A Multi-Omics View of Maize’s (Zea mays L.) Response to Low Temperatures During the Seedling Stage

Maize (<i>Zea mays</i> L.) is highly sensitive to temperature during its growth and development stage. A 1 °C drop in temperature can delay maturity by 10 days, resulting in a yield reduction of over 10%. Low-temperature tolerance in maize is a complex quantitative trait, and different germplasms exhibit significant differences in their responses to low-temperature stress. To explore the differences in gene expression and metabolites between B144 (tolerant) and Q319 (susceptible) during germination under low-temperature stress and to identify key genes and metabolites that respond to this stress, high-throughput transcriptome sequencing was performed on the leaves of B144 and Q319 subjected to low-temperature stress for 24 h and their respective controls using Illumina HiSeq^TM 4000 high-throughput sequencing technology. Additionally, high-throughput metabolite sequencing was conducted on the samples using widely targeted metabolome sequencing technology. The results indicated that low-temperature stress triggered the accumulation of stress-related metabolites such as amino acids and their derivatives, lipids, phenolic acids, organic acids, flavonoids, lignin, coumarins, and alkaloids, suggesting their significant roles in the response to low temperature. This stress also promoted gene expression and metabolite accumulation involved in the flavonoid biosynthesis pathway. Notably, there were marked differences in gene expression and metabolites related to the glyoxylate and dicarboxylate metabolism pathways between B144 and Q319. This study, through multi-omics integrated analysis, provides valuable insights into the identification of metabolites, elucidation of metabolic pathways, and the biochemical and genetic basis of plant responses to stress, particularly under low-temperature conditions.