Supplementary Table 2: Marker-trait associations (q ≤ 0.05) obtained with the multiple regression model (1) in the ALL population. The amount of variance (in %) explained by the marker is given by the R2 statistic.

Marker allele / Chr.
No. / Allele frequencyb / CQA
q (R2) / CQS
q (R2) / TSC
q (R2) / TY
q (R2) / TSY
q (R2)
G6pdh-4b / II / 96/240 / 0.044 (1.9)
↓ d / ns c / ns / ns / ns
G6pdh-4d / II / 40/238 / 0.000 (9.2)
↓ / 0.000 (10.4)
↓ / 0.000 (6.9)
↓ / ns / ns
Stp23-8b (7a, 7b)a / III / 66/243 / 0.002 (3.9)
↑ / 0.000 (9.0)
↑ / 0.000 (11.4)
↑ / ns / 0.002 (6.7)
↑
Stp23-8a / III / 126/238 / ns / 0.003 (5.2)
↑ / 0.000 (9.6)
↑ / ns / 0.002 (5.9)
↑
Stp23-7c / III / 69/243 / ns / ns / 0.029 (2.8)
↑ / ns / ns
Pain1-5b / III / 104/239 / ns / 0.048 (2.5)
↓ / 0.002 (5.3)
↓ / ns / ns
PainI-9a (8c, 5c) a / III / 67/241 / 0.001 (4.4)
↑ / 0.000 (10.4)
↑ / 0.000 (12.0)
↑ / ns / 0.003 (5.3)
↑
PainI-5d / III / 25/242 / ns / ns / 0.045 (2.4)
↑ / ns / ns
SssI-4b (7a) a / III / 152/239 / 0.004 (3.7)
↑ / 0.000 (6.6)
↑ / 0.000 (7.2)
↑ / ns / 0.012 (4.3)
↑
StpL-3b / V / 121/242 / 0.000 (5.3)
↓ / 0.000 (7.3)
↓ / 0.000 (7.0)
↓ / ns / 0.033 (3.3)
↓
StpL-3d / V / 79/243 / ns / 0.021 (3.5)
↓ / ns / ns / ns
StpL-3e / V / 129/241 / 0.000 (6.8)
↑ / 0.000 (12.6)
↑ / 0.000 (9.3)
↑ / 0.000 (7.7)
↓ / ns
StpL-3c / V / 76/243 / ns / 0.048 (2.5)
↓ / 0.000 (6.4)
↓ / ns / ns
StpL-3i / V / 22/243 / ns / ns / 0.019 (3.3)
↑
Sut2-11a (7a, 8a, 12a, 6c, 9c)a / V / 80/239 / 0.037 (2.0)
↓ / 0.047 (2.6)
↓ / ns / ns / ns
Sut2-7c (3b, 9a, 11b) a / V / 157/243 / ns / ns / 0.019 (3.2)
↑ / ns / ns
Sut2-7b / V / 89/243 / ns / ns / 0.014 (3.6)
↓ / ns / ns
Sut2-5b / V / 27/241 / 0.017 (2.7)
↑ / 0.026 (3.3)
↑ / 0.025 (3.0)
↑ / ns / ns
Sps-7c (3a, 3i)a / VII / 147/241 / 0.022 (2.5)
↑ / ns / ns / ns / ns
Sps-3h (3f) a / VII / 103/240 / ns / ns / 0.017 (3.5)
↓ / ns / ns
Sps-15b / VII / 165/243 / 0.034 (2.1)
↓ / ns / ns / ns / ns
Pha2-3a / VII / 97/240 / ns / 0.001 (6.3)
↓ / 0.004 (4.7)
↓ / ns / ns
Pha2-3c / VII / 160/234 / ns / ns / 0.029 (2.9)
↓ / ns / 0.026 (3.5)
↓
Sus3-1a (Sus3/STM1043-a, Sus3/STM1097-a)a / VII / 130/237 / ns / 0.020 (3.7)
↓ / ns / ns / ns
AGPsb-6b / VII / 109/241 / ns / 0.040 (2.9)
↓ / ns / ns / ns
AGPsb-2a / VII / 103/242 / ns / ns / 0.036 (2.6)
↓ / ns / ns
GP171-a / VIII / 115/242 / 0.000 (5.7)
↓ / 0.000 (7.5)
↓ / 0.003 (4.9)
↓ / ns / ns
InvGE-6f (InvGF-4d)a / IX / 73/243 / 0.034 (2.2)
↑ / 0.040 (2.8)
↑ / ns / ns / ns
STM3012-c / IX / 135/232 / ns / 0.011 (4.3)
↓ / ns / ns / ns
STM3012-a / IX / 143/241 / 0.045 (1.8)
↓ / 0.041 (2.7)
↓ / ns / ns / ns
STM3012-b / IX / 54/235 / ns / ns / 0.044 (2.5)
↑ / ns / ns
StpH-13a / IX / 117/242 / 0.045 (1.8)
↑ / 0.040 (2.8)
↑ / ns / ns / ns
StpH-13c / IX / 50/242 / 0.045 (1.8)
↑ / ns / ns / ns / ns
STM3023b-e / IX / 32/236 / 0.034 (2.2)
↑ / 0.048 (2.6)
↑ / 0.033 (2.8)
↑ / ns / ns
Rca-1a / X / 80/241 / 0.000 (6.9)
↓ / 0.016 (3.8)
↓ / ns / ns / ns
pCD141-3b / X / 99/237 / 0.035 (2.1)
↑ / ns / ns / ns / ns
pCD141-3c / X / 118/240 / 0.008 (3.1)
↓ / 0.028 (3.1)
↓ / 0.007 (4.2)
↓ / ns / ns
pCD141-3a / X / 32/241 / ns / ns / 0.033 (2.7)
↑ / ns / ns
GP250-a / XI / 144/242 / 0.045 (1.8)
↓ / ns / ns / ns / ns
St1.1_HaeIII_b
(St1.1_HinfI_a) a / XI / 161/242 / 0.045 (1.8)
↑ / ns / 0.033 (2.7)
↑ / ns / 0.048 (2.9)
↑
STM0037-a / XI / 58/239 / 0.036 (2.0)
↑ / 0.043 (2.7)
↑ / 0.002 (5.5)
↑ / ns / ns
STM0037-c / XI / 72/239 / 0.030 (2.3)
↓ / ns / ns / ns / ns
STM0037-g / XI / 166/236 / ns / ns / 0.003 (5.1)
↓ / ns / 0.025 (3.8)
↓
Dbe-5c / XI / 130/233 / ns / ns / ns / ns / 0.026 (3.5)
↓
Dbe-5f / XI / 156/231 / ns / 0.028 (3.3)
↑ / ns / ns / ns
Dbe-5g / XI / 37/234 / 0.045 (1.8)
↑ / ns / ns / ns / ns

aMarker fragments shown in parenthesis are in nearly absolute LD, have identical or highly similar distribution in the population and show similar associations.

b Allele frequency is expressed as: number of genotypes having the marker allele/number of genotypes scored.

c Not significant, q > 0.05.

d Direction of effect: ↑ the marker allele has a positive effect on the trait (better chip quality, higher tuber starch content, yield and starch yield), ↓ the marker allele has a negative effect on the trait (lower chip quality, tuber starch content, yield and starch yield).

1