Genetic mapping reveals a marker for yellow skin in watermelon (Citrullus lanatus L.)

As a diverse species, watermelon [Citrullus lanatus (Thunb.) Matsum. &Nakai var. lanatus] has different kinds of fruit sizes, shapes, flesh colors and skin colors. Skin color is among the major objectives for breeding. Yellow skin is an important trait in watermelon, but the underlying genetic mechanism is unknown. In this study, we identified a locus for yellow skin through BSA-seq and GWAS. A segregation analysis in F(2) and BC(1) populations derived from a cross of two inbred lines ‘94E1’(yellow skin) and ‘Qingfeng’(green skin) suggested that skin color is a qualitative trait. BSA-seq mapping confirmed the locus in the F(2) population, which was detected on chromosome 4 by GWAS among 330 varieties. Several major markers, namely, 15 CAPS markers, 6 SSR markers and 2 SNP markers, were designed to delimit the region to 59.8 kb region on chromosome 4. Utilizing the two populations consisting of 10 yellow and 10 green skin watermelons, we found a tightly linked functional SNP marker for the yellow skin phenotype. The application of this marker as a selection tool in breeding programs will help to improve the breeder’s ability to make selections at early stages of growth, thus accelerating the breeding program.