Haplotype-resolve genome assembly and resequencing provide insights into the origin and domestication of modern rose

Author:

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

Abstract

AbstractModern 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 tetraploidR. hybrida‘Samantha’ and a genome variation map of 233Rosaaccessions involving various wild species, and old and modern cultivars. The two subgenomes of ‘Samantha’ show no significant global bias in gene loss but substantial expression bias, and homoeologous exchanges are frequently observed between subgenomes. Population genomic and genomic composition analyses reveal the contributions of wildRosaspecies to modern roses, and highlight thatR. odorataand its derived cultivars contribute more to modern roses thanR. chinensis‘Old Blush’. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous flowering, floral organ identity, 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.

Publisher

Cold Spring Harbor Laboratory

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