Abstract 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).

中文翻译：

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基于SNP的CAPS标记对甜瓜形态和果实品质相关性状的遗传连锁作图和QTLs鉴定

摘要 瓜类表现出巨大的形态和果实品质性状多样性，这些性状仍在世界范围内的育种研究中进行研究。由于具有惊人的优势，基于单核苷酸多态性 (SNP) 的遗传标记被广泛用于解析推定的 QTL/基因。在这项研究中，我们通过使用全基因组重测序和新开发的基于 SNP 的切割扩增多态性序列 (CAPS) 标记，报道了甜瓜子房、果实和种子性状的遗传连锁作图和 QTL 检测。两个不同的甜瓜系的重测序分析暴露了参考基因组中 1400 万（96%，360Mb）和 2000 万（85.62%，319Mb）重测序读数、404083 个候选 SNP 和 6474 个 CAPS 位点。一个由 148 个个体组成的 F2 作图群体使用 163 个 SNP-CAPS 标记进行基因分型，用于遗传连锁作图，跨越总遗传距离为 1545.44 cM，全基因组相邻标记之间平均为 9.48 cM。总共在差异染色体（1、2、3、4、6、8、9和12）上检测到26个推定QTL（6个主要QTL和20个次要QTL），并解释了12个表型性状的1.83 %~17.67 %的表型变异具有多效性。在这些QTLs中，鉴定出6个子房QTLs、17个果实品质QTLs和3个种子性状QTLs，许多QTLs聚集在1、9、12号染色体上。相关性和PCA分析。关键是，