1. Supplemental Fig. S1 Comparison of QTLs identified by linkage mapping and association studies on chromosomes 1, 3, 5, 6, 10, 11 and 12. SNPs were mapped on tomato EXPEN 2000 reference map (http://www.solgenomics.net). Associations detected in the 188 accessions (W) and in127S. l. cerasiformeaccessions (C) are indicated to the right of the chromosomes. Associations were estimated with K + Q model, model A: MLM model, with structure based on 20 SSR marker, model B: MLM model with structure based on 121 SNP (common font: associations detected in model A; in italic: associations detected in model B; in bold, associations detected in both models). Horizontal lines “-“ correspond to the genetic location of associated marker, associations are linked together by a vertical line when linked markers in less than 10 cM are associated to the same trait. Associated SNPs in less than 10 cM on each chromosome were grouped together. SNP which is 10 cMapart from the others were assigned as independent groups. Groups are named as consecutive number according to their genetic location on each chromosome. Traits are : FIR= firmness, FW= fruit weight, SSC= soluble solids content, SUG = total sugar content, LCN= locule number, a and L=color, TA = titratable acidity. QTLs identified by linkage mapping in the populations from crosses of S. Lycopersicum× S. l. cerasiforme (Saliba-Colombani et al. 2001), S. Lycopersicum× S. pimpinellifolium(Grandillo et al. 1996) and S. Lycopersicum× S. l. cheesmanii(Goldman et al. 1995)are shown to the left of the chromosomes (CR= QTL from S. l. cerasiforme, CE= QTL from S. l. cheesmanii, PM= QTL from S. pimpinellifolium).Only QTL co-localizing with an association are shown