Key Genes and Molecular Mechanism Investigation in the Synthesis of Maize Quercetin Based on SNP and Bioinformatics Analysis

This study aimed to reveal the potential genes and mechanisms involved in the biosynthesis of quercetin (QCT) in maize (Zea mays L.) through genome-wide association study (GWAS) and bioinformatics analysis, and provide a basis for further research on QCT. The content of QCT in 196 maize inbred lines was detected by LC-MS. The single-nucleotide polymorphism (SNPs) data from these samples were explored by Maize 55K SNP arrays, followed by population structure using fastStructure software and genome-wide association study (GWAS) analysis. Then, the SNP screening was performed with P < 1.00E-06 using Gramene software, followed by SNP annotation (150 KB up and downstream). The enrichment analysis was performed on all annotated genes. Finally, the protein-protein interaction (PPI) network analysis was performed to further reveal the relations among genes. A total of 12 SNPs were explored from original SNPs with P < 1.00E-06. The SNP annotation revealed several SNP-associated genes including Zm00001d036822 and Zm00001d007407. These genes were mainly enriched in metabolic pathway and functions like negative regulation of cell cycle phase transition. Finally, a PPI work was constructed by totally 34 annotated genes and 59 interactions. Zm00001d036822 and Zm00001d007407 might be novel candidate genes involved in the synthesis of QCT. Meanwhile, the metabolic pathway as well as negative regulation of cell cycle phase transition function might contribute to the biosynthesis of QCT.