TABLE 4

QTL effects in different environments

2 LOD (cM)WhiteBlueRedFar-red
QTLMarkerChromLODmm% 1% varLODmm% 1% varLODmm% 1% varLODmm% 1% var
Main effect loci
1 DARK1PW41(0–7)
2 LIGHT1CD.157C-Col/158L1(22–30)14.01.021229.50.916169.41.317176.70.51110
3 HYP1FD.90L-Col1(116–121)8.8−0.7−15105.7−0.6−1185.9−0.6−837.2−0.3−74
4 LIGHT2BF.221L2(32–40)10.60.715118.41.41818
+5 HYP2Erecta2(47–53)7.90.915146.60.61313
+ 6 FARRED2DF.140C2(68–71)6.70.251
7 RED3GB.97L-Col/99C3(76–80)7.6−1.0−139
8 BRZ4SC54(43–48)
9 WHITE4DF.IO8L-C0I4(46–52)4.00.494
10 BLUE4FD.167L-Col4(55–65)9.30.91513
11 FARRED4GH.433L-Col4(65–78)4.00.4107
12 BLUE5FD.207L5(0–3)4.20.6106
Epistaitic loci
Additivew.EPIlBF.269C5(19–25)0.00
Additivew.EPI2GH.117C5(36–41)−0.4−8
Interaction(BF.269C × GH.117C)5 × 55.3−1.4−1510
Germ−0.3−6−0.7−13−1.0−14−0.6−13
Total variance explained61514541
*2 LOD (cM)WhiteGADarkBRZ
QTLMarkerChromLODmm% 1% varLODmm% 1% varLODmm% 1% varLODmm% 1% var
Main effect loci
1 DARK1PW41(0–7)3.70.756
2 LIGHT1CD.157C-Col/158L1(22–30)14.01.0212210.41.21817
3 HYP1FD.90L-Col1(116–121)8.8−0.7−15105.6−0.8−1276.6−0.8−127
4 LIGHT2BF.221L2(32–40)10.60.7151110.91.32122
+5 HYP2Erecta2(47–53)8.61.392016.61.52325
+ 6 FARRED2DF.140C2(68–71)
7 RED3GB.97L-Col/99C3(76–80)
8 BRZ4SC54(43–48)13.21.32019
9 WHITE4DF.IO8L-C0I4(46–52)4.00.494
10 BLUE4FD.167L-Col4(55–65)
11 FARRED4GH.433L-Col4(65–78)
12 BLUE5FD.207L5(0–3)
Epistatic loci
Additivew.EPIlBF.269C5(19–25)0.00
Additivew.EPI2GH.117C5(36–41)−0.4−8
Interaction(BF.269C × GH.117C)5 × 5−1.4−1510
Germ−0.3−6−0.5−8−0.5−4−0.4−6
Total variance explained61432748
  • For each QTL the maximum LOD score, additive effect 2a (mm), the percentage of change in length (% 1), and the percentage of variance (% var) are shown. Positive effects indicate that the Cvi allele increases the phenotype. Italic type indicates a significant G × E interaction. The additive effects of the markers in the epistatic interaction are also shown. For the epistatic interaction the LOD increase due to the epistatic term, effect 4i (mm), percentage of change in length, and percentage of variance explained are shown. + denotes the variance explained is corrected for linkage (Kao 2000). * is the largest 2-LOD interval when the QTL was detected in multiple environments.