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

Flesh firmness (FF) is an important and complex trait for melon breeders and consumers; however, the genetic mechanism underlying FF is unclear. Here, P5 melon, whose fruit is soft, and P10 melon, whose fruit is hard, were crossed to generate F2s, and 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 1356.49 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 (Chr.) 2. Using 429 F2 individuals derived from a cross between P5 and P10, we defined the ff2.1 locus to a 28.3 kb region harbouring three functional genes.These results not only provide a new candidate QTL for melon FF breeding but also a theoretical foundation for research on the mechanism underlying melon gene function.