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. 2013 Oct 11;3(12):2131–2146. doi: 10.1534/g3.113.007195

Table 4. Summary of significant QTL for horticultural traits.

Trait Class Trait Code Trait Group Year Location(s) Peak Marker or Interval Peak LOD/Threshold LOD R2
Maturity DAP1st Time to first ripe fruit (d) Hort5-1 2009 3 & 4 TG358 7.24/1.60 0.42
2010 3 TG358 7.06/1.68 0.51
2010 4 TG358 4.82/1.70 0.41
Hort5-3 2009 3 & 4 At2g31970–At4g12590 2.88/1.60 0.16
2010 3 At2g31970 2.06/1.68 0.11
DAP50 Time to 50% ripe fruit (d) Hort5-1 2009 3 TG358 4.42/1.71 0.29
2009 4 TG358 4.90/1.67 0.30
2010 3 TG358 3.26/1.63 0.30
2010 4 TG358 6.19/1.79 0.49
Yield YLD Yield Hort5-1 2009 3 TG358 13.42/1.63 0.65
2009 4 TG358 10.09/1.75 0.54
2010 3 TG358 6.51/1.71 0.49
Hort5-3 2009 4 At2g31970–At4g12590 3.40/1.75 0.16
Fruit size/shape FH Fruit height Hort5-1 2009 3 TG358 10.20/1.79 0.42
2009 4 TG358 5.14/1.68 0.24
2010 3 TG358 4.49/1.63 0.39
2010 4 TG358 4.77/1.76 0.41
Hort5-3 2009 3 At2g31970–At4g12590 2.52/1.79 0.07
FW Fruit width Hort5-2 2009 3 & 4 At3g17210 4.11/1.64 0.27
FS Fruit shape (H:W) Hort5-1 2009 3 TG358 4.97/1.69 0.16
2009 4 TG358 2.04/1.53 0.05
Hort5-2 2009 3 At5g49510 3.86/1.69 0.12
2009 4 At5g49510 4.24/1.53 0.12
Hort5-4 2009 4 TG69 2.55/1.53 0.07
FP Fruit size Hort5-1 2009 3 TG358 6.83/1.69 0.38
2009 4 TG358 1.71/1.64 0.13
2010 3 TG358 2.85/1.74 0.27
2010 4 TG358 2.25/1.87 0.16
Hort5-2 2009 3 TG23 2.74/1.69 0.12
Hort5-4 2009 3 At4g12590 2.15/1.69 0.09
30Wt Fruit weight Hort5-1 2009 3 TG358 7.03/1.79 0.34
2009 4 TG358 5.09/1.58 0.29
2010 3 TG358 4.99/1.56 0.36
2010 4 TG358 4.72/1.80 0.39
Hort5-2 2009 3 TG23 3.85/1.79 0.15
2009 4 At3g17210 2.07/1.58 0.10
SW Seed weight Hort5-1 2009 3 & 4 T0536 2.08/1.60 0.06
Fruit quality Brix Brix Hort5-1 2009 4 TG358 4.44/1.60 0.21
Hort5-3 2009 3 At2g31970–At4g12590 7.18/1.74 0.45
2009 4 At4g12590 6.66/1.60 0.39
Hort5-4 2010 4 T1541–TG69 4.73/1.65 0.41
pH pH Hort5-1 2009 3 TG358 2.54/1.68 0.18
Plant architecture CD Canopy density Hort5-1 2009 4 TG358 2.31/1.72 0.17
Hort5-4 2009 3 TG69 3.92/1.55 0.27
HAB Plant habit Hort5-1 2010 3 & 4 TG358 4.36/1.75 0.38
Hort5-2 2009 1, 2, 3, 4 At5g49510 3.65/1.69 0.25
H Plant height Hort5-1 2009 3 & 4 TG358 5.81/1.73 0.32
2010 1 & 2 TG358 3.68/1.74 0.33
