SLAF marker based QTL mapping of fruit-related traits reveals a major-effect candidate locus ff2.1 for flesh firmness in melon

Abstract

Flesh firmness (FF) is an important and complex trait for melon breeders and consumers. However, the genetic mechanism underlying FF is unclear. Here, a soft fruit melon (P5) and a hard fruit melon (P10) were crossed to generate F2, and the FF and fruit-related traits were recorded for two years. By performing quantitative trait locus (QTL) specific-locus amplified fragment (SLAF) (QTL-SLAF) sequencing and molecular marker-linkage analysis, 112 844 SLAF markers were identified, and 5 919 SNPs were used to construct a genetic linkage map with a total genetic distance of 1 356.49 cM. Ten FF- and fruit-related QTLs were identified. Consistent QTLs were detected for fruit length (FL) and fruit diameter (FD) in both years, and QTLs for single fruit weight (SFW) were detected on two separate chromosomes in both years. For FF, the consistent major locus (ff2.1) was located in a 0.17-Mb candidate region on chromosome 2. Using 429 F2 individuals derived from a cross between P5 and P10, we refined the ff2.1 locus to a 28.3-kb region harboring three functional genes. These results provide not only a new candidate QTL for melon FF breeding but also a theoretical foundation for research on the mechanism underlying melon gene function.