Fig. 5: A key TIP for tomato flavor.

a Manhattan plot of SNP- and TIP-based GWAS (circles and diamonds, respectively) for 2-phenylethanol. b qq-plot depicting observed and expected distribution of p values for SNP- and TIP-GWAS (gray circles and black diamonds, respectively). c Detailed view of the Manhattan plot for 2-phenylethanol spanning Solyc02g079490 (PPEAT). d. 2-phenylethanol levels in accessions carrying or not the intronic COPIA insertion. Statistical significance for differences was obtained using one-sided t test. e. PPEAT expression level in accessions carrying or not the intronic COPIA insertion. Statistical significance for differences was obtained using two-sided MWU test. f Genome Browser view of full-length cDNA nanopore reads from accessions carrying or not the intronic COPIA insertion. g PPEAT transcript isoforms, protein products, and abundance of transcript isoforms in accessions carrying or not the associated TE insertion. Data are mean ± s.d., and statistical significance for differences was obtained using two-sided MWU test. h Frequency (%) of the intronic COPIA-containing allele in each of the five tomato groups. PPEAT putative 2-phenylethanol acyl transferase. For each boxplot, the lower and upper bounds of the box indicate the first (Q1) and third (Q3) quartiles, respectively, the center line indicates the median, and the whiskers represent data range, bounded to 1.5 * (Q3–Q1). Source data of Fig. 5d, e, g, h are provided as a Source Data file.