Supplementary Figure 10: Physical structure of key recombinants showing markers used to delineate mapping interval for fruit firmness QTL on IL3-4

The fruit firmness QTL shown in Supplementary 9 is in a region of the tomato genome with suppressed recombination. The recombinants were identified and the mapping interval determined using markers derived from the tomato genome sequence (G- markers) or from the tomato genetic map (https://solgenomics.net/ and also see Supplementary Table 8). The numbers under each marker are the physical distance in bp along tomato chromosome 3 based on the tomato genome SLv2.50 build (https://solgenomics.net/). G690* is a marker in pectate lyase gene. TG599 defines the proximal end of the IL3-4 introgression (https://solgenomics.net/). The physical distance between TG599 and G950 = 1091323bp and between TG129 and G950 = 1785601bp. Lines possessing the M82 S.lycopersicum allele (pink) at G690 were significantly (P≰0.002) softer, in both the outer and inner pericarp tissues, than those with the IL3-4 S. pennellii allele (green) at the same position. The mean texture values for the outer and inner pericarp (two technical replicates for each measurement) for lines carrying the S. lycopersicum and S. pennellii alleles at G690 were compared by Analysis of Variance by fitting a linear mixed model with allelic variant as the fixed effect and plant, fruit within plant and technical replicate within fruit as random effects. This ensured that, within the analysis, the variation between means of plants having the different alleles at G690 was compared to the variation between plants of the same genotype at this position. Mean values for the outer pericarp were 0.528 and 1.204N for the lines with S. lycopersicum and S. pennellii alleles at G690, respectively (SED, 0.1267 with 6 df) and for the inner pericarp the values were 0.817 and 1.480N (SED 0.11862 with 6 df).