ArticleNature genetics2023
A graph-based genome and pan-genome variation of the model plant Setaria.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.
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132 citing papers in PubMed, 200 citations in OpenAlex.
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
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- Multi-environment dissection of the genetic architecture of grain color and milling-related recovery traits in foxtail millet.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Graph-based pangenomics reveals the genetic basis of agronomic traits in tomato fruits.Horticulture research · 2026Article
- Advances in genomics-driven genetic decoding and genomic design breeding in tomato.Horticulture research · 2026Article
- Accelerating iron biofortification in millets: progress, challenges, and future prospects.Planta · 2026Review
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- Genome-wide association analysis and candidate gene identification for plant height in Shanxi local foxtail millet varieties.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
- Graph-based pan-genome reveals structural variations associated with agronomic traits in mung bean.Nature genetics · 2026Article
- Genomic analysis of 3,330 accessions provides insights into the evolutionary history and self-incompatibility locus of the Brassica A genome.Nature genetics · 2026Article
- A domestication gene links plant architecture and nitrogen metabolism to enhance yield in foxtail millet.Nature communications · 2026Article
- Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties.Nature communications · 2026Article
- Abiotic Stress Tolerance in Foxtail Millet (Plants (Basel, Switzerland) · 2026Review
- A fast method for breeding by design via G × E interactions detected in large-scale climatic, phenomic and genomic data.National science review · 2026Article
- Pangenomic analyses of rose uncover widespread structure variation and empower genomics-directed breeding.Nature genetics · 2026Article
- The Genome-Wide Identification and Expression Analysis of the AMT Gene Family in Foxtail Millet.Biology · 2026Article
- Investigating the functions of glycosyl hydrolase family 1 in foxtail millet through an integrated genome-wide survey, expression profiling, and variation analysis.BMC plant biology · 2026Article
72 more citing papers are in PubMed but not listed here.
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Authors and funding
46 authors at 16 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.
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