Abstract
Background: Goji (Lycium spp., 2n = 24) is a perennial woody plant bearing functional properties. 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 fewer studies have attempted on genomic regions corresponding to the fruit traits.Results: In this study, we established high-resolution map using SLAF-seq for de novo SNPs detection, based on 305 F1 offspring derived from L. chinense and L. barbarum. This genetic map contained 3,495 SNP markers on 12 LGs, spanning 1,649.03 cM with 0.47 cM average interval. Female and male parents had sequencing depth of 72.43-fold and 60.43-fold, respectively, while 15.23-fold detected for individuals. Phenotype data were obtained for 2 years and included 3rd year data as an average. QTL mapping analysis resulted in 117 QTLs corresponding to all traits, of which 23 QTLs in 2 years and 6 QTLs in 3rd years were detected. 6 promising QTLs, qFW10-3.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1 and qLA10-2.1 were discovered influencing fruit weight, fruit length and leaf size related attributes covering an interval ranged 13.74-76.61 cM on LG10 with peak LOD up to 14.21 and PVE 19.3%. Additionally, 3 QTLs, qFS-1, qFS-2 and qFF-1, targeting fruit sweetness and fruit firmness were also identified in this study. Strikingly, among stable QTLs, qFL10-2.1, was co-localized to qLL10-2.1, qLD10-2.1, qLA10-2.1 and harbored significantly similar markers distribution, while qLL10-2.1 was the major and stable QTL with LOD ranged from 8.71-14.21 and PVE 12.3-19.3%. As LG10 harbored most of the fruit and leaf size related QTLs, we might speculate that it could be a hotspot region regulating fruit size and plant architectures.Conclusions: This report highlighted that the high-density linkage map construction using SLAF-seq is an important means for profound QTL mapping approach. Substantially, we utilized highly saturated genetic map to find out genetic locus targeting fruit and leaf size related attributes under QTL mapping. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry. Moreover, these findings would facilitate to assemble reference genome, determining potential candidate genes and marker-assisted breeding.
Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)
