Identification of a novel locus controlling canary yellow flesh color in watermelons.

The flesh color of watermelon is an important trait that is determined by carotenoid composition and affects consumers' fruit desirability. Although a complete dominant control by locus () for canary yellow flesh (CY) over red flesh has been reported, red and CY colors frequently appear as a mixed pattern in the same flesh (incomplete canary yellow, ICY) in F and inbred lines carrying dominant alleles. Therefore, we examined the genetic control of the mixed color pattern in ICY using whole-genome resequencing of three ICY (ICY group) and three CY inbred lines (CY group), as well as genetic linkage mapping of an F population. The segregation pattern in 135 F plants indicated that CY is controlled by a single locus (named ) dominant over ICY. The whole-genome resequencing of ICY and CY inbred lines revealed an ICY/CY-specific region of approximately 27.60-27.88 Mb on Chr. 2 that was polymorphic between the ICY and CY groups. Our genetic map, using nine cleaved amplified polymorphic sequence markers developed based on the single-nucleotide polymorphisms from the ICY/CY-specific region, confirmed that is located on Chr. 2 and cosegregated with the marker (M7) derived from a non-synonymous single-nucleotide polymorphism of the pentatricopeptide repeat (PPR) gene (, ). Additionally, 27 watermelon inbred lines of ICY, CY, and red flesh were evaluated using previously reported ( locus)-based markers and our locus-linked -based marker (M7). As a result, dominant alleles at the locus were required to produce CY, in addition to dominant alleles at the locus, while a recessive homozygous genotype at the locus gave the red flesh irrespective of the genotype at the locus. Using a -based cleaved amplified polymorphic sequence developed in this study and -based markers, watermelon cultivars with CY, ICY, and red flesh could be successfully discerned, implying that the combined use of these markers will be efficient for marker-assisted selection of flesh color in watermelon breeding.