Identification of a cluster of oligonucleotide repeat sequences and its practical implication in melon (Cucumis melo L.) breeding

A cluster of oligonucleotide repeat sequences was identified that is linked to the melon (Cucumis melo L.) andromonoecious (a) locus, which controls andromonoecy. Six different repeat units, ranging from 11 to 49 base pairs, were clustered within a 0.6-kb intergenic region. The number of repeat units varied from two to six. After sequence analysis of diverse melon germplasms, four haplotypes of this cluster were identified. Length variations among the four haplotypes resulted from insertion or deletion of repeat sequences. Particularly, a tandem array of six repeats of 21 nucleotides was a hotspot for insertion/deletion mutations. A simple PCR-based marker was developed to identify haplotypes of this cluster based on the length polymorphism. In practice, this marker was successfully used in genetic purity tests of melon F1 hybrid cultivars. Four self-pollinated contaminants, which were confirmed by phenotypic examination in grow-out tests, were easily discriminated from 99 F1 hybrid individuals. In addition, the genetic distance between this marker and the andromonoecious (a) locus was calculated as 7.9 cM, after analyzing melon F2 populations originating from a cross between monoecious and andromonoecious parental lines. Therefore, this marker will be useful as a recombinant selection marker in marker-assisted backcrossing of monoecy in melon breeding programs.