Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose

IF 15.8 1区生物学 Q1 PLANT SCIENCES

Nature Plants Pub Date : 2024-10-11 DOI:10.1038/s41477-024-01820-x

Zhao Zhang, Tuo Yang, Yang Liu, Shan Wu, Honghe Sun, Jie Wu, Yonghong Li, Yi Zheng, Haoran Ren, Yuyong Yang, Shaochuan Shi, Wenyan Wang, Qi Pan, Lijuan Lian, Shaowen Duan, Yingxiong Zhu, Youming Cai, Hougao Zhou, Hao Zhang, Kaixue Tang, Jiaopeng Cui, Dan Gao, Liyang Chen, Yunhe Jiang, Xiaoming Sun, Xiaofeng Zhou, Zhangjun Fei, Nan Ma, Junping Gao

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Abstract

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. The haplotype-resolved genome of tetraploid modern rose, along with a variation map of 233 wild and cultivated Rosa accessions, reveals the complex genome composition of modern roses and elucidates the genomic bases of their origin and breeding.

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单倍型解析基因组组装和重新测序为现代玫瑰的起源和育种提供了启示

现代玫瑰（Rosa hybrida）是一种新近形成的种间杂交种，已成为最重要和最广泛栽培的观赏植物之一。在此，我们报告了四倍体蔷薇杂交种'Samantha'（'JACmantha'）的染色体组型解析基因组组装以及 233 个蔷薇品种的基因组变异图谱，其中包括各种野生品种、古老品种和现代栽培品种。萨曼莎'的同源染色体表现出频繁的同源交换。种群基因组和基因组组成分析揭示了野生蔷薇物种对现代蔷薇的贡献，并强调了R. odorata及其衍生栽培品种对现代蔷薇的重要贡献，就像R. chinensis 'Old Blush'一样。此外，还发现了现代玫瑰育种过程中与主要农艺性状（包括连续和重复开花、重瓣花、花衰老和抗病性）相关的选择性扫描。这项研究深入揭示了现代玫瑰起源和育种历史的遗传基础，为玫瑰改良提供了前所未有的基因组资源。

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来源期刊

Nature Plants PLANT SCIENCES-

CiteScore

25.30

自引率

2.20%

发文量

196

期刊介绍： Nature Plants is an online-only, monthly journal publishing the best research on plants — from their evolution, development, metabolism and environmental interactions to their societal significance.