Construction of a high-density genetic map for melon using ddRAD-Seq technology from a population derived from flexuosus and reticulatus botanical groups

Melon (Cucumis melo L.) is an economically important fruit crop with high phenotypic diversity, but the high-density genetic map suitable for QTL analysis of multiple phenotypes is unavailable to date. In this study, we adopted double-digest restriction-site associated DNA sequencing (ddRAD-seq) for large-scale discovery of single nucleotide polymorphisms (SNPs) and construction of a high-density genetic map in melon. A F2 population containing 140 individuals was developed from two parental lines, H581 and H906, which respectively belonged to flexuosus and reticulatus botanical groups and showed a significant phenotypic difference. Approximately 441 Gb of data containing 3.4 × 109 paired-end reads were obtained following the ddRAD-seq. Mining this dataset, 11,073 SNPs were detected between the two parents, of which 4654 valid SNPs were finally retained in the population for genetic map construction. In total, 1090 bin markers, consisting of all the 4654 SNPs, were sorted into 12 linkage groups (LGs). The total length of the bin map was 1462.30 cM, with an average marker density of 1.39 cM and a recombination rate of 3.90 cM/Mb. Haplotype map and linkage relationship heat map revealed that most of the recombination blocks were well defined in the segregating population, confirming a high accuracy of the bin map. This map could be used for discovery of QTLs/genes related to the diverse phenotypes between the two botanical groups, further facilitating molecular breeding in melon.