1. C2_At1g60640 12.5 C2_At1g78690 32.0 C2_At3g01160 83.4 C2_At2g04700 97.0 C2_At3g27310 138.0 Chr. 2 cM C2_At1g30580 0.0 C2_At4g21580 68.0 C2_At3g02300 118.0 C2_At4g37300 132.0 171 cM C2_At5g23880 53.0 C2_At1g02140 71.0 C2_At3g10220 76.9 C2_At1g74520 113.0 C2_At1g09760 133.5 C2_At1g80360 145.5 C2_At1g55170 158.5 Chr. 3 cM C2_At4g14570 4.0 C2_At3g47990 101.5 C2_At3g20240 171.0 C2_At1g28530 21.0 143 cM 01.006001.0060 01.018501.0185 02.000002.0000 02.012502.0125 02.032002.0320 02.06802.068 02.083402.0834 02.097002.0970 02.11802.118 02.13202.132 02.138002.1380 03.000403.0004 03.02103.021 03.053503.0535 03.071003.0710 03.076903.0769 03.101503.1015 03.113003.1130 03.133503.1335 03.145503.1455 03.158503.1585 03.171003.1710 C2_At5g53000C2_At5g53000 C2_At5g06370C2_At5g06370 C2_At1g30580C2_At1g30580 C2_At1g60640C2_At1g60640 C2_At1g78690C2_At1g78690 C2_At4g21580C2_At4g21580 C2_At3g01160C2_At3g01160 C2_At2g04700C2_At2g04700 C2_At3g02300C2_At3g02300 C2_At4g37300C2_At4g37300 C2_At3g27310C2_At3g27310 C2_At4g14570C2_At4g14570 C2_At1g28530C2_At1g28530 C2_At5g23880C2_At5g23880 C2_At1g02140C2_At1g02140 C2_At3g10220C2_At3g10220 C2_At3g47990C2_At3g47990 C2_At1g74520C2_At1g74520 C2_At1g09760C2_At1g09760 C2_At1g80360C2_At1g80360 C2_At1g55170C2_At1g55170 C2_At3g20240C2_At3g20240 C2bTKM6U01931133111111111333311111 C2dTKM5U06481111133111111111111111 C3cTKM6U02171111311111111111133311

2. Supplemental Figure S1. Marker position and genetic variability of the three previously uncharacterised introgression lines C2b, C2d and C3c. Marker positions are given on the respective chromosomes 2 and 3. The nature of the chromosomal segments between two markers is provided for all relevant regions in the Table with 3 representing homozygous for S. chmielewski whilst 1 represents homozygous for S. lycopersicum. All regions for which no information is given were homozygous for S. lycopersicum.

3. Supplemental Figure S2. Heat map of the metabolite profiles of the introgression lines in comparison to that of the parental control (Solanum lycopersicum cv Moneyberg) from the individual data set year 2006 under high load condition. Each square represents the effect of chromosomal segment substitution on the amount of every metabolite using false color scale. Regions of red or blue indicate that the metabolite content is increased or decreased, respectively, after the introgression of S. chmielewski LA1840 segments. For each haverst, gas chromatography-mass spectrometry was used to quantify 62 metabolites, including amino acids, organic acids, fatty acids, sugars, sugar alcohols, sugar phosphates and vitamins.

4. Supplemental Figure S3. Heat map of the metabolite profiles of the introgression lines in comparison to that of the parental control (Solanum lycopersicum cv Moneyberg) from the individual data set year 2007 under high load condition. Each square represents the effect of chromosomal segment substitution on the amount of every metabolite using false color scale. Regions of red or blue indicate that the metabolite content is increased or decreased, respectively, after the introgression of S. chmielewski LA1840 segments. For each haverst, gas chromatography-mass spectrometry was used to quantify 62 metabolites, including amino acids, organic acids, fatty acids, sugars, sugar alcohols, sugar phosphates and vitamins.

5. Supplemental Figure S4. Heat map of the metabolite profiles of the introgression lines in comparison to that of the parental control (Solanum lycopersicum cv Moneyberg) from the individual data set year 2006 under low load condition. Each square represents the effect of chromosomal segment substitution on the amount of every metabolite using false color scale. Regions of red or blue indicate that the metabolite content is increased or decreased, respectively, after the introgression of S. chmielewski LA1840 segments. For each haverst, gas chromatography-mass spectrometry was used to quantify 62 metabolites, including amino acids, organic acids, fatty acids, sugars, sugar alcohols, sugar phosphates and vitamins.

6. Supplemental Figure S5. Heat map of the metabolite profiles of the introgression lines in comparison to that of the parental control (Solanum lycopersicum cv Moneyberg) from the individual data set year 2007 under low load condition. Each square represents the effect of chromosomal segment substitution on the amount of every metabolite using false color scale. Regions of red or blue indicate that the metabolite content is increased or decreased, respectively, after the introgression of S. chmielewski LA1840 segments. For each haverst, gas chromatography-mass spectrometry was used to quantify 62 metabolites, including amino acids, organic acids, fatty acids, sugars, sugar alcohols, sugar phosphates and vitamins.

7. Supplemental Figure S6. Comparison of metabolic network obtained from S. chmielewskii IL population (A) with the previous reported obtained from S. pennellii IL population (B). A B

8. Supplemental Figure S7. Schematic representation of the metabolic changes occurring in the transition from development to ripening processes in tomato fruits of Moneyberg under high load (A) and low load (B) conditions. Data was normalize to 21 dpa. Boxes in grey and white indicate no changes and not determined, respectively. A B

9. Supplemental Figure S8. Principal component analysis of metabolite data obtained from 3 genotypes during fruit development (21, 28, 35. 42 DPA and mature stage) under two fruit load conditions (high load and low load). Green, blue and yellows represents different genotypes IL- 12d, IL-9d and Moneyberg, respectively. Triangle and square represents high load and low load condtions, respectively. Different development stages of fruit were visualized by different size of symbol (increased sized of symbol indicates the later stage of fruit development).