A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease
Abstract
:1. Introduction
2. Results
2.1. Sequencing of Small RNAs
2.2. Expression of Known miRNAs
2.3. Identification and Distribution of Novel miRNAs
2.4. Comparison of miRNAs Expression in Control and Infected Samples
2.5. Differential Regulation of miRNAs and Target Genes
2.6. Expression Analysis of miRNAs at Different Time Points of Infection
2.7. Expression Analysis of miRNAs Induced by Different Strains of R. solani
2.8. Expression Analysis of R. solani Responsive miRNAs in Wild Relatives of Rice
2.9. Mapping of R. solani-Induced miRNAs to Sheath Blight-Resistant QTL Regions
3. Discussion
4. Materials and Methods
4.1. Plant Material, Fungal Strains, and Sample Preparation
4.2. Small RNA Library Construction and Sequencing
4.3. Sequence Analysis
4.4. RT-qPCR Analysis of miRNAs and Target Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Availability of Data and Materials
References
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Sample Name | Total Number of Reads | Clean Reads before Data Filtering | Q30 (%) | Clean Reads after Data Filtering | Clean Reads (18–24 nt) | Identified Known miRNAs | Identified Novel miRNAs |
---|---|---|---|---|---|---|---|
R. solani-infected samples | |||||||
TN1 | 17,292,908 | 17,277,169 | 96.65 | 16,998,190 | 1,209,465 | 89 | 7 |
BPT5204 | 19,838,709 | 19,817,284 | 96.7 | 19,603,829 | 3,442,243 | 282 | 8 |
N22 | 12,331,370 | 12,318,143 | 96.45 | 12,028,969 | 1,563,885 | 24 | 9 |
Vandana | 15,584,456 | 15,566,007 | 96.42 | 15,179,461 | 1,082,338 | 278 | 21 |
Tetep | 16,772,072 | 16,754,325 | 96.64 | 16,346,243 | 2,601,317 | 161 | 9 |
Pankaj | 14,666,490 | 14,652,163 | 96.66 | 14,207,919 | 1,023,439 | 147 | 4 |
Control samples | |||||||
TN1 | 18,776,171 | 18,757,059 | 96.58 | 18,058,533 | 822,299 | 95 | 7 |
BPT5204 | 17,754,335 | 17,733,540 | 95.66 | 17,107,679 | 1,202,770 | 104 | 5 |
N22 | 16,568,740 | 16,549,626 | 96.38 | 15,910,033 | 1,397,952 | 24 | 2 |
Vandana | 15,698,991 | 15,682,752 | 96.48 | 14,906,413 | 1,062,798 | 154 | 6 |
Tetep | 15,304,171 | 15,283,850 | 96.11 | 14,364,145 | 986,089 | 43 | 2 |
Pankaj | 16,132,109 | 16,114,741 | 96.57 | 15,524,879 | 851,888 | 128 | 5 |
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Chopperla, R.; Mangrauthia, S.K.; Bhaskar Rao, T.; Balakrishnan, M.; Balachandran, S.M.; Prakasam, V.; Channappa, G. A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease. Int. J. Mol. Sci. 2020, 21, 7974. https://doi.org/10.3390/ijms21217974
Chopperla R, Mangrauthia SK, Bhaskar Rao T, Balakrishnan M, Balachandran SM, Prakasam V, Channappa G. A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease. International Journal of Molecular Sciences. 2020; 21(21):7974. https://doi.org/10.3390/ijms21217974
Chicago/Turabian StyleChopperla, Ramakrishna, Satendra K. Mangrauthia, Talluri Bhaskar Rao, Marudamuthu Balakrishnan, Sena Munuswamy Balachandran, Vellaisamy Prakasam, and Gireesh Channappa. 2020. "A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease" International Journal of Molecular Sciences 21, no. 21: 7974. https://doi.org/10.3390/ijms21217974