Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection
Abstract
:1. Introduction
2. Results and Discussions
2.1. Plant Morphology and Fungal Quantification
2.2. Production of Antioxidant Enzymes in Maize Shoots in Response to F. verticillioides Inoculation
2.3. Determining Differential Expression between Control and Infected Maize Shoots Using RNA-Sequencing
2.4. Gene Ontology Enrichment Analysis Reveals Possible F. verticillioides Induced Response Mechanisms in Maize
2.5. Comparing DEGs Against a Different Maize Line Infected with F. verticillioides
2.6. Validation of RNA-Sequencing by Quantitative Real-Time PCR
2.7. Analysis of Phytoalexin Accumulation
3. Conclusions
4. Materials and Methods
4.1. Fungi
4.2. Plant Growth, Inoculations and Morphology
4.3. RNA Extraction and RNA-Sequencing
4.4. RNA-Sequencing and Data Analysis
4.4.1. Analysis Using Protocol 1
4.4.2. Analysis Using Protocol 2
4.5. Gene Ontology Analysis Using agriGO
4.6. cDNA Synthesis and Quantitative Real-Time PCR
4.7. Phytoalexin Accumulation
4.8. Antioxidant Assays
4.8.1. Catalase (CAT, EC 1.11.1.6)
4.8.2. Glutathione Reductase (GR, EC 1.6.4.2)
4.9. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene Stable ID | Average Log2 Fold-Change | Ensembl/NCBI Gene Description | ¥ Enriched GO-Term |
---|---|---|---|
GRMZM2G049538 | 4.56 | Acyclic sesquiterpene synthase/ent-Kaurene synthase B | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G119975 | 3.98 | Uncharacterised LOC103646336 | |
GRMZM2G029219 | 3.45 | Carbohydrate transporter/sugar porter/transporter | |
GRMZM5G874955 | 3.33 | Uncharacterised protein | |
GRMZM2G062724 | 3.27 | Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G026922 | 3.27 | Hypothetical protein | |
GRMZM2G117971 | 3.25 | Uncharacterised protein | |
GRMZM2G087875 | 3.20 | Putative cytochrome P450 superfamily protein; Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G143139 | 3.17 | N/A | |
GRMZM2G149422 | 3.07 | Hypothetical protein | |
GRMZM2G154523 | 3.06 | Patatin T5; Uncharacterised protein | |
GRMZM2G098346 | 3.04 | Alcohol dehydrogenase 2 | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM5G892675 | 3.01 | Uncharacterised protein | |
GRMZM2G137861 | 2.99 | Wall-associated receptor kinase 2-like | |
GRMZM2G443728 | 2.95 | Potassium transporter 10 | |
GRMZM2G070011 | 2.85 | Uncharacterised protein; Vignain | |
GRMZM2G006973 | 2.73 | Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G036464 | 2.72 | Glutamine synthetase root isozyme 4 | |
GRMZM2G115451 | 2.63 | Uncharacterised protein | |
GRMZM2G178546 | 2.61 | Trehalose-phosphate phosphatase | |
GRMZM2G099049 | 2.56 | N/A | |
GRMZM2G063431 | 2.53 | N/A | |
GRMZM2G427815 | 2.51 | Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G062531 | 2.50 | Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G093826 | 2.49 | Potassium high-affinity transporter | |
GRMZM2G110504 | 2.46 | Uncharacterised LOC100278648 | |
GRMZM2G007151 | 2.42 | Uncharacterised protein | |
GRMZM2G130173 | 2.41 | Metallothionein-like protein type 2; Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G477503 | 2.36 | Uncharacterised protein | |
AC217947.4_FG002.2 | 2.24 | N/A | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G026470 | 2.22 | Soluble inorganic pyrophosphatase; Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G091456 | 2.21 | Putative Uncharacterised protein | |
