] |
LOC_Os05g40180 | OsSTN8 | Serine/threonine protein kinase | up | [44] |
LOC_Os06g14620 | RNRS1 | A small subunit of ribonucleotide reductase | up | [45] |
LOC_Os09g21250 | YLC1 | A DUF3353 superfamily gene | up | [46] |
LOC_Os12g36194 | WSL12 | Nucleoside diphosphate kinase 2 | up | [47] |
Hormone regulatory pathways | ||||
LOC_Os06g20920 | OsJMT | Jasmonic acid carboxyl methyltransferase gene | up | [48] |
LOC_Os05g01140 | OsJMT | Jasmonic acid carboxyl methyltransferase | down | [49] |
Signal pathway | ||||
LOC_Os03g03990 | OscpSRP43 | A chloroplast signal recognition particle 43 | up | [37] |
LOC_Os11g05552 | YGL138(t) | Putative signal recognition particle 54 kDa protein | up | [38] |
LOC_Os05g40180 | OsSTN8 | Serine/threonine protein kinase | up | [44] |
LOC_Os12g36194 | WSL12 | Nucleoside diphosphate kinase 2 | up | [47] |
Transcription factor | ||||
LOC_Os06g05350 | OsWHY1 | WHIRLY family transcription factor | up | [50] |
LOC_Os02g12790 | OsCGA1 | GATA family transcription factor | up | [51,52] |
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Yao, Y.; Zhang, H.; Guo, R.; Fan, J.; Liu, S.; Liao, J.; Huang, Y.; Wang, Z. Physiological, Cytological, and Transcriptomic Analysis of Magnesium Protoporphyrin IX Methyltransferase Mutant Reveal Complex Genetic Regulatory Network Linking Chlorophyll Synthesis and Chloroplast Development in Rice. Plants 2023, 12, 3785. https://doi.org/10.3390/plants12213785
Yao Y, Zhang H, Guo R, Fan J, Liu S, Liao J, Huang Y, Wang Z. Physiological, Cytological, and Transcriptomic Analysis of Magnesium Protoporphyrin IX Methyltransferase Mutant Reveal Complex Genetic Regulatory Network Linking Chlorophyll Synthesis and Chloroplast Development in Rice. Plants. 2023; 12(21):3785. https://doi.org/10.3390/plants12213785
Chicago/Turabian StyleYao, Youming, Hongyu Zhang, Rong Guo, Jiangmin Fan, Siyi Liu, Jianglin Liao, Yingjin Huang, and Zhaohai Wang. 2023. "Physiological, Cytological, and Transcriptomic Analysis of Magnesium Protoporphyrin IX Methyltransferase Mutant Reveal Complex Genetic Regulatory Network Linking Chlorophyll Synthesis and Chloroplast Development in Rice" Plants 12, no. 21: 3785. https://doi.org/10.3390/plants12213785