A pangenome reference and population studies link structural variants with breeding traits in Gossypium hirsutum

Limited pangenome and ambiguous genomic architecture constrain comprehensive genetic variation discovery and cotton improvement. Here we assembled a telomere-to-telomere (T2T) genome for elite cultivar NDM13 and near-T2T genomes for 27 additional representatives of Gossypium hirsutum over the recent century, with transcriptomic profiling of 15 distinct tissues from each. We uncovered 51,551 one-to-one conserved orthologs across all genomes and landscapes of telomere, centromere, 45S rDNA, segmental duplication and copy number variant. We revealed hotspots of structural variation (SV) and impacts of SV, segmental duplication and copy number variant on gene expression or content alteration, as well as adversity resistances. We identified thousands of divergent SVs and genes implicated in modern breeding evolution. Combining T2T-reference-based pangenome construction and 761,536 SVs identified across 1,671 worldwide accessions with phenotypic data from 22 environments, we captured a number of hidden SVs that potentially influence critical breeding traits. These will boost genetic study and biotechnological improvement of the crop.