Marker development for erect versus pendant-orientated fruit in Capsicum annuum L.

The erect habit of fruit setting is a unique characteristic of ornamental peppers and wild pepper species. The erect habit is known to be controlled by the up locus on pepper (Capsicum annuum L.) chromosome 12. The result of a genetic analysis using Saengryeog 211 (pendant), Saengryeog 213 (erect), and their F1 and BC1 progeny demonstrated that up is a recessive gene. To develop an up-linked marker, bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) were employed using 108 F2:3 individuals. The closest AFLP marker, A2C79, was located at a genetic distance of 1.7 cM from the up locus and was converted into a cleaved amplified polymorphic sequence (CAPS) marker. This marker was mapped at a genetic distance of 4.3 cM from the up locus. When the CAPS was applied to seven ornamental lines and 27 breeding lines with erect fruit, these genotypes of 28 lines were correctly predicted. Thus, the CAPS marker will be useful for marker-assisted selection (MAS) of pepper breeding lines with the up allele at the early seedling stage.