Transcriptome and Co-Expression Network Analyses of Resistant and Susceptible Rice Cultivars in Response to Meloidogyne graminicola
Abstract
1. Introduction
2. Results
2.1. Identification of Resistance to M. graminicola in Indica Rice Cultivars
2.2. RNA-Seq Data Alignment to the Reference Genome
2.3. Comparison of the DEGs Between Resistant and Susceptible Rice Cultivars in Response to M. graminicola Infection
2.4. Weighted Gene Co-Correlation Network Analysis
2.5. Functional Analysis of Gene Modules Associated with Susceptibility and Resistance to M. graminicola
2.6. Identification of Hub Genes Correlated with Susceptibility and Resistance to M. graminicola
2.7. Validation of Hub Genes by RT-qPCR
3. Discussion
3.1. Mining of M. graminicola Resistance Resources and Molecular Mechanism
3.2. Sugar Metabolism Has an Important Role in Nematode–Host Interactions
3.3. Autophagic Degradation Pathway Regulates Plant-Nematode Immune Interactions
3.4. M. graminicola Regulate the Salicylic Acid (SA) and Brassinosteroid (BR) Signaling Pathway to Promote Nematode Parasitism
4. Materials and Methods
4.1. Plant Material and Nematode Inoculation
4.2. Nematode Infection Experiments
4.3. RNA-Seq and Differentially Expressed Gene Analysis
4.4. Weighted Gene Co-Expression Network Analysis
4.5. Differential Gene Expression Analysis and Gene Enrichment Analysis
4.6. Validation of Genes by qRT-PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Correction Statement
Abbreviations
DEGs | Differential expressed genes |
GCs | Giant cells |
RNK | Root-knot nematode |
WGCNA | Weighted gene co-expression network analysis |
SCN | Soybean cyst nematode |
GO | Gene ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
HR | Hypersensitive response |
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Zhang, S.; Xiao, Z.; Shen, K.; Lai, W.; Du, S.; Zhou, L.; Chen, J. Transcriptome and Co-Expression Network Analyses of Resistant and Susceptible Rice Cultivars in Response to Meloidogyne graminicola. Int. J. Mol. Sci. 2025, 26, 5315. https://doi.org/10.3390/ijms26115315
Zhang S, Xiao Z, Shen K, Lai W, Du S, Zhou L, Chen J. Transcriptome and Co-Expression Network Analyses of Resistant and Susceptible Rice Cultivars in Response to Meloidogyne graminicola. International Journal of Molecular Sciences. 2025; 26(11):5315. https://doi.org/10.3390/ijms26115315
Chicago/Turabian StyleZhang, Shirui, Zitong Xiao, Kexiang Shen, Wentao Lai, Shunbiao Du, Lingyan Zhou, and Jiansong Chen. 2025. "Transcriptome and Co-Expression Network Analyses of Resistant and Susceptible Rice Cultivars in Response to Meloidogyne graminicola" International Journal of Molecular Sciences 26, no. 11: 5315. https://doi.org/10.3390/ijms26115315
APA StyleZhang, S., Xiao, Z., Shen, K., Lai, W., Du, S., Zhou, L., & Chen, J. (2025). Transcriptome and Co-Expression Network Analyses of Resistant and Susceptible Rice Cultivars in Response to Meloidogyne graminicola. International Journal of Molecular Sciences, 26(11), 5315. https://doi.org/10.3390/ijms26115315