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

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’ and a genome variation map of 233 Rosa accessions 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 wild Rosa species to modern roses, and highlight that R. odorata and its derived cultivars contribute more to modern roses than R. 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.