Integrated metabolomics and transcriptomics analysis during seed germination of waxy corn under low temperature stress

BACKGROUND: Waxy corn has a short growth cycle and high multiple cropping index. However, after being planted in early spring, late autumn and winter, it is susceptible to low temperature (LT), which reduces the emergence rate and yield. Therefore, it is important to analyze the response mechanism of waxy corn under LT stress. RESULTS: All phenotype indexes of waxy corn inbred lines N28 were significantly higher than waxy corn inbred lines N67 under LT. With the increase of LT stress time, all physiological indexes showed an upward trend in N28 and N67. Differentially expressed genes (DEGs) 16,017 and 14,435 were identified in N28 and N67 compared with nongerminated control under LT germination, respectively, and differential metabolites 127 and 93 were detected in N28 and N67, respectively. In addition, the expression level of some genes involved in plant hormones and mitogen activated protein kinase (MAPK) signaling pathways was significantly up-regulated in N28. Compared with N67, flavonoid metabolites were also significantly enriched in N28 under LT germination. CONCLUSION: Under LT stress, the inbred lines N28 was significantly higher than the inbred lines N67 in the phenotypic and physiological indices of cold resistance. Compared with N67, the expression levels of some genes involved in the plant hormones and MAPK pathways were significantly up-regulated in N28, and flavonoid metabolites were also significantly enriched in N28 under LT stress. These genes and metabolites may help N28 to improve cold resistance and may be as potential target genes for cold resistance breeding in waxy corn. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04195-x.