QTL mapping of pericarp and fruit-related traits in melon (Cucumis melo L.) using SNP-derived CAPS markers

Abstract

As an important fruit vegetable crop, the quality of melon affects consumer preferences and the market value. Most quantitative trait loci (QTLs) related to fruit quality are controlled by polygenes and influenced by environmental factors. The objective of the present study was to identify QTLs for fruit quality traits in the F2 population derived from thick-skin line Elizabeth (M4-5) and thin-skin line M1-15 melons using single-nucleotide polymorphism (SNP)-derived cleaved amplified polymorphic sequence (CAPS) markers. We sequenced the melon lines M4-5 and M1-15 using next-generation sequencing (NGS) to identify CAPS loci across the assembled genome and constructed a linkage map with 195 CAPS markers to map the QTLs associated with fruit quality traits. Forty QTLs for fruit quality traits were identified with the new CAPS-based linkage map. Among these, 12 QTLs were associated with pericarp-related traits (exocarp type and thickness, pericarp thickness and firmness, and cracking) and 28 QTLs were associated with fruit-related traits (fruit length, width, and weight, and brix content). Our results suggest that the genetic components for fruit quality traits are complex and additive. The majority of QTLs for fruit quality traits were clustered around LG6 and LG9, among which two QTLs showed pleiotropic effects. The location of these QTLs with narrow genomic intervals could facilitate marker-assisted selection (MAS) application of the underlying genes in breeding programs. The findings of the present study provide the fundamentals for pyramiding the favored allele at multiple QTL locations into elite material using highly efficient molecular breeding tools.