High-resolution QTL mapping of horticultural traits in muskmelon (Cucumis melo L.) using genotyping-by-sequencing

Abstract

Muskmelon (Cucumis melo L.) is an economically and nutritionally important vegetable crop with significant genetic variability. Fruit traits significantly influence consumer preference and market value, with most quality parameters governed by multiple genes and influenced by environmental factors. High-resolution quantitative trait loci (QTL) mapping can elucidate the genetic basis of these traits, facilitating marker-assisted breeding. In this study, QTL mapping was performed for melon quality traits using an F2:4 population of 110 individuals derived from a cross between muskmelon variety Punjab Sunehri and Snap melon accession SM2012-1. The F4 population was phenotyped during the spring and rainy seasons of 2023. A genetic linkage map was constructed using the Genotyping-by-Sequencing (GBS) approach, comprising 13 linkage groups and 1962 single nucleotide polymorphism (SNP) markers. Nine horticultural traits were evaluated: days to first male flower appearance, fruit maturity, fruit weight, fruit length, fruit width, flesh thickness, fruit cavity length, cavity width and total soluble solids. QTLs were identified across both seasons on chromosomes 1, 2, 3, 5, 9, 10, and 12, explaining 7–71% of the phenotypic variance (PVE), with logarithm of odds (LOD) scores ranging from 2.6 to 8.7. Notably, overlapping QTLs for fruit weight, fruit length, and fruit maturity were consistently detected at the same positions on chromosomes 3 and 9 in both seasons. These results provide valuable insights for fine-mapping of QTLs and support the integration of marker-assisted selection (MAS) in melon breeding programs.