SNP-based high-density genetic map construction and candidate gene identification for fruit quality traits of Dimocarpus longan Lour

•A high-density genetic map of longan was constructed using SNPs.•Marker-trait association linked to fruit quality and three key candidate genes were identified.•These results provide valuable information for MAS in longan breeding programs. Longan is an economically important fruit tree that is cultivated in subtropical regions worldwide. For longan breeding, traits associated with yield and quality are considered desirable. Thus, fine mapping of quantitative trait loci (QTLs) and mining candidate genes for longan fruit yield and quality would benefit longan breeding. In this study, we constructed the first single-nucleotide polymorphism (SNP)-based genetic map of an F1 longan population using restriction site-associated DNA sequencing. A total of 1,464,790,436 clean reads were generated from 200 F1 progeny from ‘Fengliduo’ (female) × ‘Dawuyuan’ (male) and their parents. The overall integrated map contained 8014 SNP markers, which were assigned to 15 linkage groups with a total length of 2873.39 cM, an average distance of 0.36 cM, and 99.96 % of gaps having a genetic distance of