GRMZM2G366681 | 2.11 | Hypothetical protein | |
GRMZM2G034152 | 2.07 | Polyamine oxidase | |
GRMZM2G130149 | 2.07 | Uncharacterised protein | |
GRMZM2G144097 | 2.04 | Uncharacterised protein | |
GRMZM2G125669 | 2.03 | Alternative oxidase | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G144083 | 2.02 | Putative ATP dependent copper transporter | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G034302 | 2.01 | Uncharacterised protein | |
GRMZM2G036217 | 1.91 | Uncharacterised protein | |
GRMZM2G116079 | 1.86 | Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G076537 | 1.82 | Polynucleotidyl transferase, ribonuclease H-like superfamily protein | |
GRMZM2G176433 | 1.80 | Putative Uncharacterised protein | |
GRMZM2G008247 | 1.78 | Beta-glucosidase2 | |
GRMZM2G070659 | 1.77 | Hypersensitive-induced response protein | |
GRMZM2G147243 | 1.72 | IAA17-auxin-responsive Aux/IAA family member; Uncharacterised protein | |
GRMZM2G099767 | 1.63 | ATMAP70-2 | |
GRMZM2G057823 | 1.55 | Fructose-bisphosphate aldolase, cytoplasmic isozyme | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G040369 | 1.54 | Elongation factor 2 | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G168552 | 1.53 | Bundle sheath cell specific protein 1 | |
GRMZM2G020146 | 1.51 | Uncharacterised protein | |
GRMZM2G473001 | 1.48 | Phosphoenolpyruvate carboxylase 2 | |
GRMZM2G113332 | 1.42 | Uncharacterised protein | GO: 0043167 |
GO: 0046872 | |||
GO: 0043169 | |||
GRMZM2G141353 | 1.41 | Uncharacterised LOC100194210 | |
GRMZM2G146004 | −FC | Uncharacterised protein | GO: 0050896 |
AC214438.3_FG002.1 | −FC | N/A | |
GRMZM2G177077 | −1.40 | Glucose-6-phosphate 1-dehydrogenase | GO: 0005975 |
GRMZM2G047474 | −1.42 | TLD-domain containing nucleolar protein | |
GRMZM2G366659 | −1.49 | Putative trehalose phosphatase/synthase family protein | GO: 0005975 |
GRMZM5G870170 | −1.57 | MATE1 | GO: 0050896 |
GO: 0042221 | |||
GRMZM2G024733 | −1.57 | Uncharacterised LOC100304285 | |
GRMZM2G478568 | −1.63 | Nicotianamine synthase 3 | |
GRMZM2G154278 | −1.68 | Pre-mRNA-splicing factor cwc15 | |
GRMZM2G103812 | −1.70 | Uncharacterised protein | GO: 0050896 |
GO: 0042221 | |||
GRMZM2G121264 | −1.74 | Uncharacterised protein | |
GRMZM2G173085 | −1.85 | Lipase/lipooxygenase, PLAT/LH2 family protein | |
GRMZM2G079381 | −1.86 | Ferredoxin-nitrite reductase, chloroplastic | GO: 0050896 |
GO: 0042221 | |||
GRMZM2G053669 | −1.99 | Asparagine synthetase | |
GRMZM2G147687 | −2.02 | Uncharacterised protein | GO: 0005975 |
GRMZM2G358153 | −2.09 | Chitinase 1; Uncharacterised protein | GO: 0005975 |
GRMZM2G181081 | −2.21 | CIPK-like protein 1 | GO: 0050896 |
GO: 0042221 | |||
GRMZM2G422955 | −2.26 | N/A | |
GRMZM2G097641 | −2.27 | Sucrose-phosphatase 2 | GO: 0005975 |
GO: 0050896 | |||
GO: 0042221 | |||
GRMZM2G078472 | −2.32 | Asparagine synthetase | |
GRMZM2G124495 | −2.38 | Putative MYB DNA-binding domain superfamily protein; Transfactor; Uncharacterised protein | |
GRMZM2G058612 | −2.39 | F-box/LRR-repeat protein 3-like | |
GRMZM2G125775 | −2.40 | AN17 | GO: 0050896 |
GO: 0042221 | |||
GRMZM2G133675 | −2.65 | Putative HLH DNA-binding domain superfamily protein; Uncharacterised protein | |
GRMZM2G004161 | −2.92 | Uncharacterised protein | GO: 0050896 |
GO: 0042221 | |||
GRMZM2G472248 | −3.17 | Protein induced upon tuberization | GO: 0050896 |
