Exploring the characteristics of maize’s tolerance to low-temperature stress is of great significance for enhancing maize’s adaptability to such stress and for developing valuable germplasm resources. In this study, a combined analysis of genomics, transcriptomics, and metabolomics was conducted on maize 245 F7 recombinant inbred lines (RILs) to screen for candidate genes and differential metabolites controlling the cold tolerance of maize during the germination stage. Bulked segregant analysis-sequencing (BSA-seq) located four candidate regions on chromosome 1 (qSGRL1-2, qSGRL1-3, and qSGRL1-4) and chromosome 10 (qSGRL10), which altogether contained 109 candidate genes. Combined with the transcriptome sequencing results, among the genes screened by quantitative trait locus sequencing (QTL-seq), seven genes (Zm00001eb043000, Zm00001eb043620, Zm00001eb043650, Zm00001eb043680, Zm00001eb043720, Zm00001eb043400, and Zm00001eb043490) were identified as common candidate genes related to the cold tolerance of maize during the germination stage. Combined with the metabolomic analysis results, low-temperature stress induced the differential expression of relevant genes, leading to the differential accumulation of metabolites such as L-glutamic acid, 4-aminobutyric acid, and Lysophosphatidylcholine (LPC). These results enrich the information for molecular marker-assisted selection of maize tolerance to low-temperature stress and provide genetic resources for the maize varieties breeding.

Seed germination is a critical determinant of seedling establishment, stress resistance, and final yield. ABA catabolism plays a central role in releasing seed dormancy and promoting germination, and ABA8ox is the key rate-limiting enzyme in this process. In this study, we used wild-type maize B73, and ZmABA8ox1b CRISPR-Cas9 knockout mutant as materials to investigate the biological function of ZmABA8ox1b. Compared with the wild type, the zmaba8ox1b mutant significantly delayed seed germination and enhanced the sensitivity to exogenous ABA. Endogenous ABA content in mutant embryos was drastically increased, indicating that ZmABA8ox1b is essential for ABA degradation during germination. The loss of ZmABA8ox1b function led to the activation of the ABA signaling pathway and severely impaired the responsiveness to exogenous ABA. Moreover, the mutation disturbed the expression and ABA responsiveness of auxin, gibberellin, ethylene, jasmonic acid, and brassinosteroid pathways, leading to a hormonal network imbalance. In conclusion, ZmABA8ox1b positively regulates maize seed germination by coordinating ABA catabolism and multi-hormone signal crosstalk. This study preliminarily clarifies the molecular mechanism of ZmABA8ox1b in germination control and provides important gene resources and theoretical support for breeding maize varieties.