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Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits and anti-inflammatory effects

ABSTRACT: Foxtail millet, domesticated from the wild species green foxtail, provides a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail millet grains, we generated and analyzed datasets encompassing genomes, transcriptomes, metabolomes and anti-inflammatory indices from 398 foxtail millet accessions. We identified hundreds of common variants that influence numerous secondary metabolites, with significant heterogeneity in the natural variation of metabolites and their underlying genetic architectures between different sub-groups of foxtail millet. The combined results from variations in genome, transcriptome and metabolome illustrated how breeding has altered foxtail millet metabolite content. Selection for alleles of genes associated with yellow grains led to altered metabolite profiles, such as carotenoids and endogenous hormones. The importance of PSY1 (phytoene synthase 1) for millet color was validated using CRISPR-Cas9. The in vitro cell inflammation assay showed that 83 metabolites have anti-inflammatory effects. This multi-omics study illustrates how the breeding history of foxtail millet has impacted metabolites. It provides some fundamental resources for understanding how grain quality could be associated with different metabolites, and highlights future perspectives on millet genetic research and metabolome-assisted improvement.

ORGANISM(S): Foxtail Millet (setaria Italica) Setaria Italica Millet

TISSUE(S): Seeds

SUBMITTER: Xukai Li

PROVIDER: ST002168 | MetabolomicsWorkbench | Mon May 09 00:00:00 BST 2022

REPOSITORIES: MetabolomicsWorkbench

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