Expression Analysis Reveals Differentially Expressed Genes in BPH and WBPH Associated with Resistance in Rice RILs Derived from a Cross between RP2068 and TN1
Abstract
:1. Introduction
2. Results
2.1. WBPH RNA-Seq and Differential Gene Expression (DGE) Analysis
2.2. GO and KEGG-Based Enrichment Analysis
2.3. Comparative Expression Profiles of Select Genes of BPH and WBPH by qRT-PCR
3. Discussion
4. Materials and Methods
4.1. Insect Material
4.2. RNA Extraction
4.3. cDNA Library Preparation, Clustering, and RNA-Sequencing
4.4. RNA-Seq Data Analysis
4.4.1. RNA Quality Control (QC)
4.4.2. Alignment and Mapping
4.4.3. Transcript Quantification
4.4.4. Differential Gene Expression Analysis
4.4.5. Enrichment Analysis
Gene Ontology (GO)
KEGG Enrichment Analysis
4.5. Expression Analysis of Differentially Expressed BPH and WBPH Genes by Quantitative PCR (qPCR)
4.6. Data Analyses
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample Name | Raw Reads | Clean Reads | Raw Bases | Clean Bases | Error Rate (%) | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|---|---|---|
W_TN1-R1 | 24206186 | 23584788 | 7.3G | 7.1G | 0.03 | 97.91 | 93.96 | 37.47 |
W_TN1-R2 | 21448759 | 21053170 | 6.4G | 6.3G | 0.03 | 97.89 | 93.86 | 38.65 |
W_TN1-R3 | 21926318 | 21522130 | 6.6G | 6.5G | 0.03 | 97.94 | 94.02 | 37.92 |
W_TR145RS_R1 | 26899128 | 26352877 | 8.1G | 7.9G | 0.03 | 97.95 | 94.01 | 38.2 |
W_TR145RS_R2 | 23710772 | 23313968 | 7.1G | 7.0G | 0.03 | 98 | 94.09 | 38.87 |
W_TR145RS_R3 | 25541544 | 25066110 | 7.7G | 7.5G | 0.02 | 98.08 | 94.28 | 39.75 |
W_TR152SR-R1 | 22617866 | 22093361 | 6.8G | 6.6G | 0.02 | 98.16 | 94.45 | 38.2 |
W_TR152SR-R2 | 22276222 | 21481497 | 6.7G | 6.4G | 0.03 | 97.92 | 93.94 | 38.62 |
W_TR152SR-R3 | 21430485 | 20979347 | 6.4G | 6.3G | 0.03 | 97.91 | 93.89 | 38.82 |
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Anand, R.; Divya, D.; Mazumdar-Leighton, S.; Bentur, J.S.; Nair, S. Expression Analysis Reveals Differentially Expressed Genes in BPH and WBPH Associated with Resistance in Rice RILs Derived from a Cross between RP2068 and TN1. Int. J. Mol. Sci. 2023, 24, 13982. https://doi.org/10.3390/ijms241813982
Anand R, Divya D, Mazumdar-Leighton S, Bentur JS, Nair S. Expression Analysis Reveals Differentially Expressed Genes in BPH and WBPH Associated with Resistance in Rice RILs Derived from a Cross between RP2068 and TN1. International Journal of Molecular Sciences. 2023; 24(18):13982. https://doi.org/10.3390/ijms241813982
Chicago/Turabian StyleAnand, Rashi, Dhanasekar Divya, Sudeshna Mazumdar-Leighton, Jagadish S. Bentur, and Suresh Nair. 2023. "Expression Analysis Reveals Differentially Expressed Genes in BPH and WBPH Associated with Resistance in Rice RILs Derived from a Cross between RP2068 and TN1" International Journal of Molecular Sciences 24, no. 18: 13982. https://doi.org/10.3390/ijms241813982