Discovery of the Genomic Region and Candidate Genes of the Scarlet Red Flesh Color ( Y scr ) Locus in Watermelon ( Citrullus Lanatus L.)

The flesh color of watermelon ( ) is an important fruit quality trait that helps to determine fruit attractiveness and is potentially beneficial to human health. Previous inheritance analyses determined that a single dominant gene, , produces the scarlet red flesh color rather than the coral red flesh color in watermelon. However, no genomic region or gene-based molecular markers for the locus have been reported thus far. In the present study, two high-density genetic maps and whole-genome variation detection aided by genome resequencing were first map the flesh color locus to a small region on chromosome 6 based on two independent populations derived from two scarlet red-fleshed lines and two coral red-fleshed lines. Two major quantitative trait loci located in the same genomic regions were identified in the F and BC P populations and explained 90.36% and 75.1% of the phenotypic variation in flesh color, respectively. Based on the genetic variation in the two parental lines, newly developed PCR-based markers narrowed the region to 40 Kb. Of the five putative genes in this region, four encoded glycine-rich cell wall structural proteins, which implied that a new regulatory mechanism might occur between scarlet red- and coral red-fleshed in watermelon. Moreover, the genotypes of two newly developed InDel markers (InDel27_fc6 and InDel28_fc6) were completely consistent with the phenotypes in the F and BC P populations and all 56 scarlet red-fleshed watermelon accessions. The results presented here provide valuable information for marker-assisted selection of flesh color breeding and the functional validation of candidate genes in watermelon.