Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida ‘Samantha’ (‘JACmantha’) and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of ‘Samantha’ exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis ‘Old Blush’. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement.

现代玫瑰 （Rosa hybrida） 是最近形成的种间杂交品种，已成为最重要和最广泛种植的观赏植物之一。在这里，我们报告了四倍体 R. hybrida 'Samantha' （'JACmantha'） 的单倍型分辨染色体尺度基因组组装，以及涉及各种野生物种以及古老和现代栽培品种的 233 个 Rosa 种质的基因组变异图。'Samantha' 的同源染色体表现出频繁的同源交换。群体基因组和基因组组成分析揭示了野生蔷薇物种对现代玫瑰的贡献，并强调 R. odorata 及其衍生的栽培品种是现代玫瑰的重要贡献者，就像 R. chinensis 'Old Blush' 一样。此外，还确定了现代玫瑰育种过程中与主要农艺性状相关的选择性扫描，包括连续和循环开花、双花、花衰老和抗病性。这项研究为现代玫瑰起源和育种历史的遗传基础提供了见解，并为玫瑰改良提供了前所未有的基因组资源。