Collection of maize populations and provides necessary information to understand the population structures.
All annotated metabolites information including metabolites' names, classification, distribution, and chemical structural formulas.
Provides of metabolites difference between different corn groups including T-test, fold-change, and variable importance in projection (VIP).
Collection of maize phenotypes and related genetic locus, including GWAS loci, genes, and corresponding haplotypes.
Li, et al. Large-scale metabolomic landscape of edible maize reveals convergent changes in metabolite differentiation and facilitates its breeding improvement, 28 February 2025, Online now, available at Molecular Plant [https://www.cell.com/molecular-plant/fulltext/S1674-2052(25)00090-5]
The sequencing data have been uploaded to the CNCB database with the project number PRJCA020612.
Released!
Collection of more than 450 inbreds for association mapping panel (AMP) with different populations including Field; Waxy; Sweet.
452 Group INFO
Metabolite data of our panel
We conducted a study to analyze the metabolites present in maize kernels using a comprehensive LC-MS/MS-based metabolic profiling method. In total, we identified 3020 unique metabolites. Among these, we were able to annotate and classify 802 metabolites, which is a significant improvement compared to previous studies. The annotated metabolites span a wide range of classes, including flavonoids, lipids, alkaloids, amino acids, organic acids, phenolic acids, nucleotides, saccharides, alcohols, vitamins, lignans, coumarins, terpenoids, steroids, tannins, and unclassified metabolites. The flavonoid class, for example, consisted of various subclasses such as flavones, flavonols, flavone C-gly, dihydroflavone, and flavanols. This comprehensive dataset provides valuable insights into the metabolome of maize and enhances our understanding of its biochemical composition.
Annotated metabolite INFO
Differentially accumulated metabolites information
The comprehensive dataset of metabolites offers an opportunity to gain insights into the metabolic divergence during the domestication and improvement of maize. Partial least squares discriminant analysis (PLS-DA) was employed to identify the metabolites that significantly contribute to subgroup divergence. Our results indicated that 43.5% and 47.2% of the metabolite features are associated with the divergence in Field-Waxy and Field-Sweet, respectively, as evidenced by variable importance in projection (VIP) scores exceeding 0.8. Even with stringent criteria, with VIP scores exceeding 1, 28.9% and 34.0% of the metabolites were found to be significant in Field-Waxy and Field-Sweet, respectively. Furthermore, the paired t-test (adjusted for false discovery rate (FDR) < 0.05) or fold change (|Fold Change| ≥ 2 or 1.2) analysis of metabolite levels revealed that a majority of these metabolite features exhibit noteworthy divergence or significant changes.
Differentially accumulated metabolites INFO
Loci & haplotype
We conducted a comprehensive genome-wide association study (GWAS) using a linear mixed model (LMM) on a set of 20.3Mb credible single nucleotide polymorphisms (SNPs). To determine significant associations between metabolic traits and genetic variations, we applied a Bonferroni correction with a threshold of P = 4.63 × 10-8. However, it is important to note that the presence of significant genetic differences between sweet corns and other corn varieties (such as waxy and field corns) might obscure the effects of loci with underlying contributions. To overcome this limitation, we identified significant signals in sweet corns, other corn varieties, and all accessions to obtain a more comprehensive understanding of the associations. Remarkably, nearly all of the detected metabolites (755 out of 802) exhibited at least one significant association with genetic variations, with an average of 8.36 associations per metabolite. Furthermore, more than 42% (337 out of 755) of the metabolites displayed no more than 5 associations, indicating that the majority of metabolites are regulated by a small number of genes. To further investigate these candidate genes, we performed haplotype analysis for each gene.
Loci & haplotype INFO
Prediction of relative metabolite content
Comparative Analysis of Metabolites in Sweet/Waxy Corn Within a Population Level
The EMMDB
is a website database, which developed using the R Shiny package, for interactive search and download metabolome data of the maize excellent inbred lines.
For the detail of this website, check the Tutorial
submenu of the Help
menu.
This application was created by Zhiyong Li and Chunhui Li. Please send bugs and feature requests to Feedback
panel. This application uses the shiny package from RStudio.
For Mac users, we recommend using EMMDB with the Google Chrome browser or other browsers developed based on Chrominum.