Hort5-2 2009 3 & 4 At2g39950 3.53/1.73 0.19
Hort5-3 2009 1 & 2 At2g31970–At4g12590 4.05/1.73 0.27
2009 3 & 4 At2g31970–At4g12590 5.32/1.73 0.35
2010 3 At2g31970 2.96/1.80 0.28
2010 4 At2g31970 3.78/1.73 0.32
W Plant width Hort5-1 2009 1 TG358 3.05/1.65 0.22
Hort5-3 2009 3 & 4 At2g31970–At4g12590 9.28/1.67 0.55
2010 1 & 2 At2g31970–At4g12590 3.32/1.66 0.30
Hort5-4 2009 2 T1541–TG69 2.17/1.65 0.18
2010 1 & 2 TG69 3.07/1.66 0.20
SH Plant shape (H:W) Hort5-1 2009 3 & 4 TG358 11.19/1.63 0.58
Hort5-2 2009 3 & 4 At3g55800 2.34/1.63 0.08
Hort5-3 2009 1 At4g12590 3.23/1.48 0.22
Hort5-4 2010 3 & 4 TG69 2.11/1.65 0.21
SZ Plant size Hort5-1 2009 1 & 2 TG358 3.54/1.73 0.24
2010 1 & 2 TG358 3.61/1.80 0.27
Hort5-2 2009 3 & 4 At2g39950 2.70/1.62 0.14
2010 1 & 2 At3g17210 1.88/1.80 0.13
Hort5-3 2009 3 & 4 At2g31970–At4g12590 5.29/1.62 0.35
2010 3 & 4 At2g31970–At4g12590 2.69/1.67 0.32
Trait Class Trait Code Trait Group Year Location(s) Allele Direction 1-LOD Support Interval Flanking Markers
Maturity DAP1st Time to first ripe fruit (d) Hort5-1 2009 3 & 4 (+) 0.0–0.3 TG358-T0536
2010 3 (+) 0.0–0.3 TG358-T0536
2010 4 (+) 0.0–0.3 TG358-T0536
Hort5-3 2009 3 & 4 (+) 7.3–9.9 At5g49510-T1541
2010 3 (+) 6.3–9.5 At5g49510-T1777
DAP50 Time to 50% ripe fruit (d) Hort5-1 2009 3 (+) 0.0–0.3 TG358-T0536
2009 4 (+) 0.0–0.3 TG358-T0536
2010 3 (+) 0.0–0.3 TG358-T0536
2010 4 (+) 0.0–0.3 TG358-T0536
Yield YLD Yield Hort5-1 2009 3 (−) 0.0–0.3 TG358-T0536
2009 4 (−) 0.0–0.3 TG358-T0536
2010 3 (−) 0.0–0.3 TG358-T0536
Hort5-3 2009 4 (−) 6.3–9.9 At5g49510-T1541
Fruit size/shape FH Fruit height Hort5-1 2009 3 (−) 0.0–0.3 TG358-T0536
2009 4 (−) 0.0–0.3 TG358-T0536
2010 3 (−) 0.0–1.3 TG358-cLEX13G5
2010 4 (−) 0.0–0.3 TG358-T0536
Hort5-3 2009 3 (−) 7.7–11.9 At2g31970-TG69
FW Fruit width Hort5-2 2009 3 & 4 (+) 5.0–6.3 At2g39950-At5g49510
FS Fruit shape (H:W) Hort5-1 2009 3 (−) 0.0–0.3 TG358-T0536
2009 4 (−) 0.0–0.3 TG358-T0536
Hort5-2 2009 3 (−) 5.0–8.7 At2g39950-At4g12590
2009 4 (−) 5.5–7.6 At2g39950-TG60
Hort5-4 2009 4 (−) 10.9–12.3 T1541-At3g55360
FP Fruit size Hort5-1 2009 3 (−) 0.0–0.3 TG358-T0536
2009 4 (−) 0.0–1.8 TG358-U221402
2010 3 (−) 0.0–1.3 TG358-cLEX13G5
2010 4 (−) 0.0–0.3 TG358-T0536
Hort5-2 2009 3 (+) 5.0–6.3 At2g39950-At5g49510
