Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies
Abstract
:1. Introduction
2. Results
2.1. N Enrichment Promotes Tillers in a Different Pattern between NPB and YD6
2.2. Tiller Number Is Related with N and Carbohydrate Content
2.3. RNA-Seq Data Quality and Assembly
2.4. Validation of Selected DEG Confirms RNA-Seq Data Reliability
2.5. Differentially Expressed Genes (DEGs) in Response to N Rate
2.6. Gene Ontology (GO) Analysis and KEGG Clustering
2.7. Alternative Splicing Transcripts and Novel Genes
2.8. Identifition of Weighted Gene Co-Expression Network
2.9. Construction of the Gene Co-Expression Networks and Identification of Candidate Hub Genes
2.10. Expression Profiles of Tiller Related Genes and Their Network
2.11. Expression Profiles of No Apical Meristem Family Genes, Carbohydrate, and N Metabolism and Transport-Related Genes
3. Discussion
3.1. Reducing N Input to Low or Moderate Rate Is Still Good to Promote Enough Tillers
3.2. Most of the Tiller Genes Are Not Drastically Respond to N Rate
4. Materials and Methods
4.1. Plant Materials
4.2. Growth Conditions, N Rate Treatment and Measurement
4.3. Samples Preparation for RNA Extraction, cDNA Library Construction and Sequencing
4.4. RNA-Seq Data Processing and Gene Expression Calculation
4.5. Novel Gene, Alternative Splicing and Enrichment Analysis
4.6. Quantitative Real Time RT-PCR Validation
4.7. Co-Expression Network Analysis for Construction of Modules
4.8. Statistical Analysis of Genes Expression Data in a Specific Pathway
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
AS | Alternative splicing |
DEGs | Differentially expressed genes |
FPKM | Fragments per kilo-base per million reads |
GO | Gene ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
N | Nitrogen |
NAM | No apical meristem |
qRT-PCR | Quantitative real-time polymerase chain reaction |
RNA-Seq | RNA-sequencing |
SAM | Shoot apical meristem |
WSC | Water soluble carbohydrate |
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Gene Name | Description | KME Value |
---|---|---|
Light yellow module (M18) with positive correlation associated with the tillers | ||
LOC_Os04g09390 | HEV3 - Hevein family protein precursor, expressed | 0.97 |
LOC_Os01g03680 | BBTI8 - Bowman-Birk type bran trypsin inhibitor precursor, expressed | 0.95 |
LOC_Os08g28880 | patatin, putative, expressed | 0.94 |
LOC_Os10g08780 | expressed protein | 0.94 |
LOC_Os01g03360 | BBTI5 - Bowman-Birk type bran trypsin inhibitor precursor, expressed | 0.94 |
LOC_Os02g35200 | VP15, putative, expressed | 0.88 |
LOC_Os07g43670 | ribonuclease T2 family domain containing protein, expressed | 0.85 |
LOC_Os04g01690 | pyridoxal-dependent decarboxylase protein, putative, expressed | 0.85 |
LOC_Os04g25650 | cysteine-rich receptor-like protein kinase, putative, expressed | 0.85 |
LOC_Os05g02670 | kinesin motor domain containing protein, putative, expressed | −0.80 |
Green module (M3) with negative correlation associated with the tillers, N rate in leaf and stem | ||
LOC_Os10g13940 | MATE efflux protein, putative, expressed | 0.98 |
LOC_Os07g28890 | ethylene-responsive protein related, putative, expressed | 0.98 |
LOC_Os01g12720 | protein kinase domain containing protein, expressed | 0.98 |
LOC_Os07g47210 | GDSL-like lipase/acylhydrolase, putative, expressed | 0.97 |
LOC_Os01g18630 | aspartic proteinase oryzasin-1 precursor, putative, expressed | 0.95 |
LOC_Os02g19770 | eukaryotic translation initiation factor 1A, putative, expressed | 0.94 |
LOC_Os09g36580 | thaumatin, putative, expressed | 0.93 |
LOC_Os05g03530 | tetraspanin family protein, putative, expressed | 0.90 |
LOC_Os04g07280 | AGAP002737-PA, putative, expressed | 0.90 |
LOC_Os02g53500 | RFC5 - Putative clamp loader of PCNA, replication factor C subunit 5, expressed | −0.92 |
Blue module (M10) with positive correlation associated with the N rate in leaf and stem | ||
LOC_Os08g44290 | RNA recognition motif containing protein, putative, expressed | 0.98 |
LOC_Os03g61260 | ribosomal L18p/L5e family protein, putative, expressed | 0.98 |
LOC_Os03g04530 | cytochrome P450, putative, expressed | 0.95 |
LOC_Os09g36700 | ribonuclease T2 family domain containing protein, expressed | 0.94 |
LOC_Os02g52150 | heat shock 22 kDa protein, mitochondrial precursor, putative, expressed | 0.91 |
LOC_Os03g07960 | expressed protein | 0.88 |
LOC_Os10g41100 | CCT motif family protein, expressed | 0.84 |
LOC_Os11g34880 | NB-ARC domain containing protein, expressed | −0.70 |
LOC_Os11g05480 | transcription factor, putative, expressed | −0.76 |
LOC_Os01g40499 | S-locus lectin protein kinase family protein, putative, expressed | −0.82 |
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Zhang, X.; Zhou, J.; Huang, N.; Mo, L.; Lv, M.; Gao, Y.; Chen, C.; Yin, S.; Ju, J.; Dong, G.; et al. Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies. Int. J. Mol. Sci. 2019, 20, 5922. https://doi.org/10.3390/ijms20235922
Zhang X, Zhou J, Huang N, Mo L, Lv M, Gao Y, Chen C, Yin S, Ju J, Dong G, et al. Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies. International Journal of Molecular Sciences. 2019; 20(23):5922. https://doi.org/10.3390/ijms20235922
Chicago/Turabian StyleZhang, Xiaoxiang, Juan Zhou, Niansheng Huang, Lanjing Mo, Minjia Lv, Yingbo Gao, Chen Chen, Shuangyi Yin, Jing Ju, Guichun Dong, and et al. 2019. "Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies" International Journal of Molecular Sciences 20, no. 23: 5922. https://doi.org/10.3390/ijms20235922