Combinatorial analysis of transcription and metabolism reveals the regulatory network associated with antioxidant substances in waxy corn

Abstract Maize is an essential source of nutrition for humans and animals and is rich in various metabolites that determine its quality. Different maize varieties show significant differences in metabolite content. Two kinds of waxy maize parental materials, S181 and 49B, created by the Chongqing Academy of Agricultural Sciences, are widely grown in China. S181 shows higher starch and sugar contents than 49B. This study generated metabolic profiles to assess the differences between the two varieties. A total of 674 metabolites that were significantly differentially expressed between the two varieties were identified by gas chromatography and untargeted metabolomics technology. These metabolites were associated with 21 categories, including antioxidant metabolites. Moreover, 6415 differentially expressed genes (DEGs) were identified by RNA-seq. Interestingly, these DEGs comprised starch and sugar synthesis pathway genes and 72 different transcription factor families. Among these, six families that were reported to play an essential role in plant antioxidant action accounted for 39.2% of the transcription factor families. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) classification, the DEGs were mainly involved in amino acid biosynthesis, glycolysis/glucose metabolism, and the synthetic and metabolic pathways of antioxidant active substances. Furthermore, the correlation analysis of transcriptome and metabolomics identified five key transcription factors (ZmbHLH172, ZmNAC44, ZmNAC-like18, ZmS1FA2, ZmERF172), one ubiquitin ligase gene (ZmE2 5A) and one sucrose synthase gene (ZmSS1). They likely contribute to the quality traits of waxy corn through involvement in the metabolic regulatory network of antioxidant substances. Thus, our results provide new insights into maize quality-related antioxidant metabolite networks and have potential applications for waxy corn breeding.