Serial Transcriptome Analysis Reveals Genes Associated with Late Blight Resistance in Potato Cultivar Qingshu 9
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Preparation of Spore Suspension and Incubation
2.3. Collection of Samples and Microscopic Examination
2.4. RNA Extraction, Library Preparation, and Sequencing
2.5. Analysis of the Differentially Expressed Genes
2.6. GO and KEGG Enrichment Analyses of DEGs
2.7. Transcription Factor (TF) Analysis of DEGs
2.8. Comparative Analysis of Plant R Gene Database (PRGDB)
2.9. Validation of the Expression of DEGs by qRT-PCR
3. Results
3.1. Leaves at 0, 24, 48, 72 hpi Were Chosen to Prepare in Planta Materials
3.2. A Large Amount of Credible Data Were Obtained through Transcriptome Sequencing
3.3. 24 hpi and 48 hpi Are Important in the Immune Response of Qingshu 9
3.4. DEGs among the Groups Are Enriched in Different GO Terms and KEGG Pathways
3.5. Transcription Factors Play Crucial Roles in Qingshu 9’s Resistance Response
3.6. Comparison of Results between DEGs and Plant R Gene Database
3.7. The Results of qRT-PCR and RNA-Seq Are Consistent
4. Discussion
4.1. Potato Cultivar Qingshu 9 Contains Special Resistance to P. infestans
4.2. Transcription Analysis of Qingshu 9 Infected by P. infestans
4.3. Transcription Factors May Play an Important Role in the Resistance Response to P. infestans in Qingshu 9
4.4. Protein Kinases May Participate in the Interaction between Qingshu 9 and P. infestans
4.5. Disease Resistance-Related Genes May Enhance the Disease Resistance of Qingshu 9
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | Forward Primer (5′-3′) | Reverse Primer (5′-3′) |
---|---|---|
PGSC0003DMG400003863 (Zinc finger protein 593) | TCAAGACGAAGAAGCACAGGAAGC | AGCAGCTAAGTCGGCATCAAGTTG |
PGSC0003DMG400005113 (PR1 protein) | GCGGCTGGTGCTGTGAAGATG | ACCTGACTCTAGCACAACCGAGAC |
PGSC0003DMG400022159 (Heat shock cognate protein 80) | AGCTGAGAAGGTTGTTGTGACCAC | CAGGTCCTTGAGCCTACGTTCTTC |
PGSC0003DMG400029732 (Auxin repressed/dormancy associated protein) | TACCAGAGGTCTCTGTCGATGCC | GTAGGAGCGTTAGGATGAGAAGGC |
PGSC0003DMG400019435 (Wound-induced protein WIN2) | CAACTTGTGTTGCAGCCAATTCGG | CAGCGGCTCTGGCAACCTTG |
PGSC0003DMG400010173 (Avr9/Cf-9 rapidly elicited protein 140) | GGTCCAATTGCTGGGATTCT | CGTCACTGGAATAACCACCTTAT |
PGSC0003DMG400005835 (WRKY transcription factor-30) | ACATACCGAGGCTCCCATAA | TTGCTGCCCTGTTGGATAAA |
PGSC0003DMG400008337 (MYB21) | GGCATCTGGAATTGGAAACAG | CTAACATCAGGGCGGAGATAAT |
PGSC0003DMG400022134 (Salicylic acid-induced protein 19) | GAAATTCCTGAAGTGGCATGTG | GATACGGTGGCTCTGTTTGT |
GenBank No. X83206 | AGATGCTTACGCTGGATGGAATGC | TTCCGGTGTGGTTGGATTCTGTTC |
Sample | Raw Reads | Clean Reads | Uniquely Mapped Reads | Average Mapped Rate | Average Raw Reads | Average Gene Number |
