Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry

SUMMARY Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of Prunus campanulata ‘Plena’ (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high‐quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome‐wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry. Significance Statement Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry.