ArticleGenome biology2021
Cotton pan-genome retrieves the lost sequences and genes during domestication and selection.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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97 citing papers in PubMed.
- Cotton Salt Stress Resilience: Integrating Physiological, Molecular, and Agronomic Strategies for Next-Generation Breeding.Plant, cell & environment · 2026Review
- Regulatory divergence of homoeologs underlies network optimization for fiber improvement in domesticated cotton.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Pan-Genome Analysis of theGenes · 2026Article
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Genomic reconstruction of upland cotton domestication uncovers staged selection, gene flow, and flowering-time adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Three Decades of China's Bt Cotton: Achievements and Insights.Plant biotechnology journal · 2026Review
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Integrating pan-genome analysis, GWAS, and interpretable machine learning to prioritize trait-associated structural variations in Setaria italica.Plant communications · 2026Article
- Harnessing genomic resources for passion fruit improvement: Progress and prospects.The plant genome · 2026Review
- Bridging the Divide: Integrating Cottonseed Oil Content with Agronomic Trait Improvement in Upland Cotton (Plants (Basel, Switzerland) · 2026Review
- Pan-genome of wild and cultivated rice uncovers genetic diversity, lost and selected sequences during rice domestication.Rice (New York, N.Y.) · 2026Article
- Excavation and effect analysis of interaction sites between upland cotton yield and fiber quality traits and environmental factors.BMC plant biology · 2026Article
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- Speed breeding in upland cotton (Frontiers in plant science · 2026Review
- Genomic and epigenomic coordination maintains subgenome transcriptional balance in allotetraploidHorticulture research · 2026Article
- Graph pan-genome advances genetic discoveries and the improvement of eggplant.Horticulture research · 2026Article
- High-quality draft genome assembly and functional annotation ofFrontiers in plant science · 2026Article
- Comparative single-cell transcriptomic map reveals divergence in leaves between two cotton species at cell type resolution.Journal of advanced research · 2026Article
37 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMillennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components.
resultsWe construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci.
conclusionsThis variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.
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