Fig. 4: SV-based GWAS identify additional association signals for tomato fruit flavor.
a, Density of SNPs and SVs used in GWAS and genome-wide distribution of quantitative trait loci (QTLs) with top 200 PVE. b, Number of QTLs detected by different categories of markers. SNP, QTLs that could only be identified by SNPs; SV, QTLs that could only be identified by SVs; SNP_SV, QTLs detected by both SNPs and SVs. c–f, Local Manhattan plots for geranylacetone content (c), SlFM1955 (kaempferol-sinapylglucosyl-xylosylrhamnoside (d), SlFM0306 (2′-deoxyadenosine monohydrate (e) and SlFM1209 (tricin 7-O-hexoside) (f) (left panel), and corresponding box plots in accessions carrying distinct alleles (right panel). In Manhattan plots, triangles denote SVs and points illustrate SNPs. Genome-wide threshold for GWAS (7.58 × 10−7) is marked using red dashed lines. In box plots, the 25% and 75% quartiles are shown as lower and upper edges of boxes, respectively, and central lines denote the median. The whiskers extend to 1.5 times the interquartile range. Data beyond the end of the whiskers are displayed as black dots. P-values were computed from two-tailed Student’s t test. ng/gfw, nanograms per gram of fresh weight; c.p.s., counts per second; REF, accessions with homozygous reference (S. galapagense) type of allele; ALT, accessions possessing homozygous alternative allele. Numbers of samples for REF in box plots in c, d, e and f are 305, 288, 290 and 280, respectively. Numbers of samples for ALT in box plots in c, d, e and f are 16, 5, 5 and 7, respectively.
