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Background  Goji ( Lycium  spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits.    Results  In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F 1  individuals derived from  L. chinense  and  L. barbarum  and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3495 SLAF markers on 12 LGs, spanning 1649.03 cM with 0.47 cM average interval. Female and male parents and F 1  individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018–2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. Six Promising QTLs ( qFW10–6.1 ,  qFL10–2.1 ,  qLL10–2.1 ,  qLD10–2.1 ,  qLD12–4.1 ,  qLA10–2.1 ) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32–71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness ( qFS3–1 ,  qFS5–2 ) and fruit firmness ( qFF10–1 ) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular,  qFL10–2.1  was co-located with  qLL10–2.1 ,  qLD10–2.1  and  qLA10–2.1  among stable QTLs, harbored tightly linked markers, while  qLL10–1  was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures.    Conclusions  This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.

Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)