---|---|---|---|---|---|---|
Pi0h_1 | 45,925,462 | 45,011,852 | 34,474,929 | 77.58% | 47,753,443 | 24,251 |
Pi0h_2 | 54,412,460 | 52,408,268 | 42,404,666 | |||
Pi0h_3 | 42,922,408 | 41,532,392 | 31,252,486 | |||
Pi24h_1 | 44,129,574 | 42,199,746 | 33,418,531 | 77.82% | 50,630,987 | 23,579 |
Pi24h_2 | 61,477,952 | 57,247,998 | 46,896,846 | |||
Pi24h_3 | 46,285,436 | 44,600,984 | 32,263,042 | |||
Pi48h_1 | 47,926,188 | 45,964,682 | 36,934,989 | 75.99% | 49,302,732 | 23,412 |
Pi48h_2 | 48,552,120 | 46,549,340 | 33,115,129 | |||
Pi48h_3 | 51,429,890 | 48,463,464 | 37,059,231 | |||
Pi72h_1 | 44,484,052 | 42,866,804 | 32,606,650 | 74.79% | 48,372,645 | 23,736 |
Pi72h_2 | 54,973,320 | 53,716,862 | 42,717,598 | |||
Pi72h_3 | 45,660,564 | 44,668,070 | 30,717,314 |
Sample | Pi0h_1 | Pi0h_2 | Pi0h_3 | Pi24h_1 | Pi24h_2 | Pi24h_3 | Pi48h_1 | Pi48h_2 | Pi48h_3 | Pi72h_1 | Pi72h_2 | Pi72h_3 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Pi0h_1 | 1 | |||||||||||
Pi0h_2 | 0.99 | 1 | ||||||||||
Pi0h_3 | 0.99 | 0.99 | 1 | |||||||||
Pi24h_1 | 0.49 | 0.51 | 0.54 | 1 | ||||||||
Pi24h_2 | 0.57 | 0.57 | 0.60 | 0.90 | 1 | |||||||
Pi24h_3 | 0.44 | 0.45 | 0.49 | 0.84 | 0.73 | 1 | ||||||
Pi48h_1 | 0.88 | 0.89 | 0.89 | 0.54 | 0.60 | 0.49 | 1 | |||||
Pi48h_2 | 0.73 | 0.73 | 0.76 | 0.55 | 0.60 | 0.58 | 0.90 | 1 | ||||
Pi48h_3 | 0.89 | 0.88 | 0.88 | 0.42 | 0.51 | 0.39 | 0.95 | 0.82 | 1 | |||
Pi72h_1 | 0.83 | 0.84 | 0.84 | 0.66 | 0.74 | 0.55 | 0.87 | 0.74 | 0.84 | 1 | ||
Pi72h_2 | 0.87 | 0.88 | 0.86 | 0.59 | 0.66 | 0.49 | 0.88 | 0.69 | 0.88 | 0.96 | 1 | |
Pi72h_3 | 0.84 | 0.85 | 0.85 | 0.69 | 0.75 | 0.54 | 0.87 | 0.72 | 0.83 | 0.98 | 0.96 | 1 |
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He, M.; Zhou, Y.; Ye, G.; Zheng, J.; Meng, Y.; Wang, J.; Shan, W. Serial Transcriptome Analysis Reveals Genes Associated with Late Blight Resistance in Potato Cultivar Qingshu 9. Agronomy 2021, 11, 1919. https://doi.org/10.3390/agronomy11101919
He M, Zhou Y, Ye G, Zheng J, Meng Y, Wang J, Shan W. Serial Transcriptome Analysis Reveals Genes Associated with Late Blight Resistance in Potato Cultivar Qingshu 9. Agronomy. 2021; 11(10):1919. https://doi.org/10.3390/agronomy11101919
Chicago/Turabian StyleHe, Miaomiao, Yun Zhou, Guangji Ye, Jie Zheng, Yuling Meng, Jian Wang, and Weixing Shan. 2021. "Serial Transcriptome Analysis Reveals Genes Associated with Late Blight Resistance in Potato Cultivar Qingshu 9" Agronomy 11, no. 10: 1919. https://doi.org/10.3390/agronomy11101919
APA StyleHe, M., Zhou, Y., Ye, G., Zheng, J., Meng, Y., Wang, J., & Shan, W. (2021). Serial Transcriptome Analysis Reveals Genes Associated with Late Blight Resistance in Potato Cultivar Qingshu 9. Agronomy, 11(10), 1919. https://doi.org/10.3390/agronomy11101919