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Abstract：
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.
摘要：
棉花(GossypiumhirsutumL.)是全球主要的可再生纤维作物，然而，由于基因型特异性性状和品种之间复杂的相互作用，其产量和纤维质量显示出高变异性，管理实践和环境因素。由于建立基因库狭窄，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，取决于准确的品种特异性数据。在这里，我们通过为三个现代棉花品种（\'UGA230\'，\'UA48\'和\'CSX8308\')并更新\'TM-1\'棉花遗传标准参考。尽管假设遗传一致性，在四个基因组中观察到相当大的序列和结构变异，与来自“皮马”棉花的古老和正在进行的基因组渗入重叠，基因调控机制和表型性状差异。跨纤维发育的差异表达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的独特的纤维品质性状。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。
