Figure S2. Genetic maps and QTL locations for ‘Beihong’ (BH, maternal parent) × and ‘E.S.7-11-49’ (ES, paternal parent). Markers are listed to the right.

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Figure S2. Genetic maps and QTL locations for ‘Beihong’ (BH, maternal parent) × and ‘E.S ’ (ES, paternal parent). Markers are listed to the right of each LG and genetic distances on the left. The SNP markers in blue are common to both parents. QTLs controlling sugar- and acid-related traits are shown in bar and represented by blue arrows extended by lines. Confidence intervals of QTLs are according to their scale on genetic map. Distances are in Kosambi cM. The year of observation is denoted by 11, 12 and 13 for 2011, 2012 and 2013, respectively. SSC represents soluble solid content, G/F is the glucose-to-fructose ratio and β ratio is the tartaric acid-to-malic acid ratio.

BH LG01ES LG SSC G/F11 BH LG02ES LG02

G/F11 α ratio11 BH LG03ES LG Fructose12 BH LG04ES LG04

BH LG05-1ES LG05BH LG Malic11 Total acid11 BH LG06ES LG06

G/F BH LG07 ES LG07

BH LG08-1ES LG08BH LG G/F12 BH LG09ES LG09

BH LG10ES LG Fructose BH LG11ES LG11

_ BH LG12 ES LG12

BH LG13 ES LG13 Total acid12

Fructose11 BH LG14ES LG14 Glucose11, Total sugar11 Glucose11 Total sugar11 SSC11Fructose11 Glucose11 Total sugar11 SSC11

BH LG15-2ES LG15BH LG BH LG16ES LG16

Fructose11 BH LG17ES LG17 G/F13

Total acid12 Malic11 β ratio12 SSC12 Malic12 β ratio11, 12 Malic11, 12 β ratio11, 12 Total acid12 BH LG18 ES LG18 Malic12 Total acid12 β ratio11

BH LG19ES LG19