Markers for selection of three alleles of ClSUN25-26-27a (Cla011257) associated with fruit shape in watermelon

Fruit shape is an economically important trait in many horticultural crops. The genes and mechanisms underlying fruit shape variation are poorly understood in watermelon. A deletion (DEL) in ClSUN25-26-27a (Cla011257), a member of the SUN gene family, has been shown to be associated with elongated fruit. In the current study, we sequenced ClSUN25-26-27a in three watermelon cultivars with different fruit shape indices (FSIs). A novel allele containing a non-synonymous point mutation in exon 3 was identified in Klondike Black Seeded. KASP assays (ClSUN-1 and ClSUN-2) were developed to distinguish three ClSUN25-26-27a alleles (WT, KBS, and DEL), and their effects on ovary and fruit shape traits were determined in a cultivar panel and segregating populations. The different alleles showed a significant association with ovary and fruit length and shape as well as the angles of the distal and proximal ends. These effects were primarily pre-anthesis. The KASP assays can serve as tools for marker-assisted selection (MAS) of fruit length and shape in watermelon. This study highlights the allelic variation in ClSUN25-26-27a and its association with fruit shape in watermelon.