Molecular Mapping of Candidate Gene Regulating the Fruit Stripe Trait in Watermelon

Fruit quality traits are important commercial traits that directly affect the market value. The rind stripe is the primary determinant of watermelon fruit quality, but its genetic basis and underlying gene (s) are not well understood. In this study, two contrasted watermelon inbred lines (non-striped "K2" and striped "L1") were crossed to derive the F2:3 mapping population, and fine genetic mapping of fruit stripping was performed. Genetic segregation analysis proposed that the striped-rind pattern is regulated by the gene locus (ClSP) and dominant to the non-stripped rind pattern. Fine genetic mapping of the detected gene locus on chromosome 06 revealed six functionally annotated genes in the delimited genetic interval of 62.5 kb. Multiple pair-wise sequences evidently proved that Cla97C06G126560 is the candidate gene for ClSP, encoding the polygalacturonase-1 non-catalytic subunit beta (ClGP1). Two non-synonymous SNPs inside ClGP1 were identified between the two contrasted parental lines. Real-Time Quantitative PCR (RT-qPCR) significantly revealed the low expressions profiling of ClSP gene in the striped rind line "L1" as compared to the striped line "L1". A widely collected panel of 144 watermelon accessions with extreme fruit stripe variations were selected to develop the natural population, and a preliminary genome-wide association study (GWAS) confirmed the same genetic locus on chromosome 6, regulating the watermelon fruit striping pattern. The sequence analysis verified that two SNPs "SNP28280025 (A-C) and "SNP28281451 (G-C)" in the Cla97C06G126560 gene were found to be related in 49 striped-type watermelon varieties out of 144 natural watermelon lines. All of the findings strongly suggest that the ClSP gene regulates the presence or absence of the watermelon fruit stripe. Our illustrated outcomes are expected to provide potential insights for further genetic improvement of watermelon fruit varieties and also help to understand the genetic mechanism of the ClSP gene