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 <5 cM. Based on two successive years of fruit phenotyping and this high-density linkage map, 17 stable QTLs were identified, including 12 for single fruit weight (SFW) and 5 for edible rate, but no stable QTLs were identified for soluble solid content. Finally, three key candidate genes, namely, Dlo_007693.1 (DlEXP4), Dlo_011045.1 (DlCNR8), and dlo_034894.1 (DlCYP450), for SFW were identified based on RNA sequencing data and quantitative reverse-transcription polymerase chain reaction. In conclusion, this is the first study on the construction of a high-density genetic map of longan using next-generation sequencing based on the largest mapping population. These results provide valuable information for marker-assisted selection breeding and mining of candidate genes related to fruit traits in longan.

龙眼是一种经济重要的果树，在世界各地的亚热带地区种植。对于龙眼育种，认为与产量和品质相关的性状是可取的。因此，对数量性状基因座（QTL）进行精细定位和挖掘候选基因以获得龙眼果实的产量和品质将有利于龙眼育种。在这项研究中，我们使用限制性酶切位点相关的DNA测序构建了F ₁龙眼种群的第一个基于单核苷酸多态性（SNP）的遗传图谱。从200 F ₁总共产生1,464,790,436次干净读取后代来自“凤头多”（雌性）ד大五元”（雄性）及其父母。整体整合图包含8014个SNP标记，这些标记被分配给15个连锁组，总长度为2873.39 cM，平均距离为0.36 cM，遗传距离小于5 cM的缺口为99.96％。基于连续两年的水果表型分析和高密度连锁图谱，共鉴定出17个稳定的QTL，其中单果重（SFW）为12个，食用率为5个，但可溶性固形物未鉴定到稳定的QTL。最后，三个关键候选基因，即Dlo_007693.1（DlEXP4），Dlo_011045.1（DlCNR8）和dlo_034894.1（DlCYP450），基于RNA测序数据和定量逆转录聚合酶链反应确定了SFW。总而言之，这是首次使用基于最大作图群体的下一代测序技术构建龙眼高密度遗传图谱的研究。这些结果为标记辅助选择育种和挖掘与龙眼果实性状相关的候选基因提供了有价值的信息。