Development and Use of Chloroplast Simple Sequence Repeat Markers for the Identification of Big-Bracted Cornus Species

Big-bracted dogwoods (Cornus spp.) including C. florida and C. kousa are commonly grown ornamental flowering trees utilized in landscapes across temperate regions of the U.S., Europe, and Asia. Interspecific hybrids can be created among this group of species. While F₁ hybrids tend to be intermediate in phenotype between the parents, later generation crosses and backcrosses are highly variable, making it is impossible to accurately determine species lineage based purely on physical characteristics. Fortunately, molecular tools such as chloroplast simple sequence repeat (cpSSR) markers can be used to help discern maternal lineages. In this study, 14 cpSSRs were mined from the Cornus florida plastid genome. Each marker was amplified in four C. florida and six C. kousa cultivars to identify amplicon sizes that correlate to each species. These markers were then tested in 13 C. kousa x C. florida hybrids with known pedigree records. Three of the 14 markers consistently discerned C. kousa from C. florida and accurately identified the maternal C. kousa lineage in all 13 interspecific hybrids. We then used those three markers to examine 14 seedling selections with uncertain maternal backgrounds, where the phenotype of the trees was in stark contrast to pedigree records. Results showed that the three markers amplified maternal C. florida alleles in all 14 seedlings, agreeing with their phenotypes. In summary, three chloroplast SSR markers were identified that consistently distinguished C. kousa from C. florida maternal lineages. These markers provide a means to help confirm pedigrees and breeding lines and can guide future breeding decisions.