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

Foxtail millet(Setaria italica),which was domesticatedfromthewild speciesgreenfoxtail(Setaria viridis),isa richsource of phytonutrientsfor humans.To evaluate how breeding changed themetabolome offoxtail millet grains,we generated and analyzed the datasets encompassing the genomes,transcriptomes,metabolomes,and anti-inflammatory indices from 398 foxtail millet accessions.We identified hundreds of common variants that influence numerous secondary metabolites.We observed tremendous differences in natural variations of the metabolites and their underlying genetic architectures between distinct sub-groups of foxtail millet.Furthermore,we found that the selection of the gene alleles associated with yellow grains led to altered profiles of metabolites such as carotenoids and endogenous phytohormones.Using CRiSPR-mediated genome editing wevalidated the function of PHYTOENE SYNTHASE1(PSY1)gene in affecting milletgrain colorand quality.Interestingly,our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects.Taken together,ourmulti-omics study illustrates how the breeding history of foxtail millet has shaped its metabolite profile.The datasets we generated in this study also provide important resources for further understanding how millet grain quality is affected by different metabolites,laying the foundations for future millet genetic research and metabolome-assisted improvement.

Effect of water-driven changes in rice rhizosphere on Cd lability in three soils with different pH

Pot experiments were conducted to evaluate the effect of water management,namely continuous flooding(CF),intermittent flooding(IF)and non-flooding(NF),on Cd phytoavailaility in three paddy soils that differed in p H and in Cd concentrations.Diffusive gradients in thin films(DGT)technique was employed to monitor soil labile Cd and Fe concentrations simultaneously at three growth stages(tillering,heading and mature stage)of rice.The Cd phytoavailability were generally in the order of NF>IF>CF,and higher rice Cd(over permitted level,0.2 mg/kg)were only found in neutral and acidic soils under NF conditions.DGT measured soil labile Cd rather than total Cd was the most reliable predictor for Cd accumulation in rice.CF enhanced the formation of root plaques,which related to oxidation of large quantities of available Fe on root surfaces due to the O2 secretion of rice root.The Cd concentration in root plaques shared the same trend with DGT-Cd.Generally,root plaques would inhibit Cd uptake by rice under CF conditions,while under IF and NF conditions,root plaques act as a temporarily store of Cd,and soil labile Cd is the key factor that controls the transfer of Cd from soil to rice.The results of principle component analysis revealed that water management had the greatest effect on soil Cd lability and rice Cd in acidic soil.Thus,it is important to consider the availability of Cd and soil p H when assessing current agricultural practices of contaminated soil in China.