On March 20, the research team led by Professor Ma Zhiying from Hebei Agricultural University published a research paper titled “A pangenome reference and population studies link structural variants with breeding traits in Gossypium hirsutum” in the international top journal Nature Genetics. This landmark work constructed the first telomere-to-telomere (T2T) pangenome reference for cotton and revealed the structural variations and gene effects during a century of upland cotton breeding.
Cotton has shaped global history, propelled industrialization, and advanced human civilization. Crop variety innovation is the foundation of industry development; however, limited pangenome resources and ambiguous genomic architectures have hindered comprehensive discovery of genetic variations and precise improvement of breeding traits. This study first assembled the T2T genome of the high-quality upland cotton variety “Nongda Mian 13” (NDM13), along with near-T2T genomes of 27 other representative varieties spanning the past century. The researchers identified 51,551 one-to-one conserved orthologous genes present across all genomes, and mapped the chromosomal distributions of telomeres, centromeres, 45S rDNA, segmental duplications (SD), and copy number variations (CNV). They further constructed transcriptome profiles across 15 different plant tissues from 28 varieties, revealing hotspots of structural variants (SV) and demonstrating how SV, SD, and CNV influence gene expression, content variation, and stress resistance. Thousands of differential SVs associated with modern breeding evolution and their linked genes were discovered. Leveraging the NDM13-based T2T reference pangenome and phenotypic data from 22 environments (locations and years) across China’s three major cotton regions—the Yangtze River Basin, the Yellow River Basin, and the Northwestern Inland Region—the team identified over 760,000 SVs in more than 1,600 germplasm samples globally, capturing numerous SVs significantly impacting key breeding traits.
This breakthrough is likely to significantly advance genetic research and biotechnological improvement in crops.
