Identification of genes involved in the tomato root response to Globodera rostochiensis parasitism under varied light conditions

Abstract

Understanding the intricate interplay between abiotic and biotic stresses is crucial for deciphering plant responses and developing resilient cultivars. Here, we investigate the combined effects of elevated light intensity and nematode infection on tomato seedlings. Chlorophyll fluorescence analysis revealed significant enhancements in PSII quantum yield and photochemical fluorescence quenching under high light conditions. qRT-PCR analysis of stress-related marker genes exhibited differential expression patterns in leaves and roots, indicating robust defense and antioxidant responses. Despite root protection from light, roots showed significant molecular changes, including downregulation of genes associated with oxidative stress and upregulation of genes involved in signaling pathways. Transcriptome analysis uncovered extensive gene expression alterations, with light exerting a dominant influence. Notably, light and nematode response synergistically induced more differentially expressed genes than individual stimuli. Functional categorization of differentially expressed genes upon double stimuli highlighted enrichment in metabolic pathways, biosynthesis of secondary metabolites, and amino acid metabolism, whereas the importance of specific pathogenesis-related pathways decreased. Overall, our study elucidates complex plant responses to combined stresses, emphasizing the importance of integrated approaches for developing stress-resilient crops in the face of changing environmental conditions.

Keywords: Abiotic stress; Biotic stress; Cyst nematodes; RNA-seq; Stress combination.

Fig. 1

Chlorophyll a fluorescence in tomato seedlings after transferring to elevated light intensities. (A) Maximum quantum efficiency of PSII photochemistry (F_v/F_m); (B) PSII quantum yield in light-adapted leaves (F_v′/F_m′); (C) PSII quantum yield (PSII Yield); (D) non-photochemical quenching (NPQ); (E) photochemical fluorescence quenching (qP); (F) plant vitality (R_fd). Distribution of data was presented in boxplots (median, quartiles, and potential outliers) from three independent experiments, each containing 3–5 plants per treatment. Statistical analysis was performed by using two-way analysis of variance (ANOVA). Bonferroni test was used for correction for multiple comparisons

Fig. 2

Gene expression analysis in leaves and roots of tomato plants. qRT-PCR analysis of marker genes linked to photochromes, ROS metabolism, and phytohormones related to biotic stress were examined in leaves (A) and roots (B) of tomato plants after transferring to elevated light intensities. The expression levels of target genes were quantified with reference to the expression of RPL8 and SAND compared to the control (plants grown in low light intensities). The relative expression levels are shown as logarithm of fold changes relative to the copy number of a particular mRNA gene in the control sample. Results are the means (± SEM; standard error of mean) from three independent experiments. The asterisks indicate the significant differences from the control as revealed by REST (Pfaffl et al. 2002) (p < 0.05)

Fig. 3

Chlorophyll a fluorescence in infected tomato seedlings after transferring to elevated light intensities. (A) Maximum quantum efficiency of PSII photochemistry (F_v/F_m); (B) PSII quantum yield in light-adapted leaves (F_v′/F_m′); (C) PSII quantum yield (PSII yield); (D) non-photochemical quenching (NPQ); (E) photochemical fluorescence quenching (qP); (F) plant vitality (R_fd). Distribution of data was presented in boxplots (median, quartiles, and potential outliers) from three independent experiments, each containing 3–5 plants per treatment. Statistical analysis was performed by using one-way analysis of variance (ANOVA). Tukey test was used for correction for multiple comparisons

Fig. 4

Nematode infection assay on tomato roots infected by Globodera rostochiensis pathotype Ro1. The numbers of developed syncytia were counted at 14 dpi and represented as boxplots. Data was collected from three independent experiments. Statistical analysis was performed by using t-test (p < 0.05)

Fig. 5

Number of DEGs after infections with G.rostochiensis at 14 dpi in roots containing syncytia. (A) Total number of DEGs in response to different conditions. (B) Venn diagram presenting the DEGs grouped according to the changes in their expression relative to the type of comparison

Fig. 6

Gene ontology enrichment analysis within DEG groups. The KEGG pathways enriched in tomato roots due to G. rostochiensis parasitism under different light intensities

Fig. 7

Comparison of tomato transcriptomic responses to G. rostochiensis parasitism. Venn diagrams showing the number of mapped DEGs described here and in cDNA-AFLP approaches