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

期刊论文
发表日期：

2024年10月11日

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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

摘要

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.