Molecular mapping of candidate gene regulating fruit stripe trait in watermelon

Fruit rind appearance traits significantly affect the commercial market value. The molecular basis and underlying gene(s) affecting rind strip pattern are still being investigated around the world. In this study, two contrasted inbred watermelon lines (non-striped “K2” and striped “L1”) were crossed to derive three F 2 mapping populations in different environments over two years, and fine genetic mapping of a candidate gene affecting fruit stripe pattern was performed. Genetic segregation analysis and marker genotyping within three mapping populations (120-F 2A , 230-F 2B , and 155-F 2C ) collectively identified the major-effect genetic region on Chr-6 which exhibited that the striped-rind pattern is mainly regulated by the dominant gene locus ( ClSP) over the non-stripped rind pattern. Fine genetic mapping with a large mapping population of 1100-F 2 individuals and screened recombinant lines revealed six functionally annotated genes in a 62.5-kb interval. A genome-wide association study (GWAS) of a widely collected panel of 144 watermelon accessions with extreme fruit stripe variation analysis similarly confirmed the candidate genetic region on Chr-6, regulating the watermelon rind strip pattern. The pair-wise sequences alignment further proved that Cla97C06G126560 is the significant gene encoding the polygalacturonase-1 non-catalytic subunit beta ( ClGP1 ). The phylogenetic associations of the watermelon ClSP gene with homologous protein sequences of 16 different plant species revealed the highest percentage of identical sequences with melon, cucumber, and pumpkin, and depicted highly conserved domains of the BURP superfamily. Real-time quantitative PCR (RT-qPCR) significantly validated the differentiated gene expression profiling in both lines “K2” and “L1”, respectively. In addition, the sequence analysis exhibited two SNPs, “SNP28280025 (A-C)” and “SNP28281451 (G-C)” in the Cla97C06G126560 gene, that were found to be correlated in 49 striped-type watermelon accessions of GWAS material. We expect that our novel research outcomes will be valuable for understanding the detailed genetic mechanism of the ClSP gene and for further genetic improvement of watermelon varieties with the desired fruit rind appearance trait.