Fine mapping and discovery of candidate genes for rind trait in watermelon

Abstract Fine mapping and discovery of watermelon rind trait candidate genes are of great significance for modern watermelon breeding and development. In this study, we used the high-resolution genetic mapping and genome-wide genetic variation detection technology, combined with genome survey and sequencing technology, to locate and discover the candidate genes for rind traits of star watermelon varieties ‘Su XuanBai’ and ‘SHLX 21 ’. Firstly, we identified a total of eight quantitative trait loci (QTLs) related to watermelon rind traits on chromosome 6. Secondly, a total of 208,240 single nucleotide polymorphisms and 75,345 small Indels (insertions/deletions) were detected in the two parents by high-coverage re-sequencing, respectively. Based on the genetic variation of the two parents and combined with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis using the planta database, the QTL region was reduced to 0.02 Mb. Finally, we identified the six potential regulatory factors for watermelon rind traits using real-time quantitative PCR. In conclusion, our results revealed the fine localization of candidate genes for watermelon rind traits and the successful discovery of candidate genes for regulating watermelon rind traits, which is of importance for watermelon rind traits and breeding-improved watermelon varieties.