Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

棉花（ Gossypium hirsutum L.）是全球主要的可再生纤维作物，但由于基因型特异性以及品种、管理实践和环境因素之间复杂的相互作用，其产量和纤维质量表现出很大的变异性。由于创始基因库狭窄，现代育种实践可能会限制未来的产量增长。精准育种和生物技术方法提供了潜在的解决方案，具体取决于准确的品种特定数据。在这里，我们通过为三个现代棉花品种（“UGA230”、“UA48”和“CSX8308”）生成高质量参考基因组并更新“TM-1”棉花遗传标准参考来满足这一需求。尽管假设遗传一致性，但在四个基因组中观察到相当大的序列和结构变异，这些变异与来自“皮马”棉花的古老和持续的基因组渗入、基因调控机制和表型性状差异重叠。纤维发育过程中差异表达的基因与纤维生产相关，可能有助于在现代棉花品种中观察到独特的纤维品质特征。这些基因组和比较分析为未来提高全球棉花产量和可持续性的遗传努力提供了宝贵的基础。