Abstract
BACKGROUND: The North American-native ornamental tree, flowering dogwood (Cornus florida L.), has a showy bract display that can range in color from white to pink to deep red. Although many trees have white bracts, there is consumer demand for novel pigmentation in the bracts combined with other traits of interest. Because the genetic basis of all traits in flowering dogwood is unknown, combining them using traditional breeding efforts is time, labor, and space-intensive. RESULTS: We developed foundational genomic resources to establish marker-assisted selection within flowering dogwood breeding. We generated diploid, chromosome-scale, annotated genome assemblies for one pink-bracted and red-leafed tree and one white-bracted and green-leafed tree. Additionally, a phenotyping protocol for bract color and presence/absence diagnostic SNPs for bract and leaf color were established. We leveraged these resources to evaluate linkage associations and differential gene expression related to anthocyanin biosynthesis to identify candidate genes regulating bract and leaf pigmentation. Within a 14 Mb locus we identified 14 anthocyanin-related genes. Two genes, with MYB (g19533) and RING finger (g19556) binding domains, had both differential gene expression and variants with the expected segregation pattern. CONCLUSIONS: These candidate genes, diagnostic SNPs, and genomic resources will be valuable in combining pink-red bracts with other traits to advance flowering dogwood breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07836-5.