Comparison of Tomato Transcriptomic Profiles Reveals Overlapping Patterns in Abiotic and Biotic Stress Responses

Abstract

Until a few years ago, many studies focused on the transcriptomic response to single stresses. However, tomato cultivations are often constrained by a wide range of biotic and abiotic stress that can occur singularly or in combination, and several genes can be involved in the defensive mechanism response. Therefore, we analyzed and compared the transcriptomic responses of resistant and susceptible genotypes to seven biotic stresses (Cladosporium fulvum, Phytophthora infestans, Pseudomonas syringae, Ralstonia solanacearum, Sclerotinia sclerotiorum, Tomato spotted wilt virus (TSWV) and Tuta absoluta) and five abiotic stresses (drought, salinity, low temperatures, and oxidative stress) to identify genes involved in response to multiple stressors. With this approach, we found genes encoding for TFs, phytohormones, or participating in signaling and cell wall metabolic processes, participating in defense against various biotic and abiotic stress. Moreover, a total of 1474 DEGs were commonly found between biotic and abiotic stress. Among these, 67 DEGs were involved in response to at least four different stresses. In particular, we found RLKs, MAPKs, Fasciclin-like arabinogalactans (FLAs), glycosyltransferases, genes involved in the auxin, ET, and JA pathways, MYBs, bZIPs, WRKYs and ERFs genes. Detected genes responsive to multiple stress might be further investigated with biotechnological approaches to effectively improve plant tolerance in the field.

Keywords: cell wall; genome editing; phytohormones; plant stress; signaling; transcription factors; transcriptomics.

Figure 1

The intersection of up and down DEGs induced by tomato genotypes infected with fungi and bacteria (first 30 intersections). (A) Susceptible genotypes infected with fungi. (B) Resistant genotypes infected with fungi. (C) Susceptible genotypes infected with bacteria. (D) Resistant genotype infected with bacteria. In red are DEGs with the same expression trend in all the analyzed datasets.

Figure 2

Private DEGs identified in R and S genotypes to fungi, bacteria, and Tuta absoluta. CR = common DEGs among R genotypes; CS = common DEGs among S genotypes; T = tolerant; S = susceptible genotypes.

Figure 3

Genes putatively involved in biotic stress response under fungi, bacteria, TSWV, and T. absoluta infections. Blue: upregulated, red: downregulated genes. R = resistant; S = susceptible; T = tolerant genotype.

Figure 4

DEGs under various biotic stress involved in the biosynthesis of cell wall precursors. Blue: upregulated; red: downregulated. R = resistant; S = susceptible; T = tolerant genotype.

Figure 5

Heat map of DEGs participants in the signaling process. The expression pattern of DEGs identified and their function have been reported. Blue = upregulated, and red = downregulated genes. R = resistant; S = susceptible; T = tolerant genotype.

Figure 6

(A) Heatmap of DEGs induced during different abiotic stress; (B) Number of DEGs induced by different abiotic stress with a focus on private DEGs induced by tolerant and susceptible genotypes to drought. Blue = Upregulated and Red = Downregulated. R = resistant; S = susceptible; T = tolerant genotype.

Figure 7

DEGs involved in signaling, cell wall, hormones, and TFs. Blue = upregulated; red = downregulated genes.

Figure 8

Common DEGs in biotic and abiotic stress related to signaling, cell wall, hormones and transcription factors (TFs). (P) = private DEGs; R = resistant genotype; S = susceptible genotypes; T = tolerant genotype.

Figure 9

DEGs responsive to biotic and abiotic stresses, encoding for cell wall precursors, signaling proteins, hormones, and TFs. Blue = upregulated; red = downregulated genes. R = resistant; S = susceptible; T = tolerant genotypes.