Tomato Fusarium crown and root rot (FCRR) is an extremely destructive soil-borne disease. To date, studies have shown that only plants with tomato mosaic virus (TMV) resistance exhibit similar resistance to tomato Fusarium oxysporum f. sp. radicis-lycopersici (FORL) and have identified a single relevant gene, Frl, in Peruvian tomato. Due to the relative lack of research on FCRR disease-resistance genes in China and elsewhere, transcriptome data for FORL-resistant (cv. ‘19912’) and FORL-susceptible (cv. ‘Moneymaker’) tomato cultivars were analysed for the first time in this study. The number of differentially expressed genes (DEGs) was higher in Moneymaker than in 19912, and 189 DEGs in the ‘plant–pathogen interaction’ pathway were subjected to GO and KEGG enrichment analyses. MAPK and WRKY genes were enriched in major metabolic pathways related to plant disease resistance; thus, we focused on these two gene families. In the early stage of tomato infection, the content of JA and SA increased, but the change in JA was more obvious. Fourteen genes were selected for confirmation of their differential expression levels by qRT-PCR. This study provides a series of novel disease resistance resources for tomato breeding and genetic resources for screening and cloning FORL resistance genes.
J.L. and H.Y.; methodology, Y.S.; software, Y.S.; validation, Y.S., H.Y. and J.L.; formal analysis, Y.S.; investigation, Y.S.; resources, J.L.; data curation, H.Y.; writing original draft preparation, Y.S.; writing review and editing, Y.S.; visualization, Y.S.; supervision, H.Y.; project administration, J.L.; funding acquisition, J.L. and H.Y. All authors have read and agreed to the published version of the manuscript.
Figure 1. Results of inoculation. (a–c) ‘Moneymaker’ inoculated with FORL (Fusarium oxysporum f. sp. radicis-lycopersici) at 0, 3, and 6 dpi; (d–f) ‘19912’ inoculated with FORL at 0, 3, and 6 dpi.
Figure 1. Results of inoculation. (a–c) ‘Moneymaker’ inoculated with FORL (Fusarium oxysporum f. sp. radicis-lycopersici) at 0, 3, and 6 dpi; (d–f) ‘19912’ inoculated with FORL at 0, 3, and 6 dpi.
Figure 2. Trypan blue staining of tomato stem samples exposed to FORL. (a–e) ‘Moneymaker’ trypan blue staining at 0, 1, 2, 3, and 6 dpi; (f–h) ‘19912’ tomato stems dyed with trypan blue at 0, 3, and 6 dpi. Vt, vascular tissue; S, spores; Hy, hyphae; St, stomata; Np, necrotic plaque; T, trichome; HR, hypersensitive response; Ch, chloroplast.
Figure 2. Trypan blue staining of tomato stem samples exposed to FORL. (a–e) ‘Moneymaker’ trypan blue staining at 0, 1, 2, 3, and 6 dpi; (f–h) ‘19912’ tomato stems dyed with trypan blue at 0, 3, and 6 dpi. Vt, vascular tissue; S, spores; Hy, hyphae; St, stomata; Np, necrotic plaque; T, trichome; HR, hypersensitive response; Ch, chloroplast.
Figure 3. Venn diagrams presenting DEGs in diverse comparisons after FORL inoculation. (a) Venn chart of DEGs identified in the M0 vs. Frl0, M0 vs. M3, Frl0 vs. Frl3, and M3 vs. Frl3 comparisons. (b) Venn diagram of DEGs identified in the M0 vs. Frl0, M0 vs. M6, Frl0 vs. Frl6, and M6 vs. Frl6 comparisons. (c) Venn diagram of DEGs identified in the Frl0 vs. Frl6, M0 vs. M3, Frl0 vs. Frl3, and M0 vs. M6 comparisons.
Figure 3. Venn diagrams presenting DEGs in diverse comparisons after FORL inoculation. (a) Venn chart of DEGs identified in the M0 vs. Frl0, M0 vs. M3, Frl0 vs. Frl3, and M3 vs. Frl3 comparisons. (b) Venn diagram of DEGs identified in the M0 vs. Frl0, M0 vs. M6, Frl0 vs. Frl6, and M6 vs. Frl6 comparisons. (c) Venn diagram of DEGs identified in the Frl0 vs. Frl6, M0 vs. M3, Frl0 vs. Frl3, and M0 vs. M6 comparisons.
Figure 4. (a) KEGG enrichment of 189 DEGs in the ‘plant–pathogen interaction’ pathway. (b–d) GO enrichment of 189 DEGs in the ‘plant–pathogen interaction’ pathway.
Figure 4. (a) KEGG enrichment of 189 DEGs in the ‘plant–pathogen interaction’ pathway. (b–d) GO enrichment of 189 DEGs in the ‘plant–pathogen interaction’ pathway.
Figure 5. Gene co-expression network analyses via WGCNA. (a) Gene tree coloured per the relationship between genetic expression levels. Different colours denote different genetic modules and reflect different coefficients between genes. (b) Module–specimen relationship. The abscissa denotes the specimens, and the ordinate denotes the modules. The numbers in each cell denote the coefficients of association (top) and P results (bottom). The alteration from blue (low) to orange (high) denotes the DEG ranges.
Figure 5. Gene co-expression network analyses via WGCNA. (a) Gene tree coloured per the relationship between genetic expression levels. Different colours denote different genetic modules and reflect different coefficients between genes. (b) Module–specimen relationship. The abscissa denotes the specimens, and the ordinate denotes the modules. The numbers in each cell denote the coefficients of association (top) and P results (bottom). The alteration from blue (low) to orange (high) denotes the DEG ranges.
Figure 6. Genes in three modules were analysed using KEGG. (a–c) Results for the MElightcyan, MEpink, and MEblue modules, respectively.
Figure 6. Genes in three modules were analysed using KEGG. (a–c) Results for the MElightcyan, MEpink, and MEblue modules, respectively.
Figure 7. Coefficients of association between RNA sequencing and qRT-PCR results. The expression patterns of each gene in both Frl (0, 3, and 6 dpi) and MM (0, 3, and 6 dpi) were analysed. The outcomes acquired from these approaches were utilised to compute the coefficients of association (R2 values). All points denote R2 values. MM, ‘Moneymaker’; Frl, ‘19912’.
Figure 7. Coefficients of association between RNA sequencing and qRT-PCR results. The expression patterns of each gene in both Frl (0, 3, and 6 dpi) and MM (0, 3, and 6 dpi) were analysed. The outcomes acquired from these approaches were utilised to compute the coefficients of association (R2 values). All points denote R2 values. MM, ‘Moneymaker’; Frl, ‘19912’.
Figure 8. (a) DEGs related to MAPK in Frl and MM samples. (b) DEGs related to WRKY in Frl and MM samples. (c) Network analysis of ‘MAPK signalling pathway-plant’ predicting the response to FORL infection.
Figure 8. (a) DEGs related to MAPK in Frl and MM samples. (b) DEGs related to WRKY in Frl and MM samples. (c) Network analysis of ‘MAPK signalling pathway-plant’ predicting the response to FORL infection.
Figure 9. Fluctuations in (a) JA and (b) SA as a function of days after FORL infection in Frl tomato and MM tomato. JA, jasmonic acid; SA, salicylic acid; Frl, ‘19912’; MM, ‘Moneymaker’; dpi, days post-infection. Different letters indicate siginificant differences.
Figure 9. Fluctuations in (a) JA and (b) SA as a function of days after FORL infection in Frl tomato and MM tomato. JA, jasmonic acid; SA, salicylic acid; Frl, ‘19912’; MM, ‘Moneymaker’; dpi, days post-infection. Different letters indicate siginificant differences.
Figure 10. Cluster pattern of DEGs produced via MapMan. (a) DEG modulation overview for Frl tomato at 0–3 dpi. (b) DEG modulation overview for MM tomato at 0–3 dpi. (c) Biotic stress and DEG regulation in Frl tomato vs. MM tomato at 3 dpi. (d) Cell reaction and DEG regulation in Frl tomato at 0–3 dpi. (e) Cell reaction and DEG regulation in MM tomato at 0–3 dpi.
Figure 10. Cluster pattern of DEGs produced via MapMan. (a) DEG modulation overview for Frl tomato at 0–3 dpi. (b) DEG modulation overview for MM tomato at 0–3 dpi. (c) Biotic stress and DEG regulation in Frl tomato vs. MM tomato at 3 dpi. (d) Cell reaction and DEG regulation in Frl tomato at 0–3 dpi. (e) Cell reaction and DEG regulation in MM tomato at 0–3 dpi.
Table 1. Statistics for DEGs exhibiting different expression patterns.
Table 1. Statistics for DEGs exhibiting different expression patterns.
| DEG Set | Total DEGs | Upregulated | Downregulated |
| Frl0 vs. Frl3 | 7222 | 3374 | 3848 |
| Frl0 vs. Frl6 | 3545 | 1567 | 1978 |
| Frl3 vs. Frl6 | 4291 | 2398 | 1893 |
| M0 vs. M3 | 8047 | 3972 | 4075 |
| M0 vs. M6 | 4817 | 2316 | 2501 |
| M3 vs. M6 | 2944 | 1473 | 1471 |
| Frl0 vs. M0 | 6951 | 3487 | 3464 |
| Frl3 vs. M3 | 5039 | 2358 | 2681 |
| Frl6 vs. M6 | 2488 | 1222 | 1266 |