GRMZM2G176430 | −3.19 | Uncharacterised protein | |
GRMZM2G468111 | −3.58 | Uncharacterised LOC100277849 | |
GRMZM2G070172 | −3.79 | Uncharacterised protein | GO: 0005975 |
GO: 0050896 | |||
GO: 0042221 |
Up-Regulated Genes | ||||||
---|---|---|---|---|---|---|
GO Term | Ontology 1 | Description | Number in Input List | Number in BG/Ref | p-Value 2 | FDR |
GO:0043169 | F | cation binding | 16 /45 | 4135/25864 | 0.0011 * | 0.028 |
GO:0043167 | F | ion binding | 16 /45 | 4136/25864 | 0.0011 * | 0.028 |
GO:0046872 | F | metal ion binding | 16 /45 | 4124/25864 | 0.0011 * | 0.028 |
Down-regulated genes | ||||||
GO:0050896 | P | response to stimulus | 10/22 | 3551/25864 | 0.00032 * | 0.0059 |
GO:0042221 | P | response to chemical stimulus | 8/22 | 2052/25864 | 0.00018 * | 0.0059 |
GO:0005975 | P | carbohydrate metabolic process | 6/22 | 1246/25864 | 0.00048 * | 0.0060 |
Gene Stable ID | Ensembl/NCBI Gene Description | Susceptible/Resistant/Common 1 | Functional Category 2 |
---|---|---|---|
GRMZM2G125669 | Alternative oxidase | Common | Response to stress |
GRMZM2G093826 | Potassium high-affinity transporter | Common | Transport |
GRMZM5G874955 | Uncharacterised protein | Common | Transport |
GRMZM2G029219 | Carbohydrate transporter/sugar porter/transporter | Common | Transport |
GRMZM2G036464 | Glutamine synthetase root isozyme 4 | Common | Metabolic process |
GRMZM2G008247 | Beta-glucosidase 2 | Common | Cell wall |
GRMZM2G034152 | Polyamine oxidase | Common | Metabolic process |
GRMZM2G427815 | Uncharacterised protein | Common | Resistance |
GRMZM5G892675 | Uncharacterised protein | Common | Transport |
GRMZM2G087875 | Putative cytochrome P450 superfamily protein | Common | Metabolic process |
GRMZM2G020146 | Uncharacterised protein | Resistant | Metabolic process |
GRMZM2G130173 | Metallothionein-like protein type 2; Uncharacterised protein | Resistant | Unknown function |
GRMZM2G026470 | Soluble inorganic pyrophosphatase | Resistant | Metabolic process |
GRMZM2G062724 | Uncharacterised protein | Resistant | Signal transduction |
GRMZM2G178546 | Trehalose-phosphate phosphatase | Susceptible | Metabolic process |
GRMZM2G007151 | Uncharacterised protein | Susceptible | Cell component |
GRMZM2G119975 | Uncharacterised LOC103646336 | Susceptible | Metabolic process |
Metabolite | ¥ Logged Average Metabolite Accumulation | Standard Deviation | p-Value (Control/Infected) | |
---|---|---|---|---|
Control | Infected | |||
KA1 | 1.42 | 2.07 | 0.59 | 0.09 |
KA2 | 1.68 | 1.60 | 1.11 | 0.90 |
KA3 | 1.90 | 2.89 | 0.67 | 0.03 * |
KB1 | 1.68 | 2.60 | 0.54 | 0.02 * |
KB2 | 1.60 | 2.51 | 0.90 | 0.11 |
KB3 | 1.78 | 3.06 | 0.93 | 0.04 * |
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Share and Cite
Lambarey, H.; Moola, N.; Veenstra, A.; Murray, S.; Suhail Rafudeen, M. Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection. Plants 2020, 9, 1112. https://doi.org/10.3390/plants9091112
Lambarey H, Moola N, Veenstra A, Murray S, Suhail Rafudeen M. Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection. Plants. 2020; 9(9):1112. https://doi.org/10.3390/plants9091112
Chicago/Turabian StyleLambarey, Humaira, Naadirah Moola, Amy Veenstra, Shane Murray, and Mohamed Suhail Rafudeen. 2020. "Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection" Plants 9, no. 9: 1112. https://doi.org/10.3390/plants9091112