Project description: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.
2022-05-09 | ST002168 | MetabolomicsWorkbench
Project description:A high-quality genome from a medieval broomcorn millet (as Panicum miliaceum L.) grain excavated from the Areni-1 cave in Armenia
Project description:TAM 111 and TAM 112 are two popular cultivars grown in the Southern US Great Plains with significantly different protein content. Thus, to investigate likely regulatory differences, transcriptome data were analyzed from developing grains at early- and mid-filling stages.
Project description:The experiment was conducted to examine the influence of non-chloroplast genomes rearangements on chloroplast transcription in cucumber
Project description:The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts.
Project description:Here we developed a new high-throughput polymorphism detection and genotyping method based on identifying restriction cut site polymorphisms using a microarray platform. We compared the genomes of 20 individual urchins; 10 from the northern part of the species range (Boiler Bay, OR) and 10 from the southern part of the range (San Diego, CA).
