Molecular and biochemical components associated with chilling tolerance in tomato: comparison of different developmental stages

Abstract

The cultivated tomato, Solanum lycopersicum, is highly sensitive to cold stress (CS), resulting in significant losses during cultivation and postharvest fruit storage. Previously, we demonstrated the presence of substantial genetic variation in fruit chilling tolerance in a tomato recombinant inbred line (RIL) population derived from a cross between a chilling-sensitive tomato line and a chilling-tolerant accession of the wild species S. pimpinellifolium. Here, we investigated molecular and biochemical components associated with chilling tolerance in fruit and leaves, using contrasting groups of "chilling tolerant" and "chilling sensitive" RI lines. Transcriptomic analyses were conducted on fruit exposed to CS, and gene expressions and biochemical components were measured in fruit and leaves. The analyses revealed core responding genes specific to either the cold-tolerant or cold-sensitive RI lines, which were differentially regulated in similar fashion in both leaves and fruit within each group. These genes may be used as markers to determine tomato germplasm cold tolerance or sensitivity. This study demonstrated that tomato response to CS in different developmental stages, including seedling and postharvest fruit, might be mediated by common biological/genetic factors. Therefore, genetic selection for cold tolerance during early stages of plant development may lead to lines with greater postharvest fruit chilling tolerance.

Keywords: Chilling; Cold; Postharvest; Storage; Tomato.

Fig. 1

Overview of the transcriptomics of fruit response to cold stress in sensitive (5, 135, 150) and tolerant (47,65, 99) RILs. A Heat map showing the expression of differentially regulated genes (DEGs) among sensitive and tolerant RILs before cold stress. B Heat map showing the expression DEGs among sensitive and tolerant RILs after two hours of exposure. C Heat map showing the expression of 486 DEGs among sensitive and tolerant RILs after twenty-four-hour exposure to cold stress. D Gene ontology (GO) enrichment analysis of 486 DEGs from tomato fruit after twenty-four-hour exposure to cold stress using KOBAS. E The highly expressed 21 genes linked with calcium-mediated signaling among the 486 DEGs are presented. In the heat map, the dark red color denotes the highly up-regulated expression, and the sky-blue color denotes the down-regulated expression. S, cold-sensitive RILs, T, cold tolerant RILs. DEGs analysis was performed with DESeq2 R package (twofold, FDR < 0.05)

Fig. 2

Common transcriptomic response of all six RIL fruits following 24 h exposure to 1.5°C temperature. All 2454 cold-responsive DEGs identified in all six RIL fruits were bioinformatically analyzed. A Bubble plot displaying GO classification and KEGG categories classifications of commonly expressed functionally annotated 2454 DEGs from all six RILs cold-sensitive (5, 135 and 150) and cold tolerant (47,65 and 99). B Heatmap analysis presenting common response of genes included in BP term—response to heat. C Expression pattern of cluster 2, 621 DEGs. D Bubble plot displaying GO classification and KEGG categories classifications for functionally annotated DEGs commonly expressed and grouped in cluster 2. E Heatmap analysis presenting common response of genes included in the GO term—response to stimuli included in cluster 2. F Expression pattern of cluster 4, 198 DEGs. G Bubble plot displaying GO classification and KEGG categories classifications for functionally annotated DEGs commonly expressed and grouped in cluster 4. H Expression pattern of cluster 5, 270 DEGs. I Bubble plot displaying GO classification and KEGG categories classifications for functionally annotated DEGs commonly expressed and grouped in cluster 5. J Heatmap analysis presenting common response of genes included in the GO term—protein folding included in cluster 5. K Expression pattern of cluster 8, 275 DEGs. L Bubble plot displaying GO classification and KEGG categories classifications for functionally annotated DEGs commonly expressed and grouped in cluster 8. In heatmaps, the dark red color denotes up-regulated DEGs, and the sky-blue color denotes down-regulated DEGs. GO enrichment analysis of 2454 genes were done using KOBAS and PANTHER. DEGs analysis was performed with DESeq2 R package (twofold, FDR < 0.05)

Fig. 3

Susceptibility to cold stress of vegetative tissue in different tomato RILs. A, B Cold sensitive (71, 135, 150) and cold tolerant (47, 65, and 99) RILs were grown in perlite, and young plants (~ 30 days old; ~ 20–30 cm tall) were incubated at 1.5°C in the light for three days. Cold sensitive (5, 71, 90, 150) and cold tolerant (47, 49, 65, 99) RILs were grown in sand soil (C, D) or MS plates (~ 10 days old; ~ 8–10 cm tall) (E, F), and young plants were incubated in 1.5°C for 24 h followed with growth recovery at 25°C for 10 days. G Total chlorophyll content after 10 days of cold recovery of MS-grown plants. Bars with different letters indicate significant differences between sensitive and tolerant lines. One-way ANOVA p ≤ 0.05, as determined by Turkey-Kramer HSD

Fig. 4

Physiological and biochemical markers indicative of chilling injury development in leaves of different tomato RILs. The different parameters were measured in soil-grown plants (~ 30 days old), including cold-sensitive (5, 71, 90, 150) or cold-tolerant (47, 49, 65, 99) RILs. A-C The impact of cold treatment on the index of leaf injury. D index of electrolyte leakage. E H₂O₂ content. F MDA content. Additionally, (G) the index of ion leakage and (H) MDA content were measured in MS-grown seedlings (~ 10 days old) following cold stress. Data are means ± SE, n = 4; biological replicates. Different lowercase letters indicate significant differences between sensitive and tolerant lines. One-way ANOVA p ≤ 0.05, as determined by Turkey-Kramer HSD

Fig. 5

Changes in starch and sugar levels in cold-tolerant and sensitive RILs during exposure to cold stress. Sugar content was measured in leaves of soil-grown plants (~ 30 days old), including cold-sensitive (5, 71, 90, 150) or cold-tolerant (47, 49, 65, 99) RILs following 24 h in 1.5°C. A and B starch content; (C) sucrose content; (D) glucose content; and (E) fructose content. Data are means ± SE, n = 4; biological replicates. Bars with different letters indicate significant differences between sensitive and tolerant lines. One-way ANOVA p ≤ 0.05, as determined by Turkey-Kramer HSD and T_test (sucrose)

Fig. 6

Expression of specific genes in leaves of cold-tolerant or cold-sensitive RILs following by cold stress. Gene expression was measured using RT-qPCR in leaves of cold-sensitive (5, 71, 90, 150) and cold-tolerant (47, 49, 65, 99) RILs. Soil-grown plants (~ 30 days old) were exposed to cold stress at 1.5ºC for 2 or 24 h. Data are means ± SE (n = 3 biological replicates). Bars with different letters indicate significant differences between sensitive and tolerant lines. One-way ANOVA p ≤ 0.05, as determined by Turkey-Kramer HSD