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

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

doi:10.1038/s41477-024-01820-x

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

Nat Plants. 2024 Oct 11. doi: 10.1038/s41477-024-01820-x. Online ahead of print.

Authors

Zhao Zhang^#¹, Tuo Yang^#¹, Yang Liu^#¹, Shan Wu^#², Honghe Sun^#^{2

3}, Jie Wu^#¹, Yonghong Li^#⁴, Yi Zheng^{5

6}, Haoran Ren¹, Yuyong Yang⁷, Shaochuan Shi¹, Wenyan Wang¹, Qi Pan¹, Lijuan Lian⁸, Shaowen Duan⁹, Yingxiong Zhu¹⁰, Youming Cai¹¹, Hougao Zhou¹², Hao Zhang¹³, Kaixue Tang¹³, Jiaopeng Cui¹⁴, Dan Gao¹⁵, Liyang Chen¹⁵, Yunhe Jiang¹, Xiaoming Sun¹, Xiaofeng Zhou¹, Zhangjun Fei^{16

17}, Nan Ma¹⁸, Junping Gao¹⁹

Affiliations

¹ Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China.
² Boyce Thompson Institute, Ithaca, NY, USA.
³ Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
⁴ School of Food and Drug, Shenzhen Polytechnic University, Shenzhen, Guangdong, China.
⁵ Bioinformatics Center, Beijing University of Agriculture, Beijing, China.
⁶ College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China.
⁷ Kunming Yang Chinese Rose Gardening Co. Ltd., Kunming, Yunnan, China.
⁸ People's Government of Weishanzhuang Town, Daxing, Beijing, China.
⁹ Chinese Ancient Rose Garden, Beijing, China.
¹⁰ Yunnan Xinhaihui Flower Industry Co. Ltd., Tonghai, Yunnan, China.
¹¹ Shanghai Academy of Agricultural Sciences, Shanghai, China.
¹² College Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.
¹³ National Engineering Research Center for Ornamental Horticulture, Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China.
¹⁴ Beijing Botanical Garden, Beijing, China.
¹⁵ Smartgenomics Technology Institute, Tianjin, China.
¹⁶ Boyce Thompson Institute, Ithaca, NY, USA. zf25@cornell.edu.
¹⁷ USDA-ARS Robert W Holley Center for Agriculture and Health, Ithaca, NY, USA. zf25@cornell.edu.
¹⁸ Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China. ma_nan@cau.edu.cn.
¹⁹ Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China. gaojp@cau.edu.cn.

^# Contributed equally.

PMID: 39394508
DOI: 10.1038/s41477-024-01820-x

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.

Abstract

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