Transcriptome Analysis of Germinated Maize Embryos Reveals Common Gene Responses to Multiple Abiotic Stresses

Maize seeds undergo a rapid germination phase, spanning from dry seeds to radicle protrusion, which is highly susceptible to various abiotic stresses. However, the specific distinctions between responses to different abiotic stresses and the genes commonly activated across multiple stresses remain largely unreported. Here, we performed a transcriptome analysis using germinating embryos subjected to low-temperature stress (LTS), high-temperature stress (HTS), drought stress (DS), and salinity stress (SS) at two key germination stages: the imbibition saturation stage and radical protrusion stage. By comparing these samples to dry embryos, we first identified germination-related genes active at both stages. Subsequently, we compared stressed samples to non-stressed controls under standard germination conditions to exclude genes influenced solely by developmental progression. This ultimately identified 1226, 2418, 1298, and 850 DEGs stress-responsive differentially expressed genes (srDEGs) at the imbibition saturation stage for LTS, HTS, DS and SS, respectively, alongside 1995, 1437, 1741 and 1555 srDEGs at the radicle protrusion stage. Through a cross-stress comparison, we identified 214 to 1563 single-stress-responsive, 35 to 414 dual-stress-responsive, and 33 to 243 triple-stress-responsive srDEGs. Notably, we detected 44 and 235 common stress-responsive (co-srDEGs) across all four stresses at the imbibition saturation and radicle protrusion stage, respectively. These co-srDEGs were primarily associated with reactive oxygen species (ROS) metabolism, hormone signaling, and transcriptional regulation. Among the co-srDEGs, we identified 20 transcription factors (TFs) representing 11 families, which may serve as critical candidate genes for regulating multi-stress tolerance. The expression of four TFs was further verified by qPCR analysis. These findings not only highlight the differences and similarities in the regulatory networks underlying LTS, HTS, DS and SS during germination but also provide essential candidate genes for elucidating the mechanisms of seed germination in response to multiple abiotic stress.