Transcriptome-Assisted SNP Marker Discovery for Phytophthora infestans Resistance in Solanum lycopersicum L.
Abstract
:1. Introduction
2. Results
2.1. Transcriptome and Differential Gene Expression Analysis
- The comparison of control susceptible vs control resistant showed a total of 2997 differentially expressed genes—1749 downregulated and 1228 upregulated—in control susceptible individuals. The downregulated genes were annotated as involved in the regulation of cellular metabolic processes, response to stress, regulation of macromolecule metabolic processes, regulation of primary metabolic processes, and cellular response to stimuli. The upregulated genes were involved in the regulation of macromolecule metabolic processes, regulation of gene expression, regulation of cellular metabolic processes, transport, and establishment of localization.
- A comparison of susceptible infected vs resistant infected showed a total of 3473 differentially expressed genes—1465 downregulated and 2007 upregulated—in susceptible infected individuals. The downregulated genes were annotated to be involved in the regulation of cellular metabolic processes, regulation of macromolecule metabolic processes, regulation of primary metabolic processes, nucleobase-containing compound biosynthetic processes, and regulation of nitrogen compound metabolic processes. The upregulated genes were involved in the establishment of localization, transport, phosphate-containing compound metabolic processes, phosphorus metabolic processes, and regulation of cellular metabolic processes.
2.2. SNP Analysis from Transcriptome Data
2.3. Integration of Public Data for Confidence
2.4. Genotyping-Based SNP Validation
2.5. Characterization of Candidate Genes
3. Discussion
4. Materials and Methods
4.1. Plant Material, Fungal Infection, and Sampling
4.2. Library Preparation and Transcriptome Sequencing
4.3. Transcriptome Data Analysis
4.4. Variant Calling from Transcriptome Data and Integration of Publicly Available Data
4.5. Experimental Validation of SNPs
4.6. Characterization of Candidate Genes
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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SNP ID | No. of Samples | Phenotype | Alternative Allele % | Reference Allele % | Chi-Squared | p-Value |
---|---|---|---|---|---|---|
774 | 65 | Susceptible | 0.00 | 100 | 45.4 | p < 0.01 |
73 | Resistant | 37.00 | 63 | |||
893 | 67 | Susceptible | 1.50 | 98.5 | 53.4 | p < 0.01 |
73 | Resistant | 45.20 | 54.8 | |||
667 | 52 | Susceptible | 1.00 | 99 | 75.8 | p < 0.01 |
52 | Resistant | 56.70 | 43.3 | |||
390 | 53 | Susceptible | 5.70 | 94.3 | 20.5 | p < 0.01 |
43 | Resistant | 30.20 | 69.8 | |||
973 | 53 | Susceptible | 0.00 | 100 | 44.4 | p < 0.01 |
55 | Resistant | 36.40 | 63.6 | |||
022 | 70 | Susceptible | 33.60 | 66.4 | 4.8 | p < 0.05 |
81 | Resistant | 48.80 | 51.2 | |||
807 | 55 | Susceptible | 0.00 | 100 | 56.5 | p < 0.01 |
42 | Resistant | 44.00 | 56 | |||
108 | 53 | Susceptible | 1.90 | 98.1 | 80.5 | p < 0.01 |
56 | Resistant | 60.70 | 39.3 |
Variety | Literature Evidence Supporting the Phenotype of the Variety | Phenotype | Data Source |
---|---|---|---|
Stupice | Powell et al. 2014 [33] | Resistant | https://plantgarden.jp/ (accessed on 29 December 2022) |
Brandywine Red | Gevens et al. 2013 [34] | Resistant | SRR5080039 |
Matt’s Wild Cherry | Gevens et al. 2013 [34] | Resistant | SRR5079877 |
Prudens Purple | Gevens et al. 2013 [34] | Resistant | SRR5080111 |
Legend | Gevens et al. 2013 [34] | Resistant | SRR5079916 |
Cherry Roma | Gevens et al. 2013 [34] | Resistant | SRR5080059 |
Green Zebra | Gevens et al. 2013 [34] | Resistant | SRR5080064 |
Mr. Stripey | Hansen et al. 2014 [35] | Resistant | SRR5080065 |
Lemon Drop | Hansen et al. 2014 [35] | Resistant | SRR5079871 |
Mexico Midget | James 2015 [36] | Resistant | SRR5080113 |
NC1-CELBR | Hansen et al. 2014 [35] | Resistant | https://solgenomics.net/ (accessed on 29 December 2022) |
LA2093 | Merk 2010 [37] | Resistant | SRR12039813 |
LA1673 | Nowakowska et al. 2014 [38] | Resistant | DRR241605 |
San Marzano | Rodríguez et al. 2011 [39] | Susceptible | https://plantgarden.jp/ (accessed on 29 December 2022) |
Castle rock | Arafa et al. 2017 [13] | Susceptible | https://plantgarden.jp/ (accessed on 29 December 2022) |
Money Maker | Ojiewo et al. 2010 [40] | Susceptible | https://plantgarden.jp/ (accessed on 29 December 2022) |
LA4084 | Zhang et al. 2014 [41] | Susceptible | SRR1013253 |
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Deb, S.; Della Lucia, M.C.; Ravi, S.; Bertoldo, G.; Stevanato, P. Transcriptome-Assisted SNP Marker Discovery for Phytophthora infestans Resistance in Solanum lycopersicum L. Int. J. Mol. Sci. 2023, 24, 6798. https://doi.org/10.3390/ijms24076798
Deb S, Della Lucia MC, Ravi S, Bertoldo G, Stevanato P. Transcriptome-Assisted SNP Marker Discovery for Phytophthora infestans Resistance in Solanum lycopersicum L. International Journal of Molecular Sciences. 2023; 24(7):6798. https://doi.org/10.3390/ijms24076798
Chicago/Turabian StyleDeb, Saptarathi, Maria Cristina Della Lucia, Samathmika Ravi, Giovanni Bertoldo, and Piergiorgio Stevanato. 2023. "Transcriptome-Assisted SNP Marker Discovery for Phytophthora infestans Resistance in Solanum lycopersicum L." International Journal of Molecular Sciences 24, no. 7: 6798. https://doi.org/10.3390/ijms24076798