ArticleNature genetics2026
Graph pan-genome illuminates evolutionary trajectories and agronomic trait architecture in allotetraploid cotton.
Article in Nature genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- A structural variation-driven evolutionary history of upland cotton.Science China. Life sciences · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Pan-Genome Analysis of theGenes · 2026Article
- Multiple environmental test and genetic mapping jointly reveal genomic loci and associated genes underlying cotton Verticillium wilt resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 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
- Genetic dissection of plant architecture, development, and seed morphology in exotic × elite Upland cotton populations.The plant genome · 2026Article
- Genomic diversity and the domestication history of cotton (Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A pangenome reference and population studies link structural variants with breeding traits in Gossypium hirsutum.Nature genetics · 2026Article
- Comparative genomics and phylogenetic analysis of three Malvaceae species on the basis of chloroplast genomes.Frontiers in plant science · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- Synergistic improvement of high glyphosate resistance and high yield with environmental safety assessment.Frontiers in plant science · 2026Article
- Cotton genetic mapping for plant biotechnology: from markers to graph pan-genomes and sustainable breeding.Frontiers in plant science · 2026Review
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18 authors.
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Abstract
Upland cotton (Gossypium hirsutum), one of the world's major fiber crops, faces challenges from the genetic homogeneity of modern varieties. Here we present 107 gold-standard genome assemblies spanning the wild-to-domesticated continuum, revealing six large-scale structural variations, including a chromosomal reciprocal translocation and five inversions tracing the evolutionary history of cultivated cotton in the Americas. This history also involved continuous introgression from Gossypium barbadense, shaping the genetic diversity of G. hirsutum landraces and cultivars. Leveraging the graph pan-genome, we capture the sequence and structural diversity of nucleotide-binding site-leucine-rich repeat genes, uncovering pathogen-driven selection signatures and loci associated with disease resistance. A presence-absence variation genome-wide association study (GWAS) identified previously overlooked loci for key fiber traits, complementing single-nucleotide polymorphism-GWAS findings. Additionally, we construct a detailed map of large inversions, offering insights into hybridization dynamics and strategies to mitigate linkage drag. This study enhances our understanding of cotton evolution and domestication while delivering a valuable resource to enhance breeding.
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