Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq
Abstract
:1. Introduction
2. Results
2.1. Identification of Sugarcane Genotypes with Contrasting Aluminum Stress Tolerance
2.2. Phytotoxic Effects of Aluminum Ions (Al3+) on the Growth of Sugarcane Roots
2.3. De Novo Assembly of RNA-seq Reads for Generation of Reference Transcriptome
2.4. Differential Expression Analysis
2.5. Functional Annotation of Consensus Sequence (Contigs)
2.6. Differential Gene Expression Analysis of Roots Exposed to Aluminum Stress
2.7. Mapping to Functional Pathways
3. Discussion
3.1. Transcriptome Analysis
3.2. Detoxification
3.3. Signaling
3.4. ROS Protection
3.5. Signal Transduction
4. Materials and Methods
4.1. Sample Selection and Preparation of Collection
4.2. Aluminum Abundance in Root
4.3. RNA Extraction, Library Preparation, and Sequencing
4.4. De Novo Transcriptome Assembly and Gene Functional Annotation
4.5. Resequencing for Validation
4.6. Statistical Analysis
4.7. Availability of Data
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
ESTs | expressed sequence tags |
SUCEST | sugarcane EST |
SAGE | serial analysis of gene expression |
TAS | tolerant to aluminum stress |
SAS | sensitive to aluminum stress |
X-EDS | energy-dispersive X-ray spectroscopy |
C | control |
T | treatment (+Al) |
DEGs | differentially expressed genes |
FC | fold-change |
Reseq | Resequencing |
NI | not identified |
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Cultivars | Condition | Aluminum Quantification–by EDS* | |
---|---|---|---|
Root Cap | Root Elongation | ||
TAS | Control | 0.46 ± 0.02 | 0.22 ± 0.02 |
Treatment | 1.76 ± 0.03 ** | 0.44 ± 0.02 ** | |
SAS | Control | 0.41 ± 0.02 | 0.05 ± 0.02 |
Treatment | 1.37 ± 0.03 ** | 0.45 ± 0.02 ** |
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Rosa-Santos, T.M.; Silva, R.G.d.; Kumar, P.; Kottapalli, P.; Crasto, C.; Kottapalli, K.R.; França, S.C.; Zingaretti, S.M. Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq. Int. J. Mol. Sci. 2020, 21, 7934. https://doi.org/10.3390/ijms21217934
Rosa-Santos TM, Silva RGd, Kumar P, Kottapalli P, Crasto C, Kottapalli KR, França SC, Zingaretti SM. Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq. International Journal of Molecular Sciences. 2020; 21(21):7934. https://doi.org/10.3390/ijms21217934
Chicago/Turabian StyleRosa-Santos, Thiago Mateus, Renan Gonçalves da Silva, Poornasree Kumar, Pratibha Kottapalli, Chiquito Crasto, Kameswara Rao Kottapalli, Suzelei Castro França, and Sonia Marli Zingaretti. 2020. "Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq" International Journal of Molecular Sciences 21, no. 21: 7934. https://doi.org/10.3390/ijms21217934