Hort5-4 2009 3 (−) 8.7–11.9 At2g31970-TG69
30Wt Fruit weight Hort5-1 2009 3 (−) 0.0–0.3 TG358-T0536
2009 4 (−) 0.0–0.3 TG358-T0536
2010 3 (−) 0.0–0.3 TG358-T0536
2010 4 (−) 0.0–0.3 TG358-T0536
Hort5-2 2009 3 (+) 5.0–6.3 At2g39950-At5g49510
2009 4 (+) 4.0–7.3 At2g39950-TG60
SW Seed weight Hort5-1 2009 3 & 4 (+) 0.0–1.3 TG358-cLEX13G5
Fruit quality Brix Brix Hort5-1 2009 4 (+) 0.0–0.3 TG358-T0536
Hort5-3 2009 3 (+) 7.7–9.4 At2g31970-At4g12590
2009 4 (+) 7.7–9.9 At2g31970-T1541
Hort5-4 2010 4 (+) 9.5–12.3 T1777-At3g55360
pH pH Hort5-1 2009 3 (−) 0.0–0.3 TG358-T0536
Plant architecture CD Canopy density Hort5-1 2009 4 (+) 0.0–1.3 TG358-cLEX13G5
Hort5-4 2009 3 (−) 9.9–12.3 T1777-At3g55360
HAB Plant habit Hort5-1 2010 3 & 4 (−) 0.0–0.3 TG358-T0536
H Plant height Hort5-1 2009 3 & 4 (+) 0.0–0.3 TG358-T0536
2010 1 & 2 (−) 0.0–1.8 TG358-U221402
Hort5-2 2009 3 & 4 (−) 2.7–5.0 At3g55800-TG23
Hort5-3 2009 1 & 2 (+) 7.7–10.9 At2g31970-TG69
2009 3 & 4 (+) 7.3–9.4 At5g49510-At4g12590
2010 3 (+) 7.3–9.4 At5g49510-At4g12590
2010 4 (+) 6.3–9.4 At5g49510-At4g12590
W Plant width Hort5-1 2009 1 (−) 0.0–1.3 TG358-T0536
Hort5-3 2009 3 & 4 (+) 7.7–9.4 At2g31970-At4g12590
2010 1 & 2 (−) 5.9–9.4 At3g17210-At4g12590
Hort5-4 2009 2 (+) 9.9–12.3 T1777-At3g55360
2010 1 & 2 (+) 12.0–12.3 TG69-At3g55360
SH Plant shape (H:W) Hort5-1 2009 3 & 4 (+) 0.0–0.3 TG358-T0536
Hort5-2 2009 3 & 4 (−) 1.8–5.0 U221402-TG23
Hort5-3 2009 1 (+) 7.7–9.9 At2g31970-T1541
Hort5-4 2010 3 & 4 (−) 9.9–12.3 T1777-At3g55360
Plant architecture SZ Plant size Hort5-1 2009 1 & 2 (−) 0.0–0.3 TG358-T0536
2010 1 & 2 (−) 0.0–0.3 TG358-T0536
Hort5-2 2009 3 & 4 (−) 1.8–5.5 U221402-TG23
2010 1 & 2 (−) 3.0–8.7 At2g39950-At4g12590
Hort5-3 2009 3 & 4 (+) 7.3–9.4 At5g49510-At4g12590
2010 3 & 4 (+) 6.3–9.4 At5g49510-At4g12590

Group indicates coincident QTL, as defined by colocation of the 1-LOD intervals. R2 values are the proportion of phenotypic variation explained by the marker–trait association. Allele direction is the direction of the effect of the S. habrochaites allele at that QTL, in terms of the trait being measured. The 1-LOD support interval positions refer to the cM distances on the linkage map for the introgressed region from S. habrochaites. See Johnson et al. (2012) for LEAF and STEM QTL results.