Czech J. Genet. Plant Breed., 2025, 61(3):160-179 | DOI: 10.17221/45/2025-CJGPB

Transcriptome analysis reveals differential gene expression in tomato under high-temperature stress

Yun Li¹, Xin Ye¹, Lingzeng Lv¹, Na Chen^1*

¹ College of Life Science and Resources and Environment, Yichun University, Yichun, China

Tomato is a major global crop, extensively cultivated in China. However, the molecular mechanisms underlying its responses to high-temperature stress remain poorly understood. This study investigates these mechanisms by examining a heat-resistant tomato variety, Hm 2-2 (R), and a heat-sensitive variety, BY 1-2 (S), under high temperature (40 °C). Total RNA was extracted from samples taken at 0 and 24 h post-treatment, followed by RNA-sequencing (RNA-seq). Differentially expressed genes (DEGs) were screened based on the criteria of |log₂ fold change| ≥ 2 and false discovery rate ≤ 0.05. Gene ontology (GO) function annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway enrichment analysis were performed to explore the biological significance of these DEGs. The results revealed 6 038 upregulated and 2 866 downregulated DEGs in the R-0 (Hm 2-2 plants treated at 40 °C for 0 h) vs. R-24 (Hm 2-2 plants treated at 40 °C for 24 h) group and 5 297 upregulated and 3 920 downregulated DEGs in the S-0 (BY 1-2 plants treated at 40 °C for 0 h) vs. S-24 (BY 1-2 plants treated at 40 °C for 24 h) group, respectively. GO enrichment analysis indicated that the majority of DEGs were associated with biological processes, followed by cellular components and molecular functions. KEGG pathway analysis identified 130, 131, 89, and 115 regulatory (or altered) pathways in the R-0 vs. R-24, S-0 vs. S-24, S-0 vs. R-0, and S-24 vs. R-24 group comparisons, respectively. Notably, pathways related to protein processing in the endoplasmic reticulum and plant hormone signal transduction were significantly enriched, suggesting their critical roles in the tomato’s response to heat stress. Moreover, 156 transcription factors (TFs) implicated in heat stress response were identified, spanning various TF families such as MYB, AP2-EREBP, b-ZIP, bHLH, NAC, and WRKY. Quantitative RT-PCR analysis of 14 randomly selected DEGs validated the RNA-seq results confirming the reliability of the data. In summary, this study provides valuable insights into the molecular mechanisms of tomato’s responses to high-temperature stress, laying a crucial foundation for future research in this area.

Keywords: gene expression profile; heat response; quantitative RT-PCR; RNA-seq; transcription factors

Received: June 14, 2025; Revised: July 30, 2025; Accepted: July 30, 2025; Prepublished online: August 7, 2025; Published: September 5, 2025  Show citation