Genetic linkage mapping and QTLs identification for morphology and fruit quality related traits of melon by SNP based CAPS markers

•Novel SNP based CAPS markers were developed using whole genome re-sequencing data of distinct parental lines of melon.•In total, 26 QTLs (6 major and 20 minor) were identified for fruit related traits in biparental F2 population of melon.•OVL2.1, OVS1.1, FW2.1, FW9.1, FS4.1, and SW3.1 were identified as major QTLs.•The entire novelties will be valuable for future MAS in melon. Melons exhibit huge diversity of morphology and fruit quality traits, and these traits are still being investigated in worldwide breeding studies. Due to the fabulous advantages, single nucleotide polymorphisms (SNPs) based genetic markers are widely being used for dissection of putative QTLs/genes. In this study, we reported genetic linkage mapping and QTLs detection for ovary, fruit and seed traits of melon by using whole genome re-sequencing and newly developed SNPs based cleaved amplified polymorphism sequence (CAPS) markers. The re-sequencing analysis of two distinct melon lines exposed 14 million (96 %, 360 Mb) and 20 million (85.62 %, 319 Mb) re-sequenced reads, 404,083 candidate SNPs, and 6474 CAPS locus across the reference genome. An F2 mapping population comprising 148 individuals was genotyped with 163 SNP-CAPS markers for genetic linkage mapping which spanned total 1545.44 cM genetic distance and averaged 9.48 cM among whole genome adjacent markers. In total, 26 putative QTLs (6 major and 20 minor QTLs) were detected on differential chromosomes (1, 2, 3, 4, 6, 8, 9, and 12) and explained 1.83 %∼17.67 % phenotypic variations for 12 phenotypic traits with pleiotropic effects. Among these QTLs, 6 QTLs of ovary, 17 QTLs of fruit quality and 3 QTLs of seed traits were identified and many QTLs were clustered on chromosome 1, 9, and 12. A highly significant relationship and normal distribution frequency of phenotypes were also noticed in analysis of correlation and PCA. In crux, our detected QTL insights could be valuable and further investigated in unexplored botanical groups of melon by fine mapping and marker assisted selection (MAS).