Comprehensive physiological and transcriptomic analysis of seed germination in two tomato inbred lines under low-temperature stress

Abstract Low-temperatures severely limit tomato seed germination, leading to reduced crop yields. Elucidating the cold resistance regulatory mechanisms is crucial for cold-resistant breeding. This study used the cold-tolerant tomato inbred line F266 and the cold-sensitive inbred line M196 as experimental materials. Phenotypic analysis revealed that under normal-temperature conditions of 25°C, there was no significant difference in germination rates between the two inbred lines. However, under low-temperature treatment of 16°C, F266 germinated earlier and exhibited a more pronounced advantage in hypocotyl elongation. Comparative transcriptome analysis results indicate that the two lines exhibit genotype-specific differences in oxidative stress response, carbohydrate metabolism, and plant hormone signaling pathways. F266 has a stronger antioxidant response capability, with higher accumulation of galactinol, raffinose, and sucrose. At the same time, F266 has higher endogenous auxin (IAA) and gibberellin (GA₃) content, and genes related to auxin and gibberellin show differential expression. Integrative analysis further identified candidate genes from the ANN p35、GATA、CAMTA、MAPK、WRKY58、WRKY33 and bHLH150, which may mediate the interactions between the aforementioned response modules. This result provides a new theoretical basis for subsequent gene function validation, improvement of tomato cold germination traits, and the development of cold-resistant tomato breeding.