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

Abstract

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 F₁ 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 F₁ 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.

Keywords: Fruit size; Goji; High-density genetic map; Interspecific; QTL mapping; SLAF-seq.

Fig. 1

Segregation pattern of polymorphic SLAF markers for F₁ interspecific population. *The x-axis depicts segregation pattern and y-axis shows the number of markers

Fig. 2

Percentages of various types of markers detected among each linkage group. *The x-axis indicates the percentage of three types of markers: “SNP_only, InDel_only, and SNP_InDel on each linkage group, while the y-axis indicates the 12 linkage groups of the integrated map

Fig. 3

The high-density genetic map presents the distribution of SNP markers on 12 linkage groups (LGs) of goji berry (Lycium Spp.). *The black bars on each linkage group show markers distribution

Fig. 4

The high-density genetic map of goji berry and stable QTLs mapping on linkage groups detected under 2 individual year and extra year. *Different vertical color tiles represent various traits QTLs. Green, qFW_fruit weight; dark blue, qFL_fruit length; red, qFD_fruit diameter; blue violet, qFSI_fruit shape index; grey, qNof/ec_number of fruits per end cluster; brown, qNof/n_number of fruits per node; steel blue, qNos/f_number of seeds per fruit; dark magenta, q100SW_100 seed weight; teal, qLL_leaf length; orange, qLD_leaf diameter; olive, qLA_leaf area, blue, qFS_fruit sweetness, salmon, qFF_fruit firmness. Stars indicate stable QTLs identified in 2 individual years consistently

Fig. 5

Female (Lycium chinense Mill. cv. Daye) and male (Lycium barbarum L. cv. ZKLC1) parent plants, and F₁ offspring pictures. *a female plant, b male plant, c female plant leaves, d female mature fruit, e male plant leaves, f male mature fruits, g F₁ offspring leaves, h F₁ offspring mature fruits