Table 4.
Results of the QTL mapping procedure for each phenology trait
| QTL | LG | Marker a | P (cM) b | SI (cM) c | LOD | α d | PEV e |
|---|---|---|---|---|---|---|---|
|
Bud burst in indoor conditions (BBI) | |||||||
| BBI.Ib |
Ib |
I_21om_sa (L29gr.164f) |
150.9 |
9.5 |
7.86 |
0.001 gw |
3.5 |
| BBI.II.1 |
II♂-2 |
II_30_sa_pIII |
16.9 |
23.5 |
4.54 |
0.005 cw |
7.5 |
| BBI.II.2 |
II♂-2 |
II_33_sa |
42.1 |
17.5 |
4.22 |
0.007 cw |
excl |
| BBI.II.3 |
II♂-2 |
II_35_sa (L12b.203f) |
80.6 |
12 |
6.20 |
0.006 gw |
7.1 |
| BBI.VII |
VII |
Ro4b |
64.4 |
48.5 |
3.04 |
0.032 cw |
excl |
| BBI.IX |
IX |
IX_1_sa |
56.6 |
10 |
3.60 |
0.010 cw |
3.2 |
| BBI.X.1 |
X |
X-4 |
83.7 |
41 |
3.55 |
0.015 cw |
excl |
| BBI.X.2 |
X |
X-21_sa (L3gr.227f) |
140.2 |
19.2 |
3.36 |
0.023 cw |
2.8 |
| BBI.A |
A |
XVI-13_sa |
17.0 |
35 |
3.95 |
0.001 cw |
6.2 |
| BBI total sum of explained variance |
30.3 |
||||||
|
Bud burst in field conditions year 2009 (BBF09) | |||||||
| BBF09.Ib |
Ib |
XVI_12_om_sa_pI |
99.5 |
13 |
6.65 |
0.001 gw |
10.3 |
| BBF09.II |
II♂-2 |
II_24_sa |
59.9 |
74.5 |
2.78 |
0.038 cw |
2.0 |
| BBF09.IV |
IV |
IV_20_sa (L2gr.226f) |
71.1 |
87.9 |
3.00 |
0.028 cw |
excl |
| BBF09.VI |
VI-1 |
VI_15_sa (L13y.371) |
48.6 |
22.5 |
5.24 |
0.011 gw |
3.7 |
| BBF09.VII |
VII |
VII-3b |
43.6 |
70.5 |
2.78 |
0.043 cw |
excl |
| BBF09.X |
X |
X_19_sa |
116.7 |
32.5 |
4.19 |
0.003 cw |
1.4 |
| BBF09.XIV |
XIV♂ |
XIV_18_sa_pIII |
85.9 |
17 |
5.89 |
0.003 gw |
4.4 |
| BBF09.XVIII |
XVIII |
XVIII_6_sa |
14.6 |
18.5 |
3.25 |
0.018 cw |
4.5 |
| BBF09.A |
A |
XVI_13_sa |
34.9 |
18.5 |
2.77 |
0.001 cw |
excl |
| BBF09.B |
B |
SB945 |
27.7 |
42.3 |
2.28 |
0.049 cw |
1.3 |
| BBF09 total sum of explained variance |
27.6 |
||||||
|
Bud burst in field conditions year 2010 (BBF10) | |||||||
| BBF10.Ia |
Ia |
SB331 |
170.3 |
36.3 |
4.60 |
0.005 cw |
1.9 |
| BBF10.Ib.1 |
Ib |
I_51om_sa |
107.2 |
28 |
3.78 |
0.022 cw |
excl |
| BBF10.Ib.2 |
Ib |
I-32_sa |
215.5 |
71.5 |
3.63 |
0.026 cw |
4.2 |
| BBF10.II |
II♂-2 |
R_41_sa_pI |
20.9 |
17 |
13.32 |
0.001 gw |
14.1 |
| BBF10.VI.1 |
VI-1 |
VI-3d |
8.3 |
15.5 |
7.96 |
0.005 gw |
7.3 |
| BBF10.VI.2 |
VI-1 |
SB496 |
61.8 |
13 |
4.04 |
0.005 cw |
excl |
| BBF10.VII |
VII |
Ph18 |
52.2 |
28.5 |
4.78 |
0.002 cw |
1.0 |
| BBF10.VIII.1 |
VIII-2 |
VIII_3_sa |
32.7 |
29.3 |
4.75 |
0.001 cw |
5.6 |
| BBF10.VIII.2 |
VIII-3 |
VIII_20_sa_pI |
41.4 |
33 |
6.72 |
0.025 gw |
3.4 |
| BBF10.IX.1 |
IX |
IX_5_sa |
36.9 |
47.5 |
3.79 |
0.008 cw |
2.1 |
| BBF10.IX.2 |
IX |
R_60_sa_pI |
78.2 |
23.9 |
3.73 |
0.011 cw |
3.5 |
| BBF10.X |
X |
Ph2 |
45.9 |
25 |
4.92 |
0.002 cw |
3.2 |
| BBF10.XIV |
XIV♂ |
XIV-4_sa |
82.3 |
19 |
3.38 |
0.019 cw |
excl |
| BBF10.XVII |
XVII |
II_37_sa_pI |
123.8 |
23.5 |
3.19 |
0.041 cw |
excl |
| BBF10.XVIII |
XVIII |
XVIII_6_sa |
14.6 |
28 |
4.34 |
0.002 cw |
3.0 |
| BBF10.A |
A |
XVI-13_sa |
35.0 |
22 |
3.05 |
0.001 cw |
3.9 |
| BBF10 total sum of explained variance |
53.2 |
||||||
|
Growth Cessation in indoor conditions (GCI) | |||||||
| GCI.Ib |
Ib |
XVII_8om_sa |
182.8 |
34 |
3.93 |
0.015 cw |
5.4 |
| GCI.II |
II♂-2 |
II_35_sa |
84.8 |
14 |
4.70 |
0.006 cw |
4.6 |
| GCI.V |
V♂ |
V-5_sa |
52.8 |
24 |
5.22 |
0.028 gw |
11.5 |
| GCI total sum of explained variance |
21.5 |
||||||
|
Growth cessation in field conditions year 2008 (GCF08) | |||||||
| GCF08.Ia |
Ia |
R_29_sa |
42.0 |
37.5 |
3.38 |
0.043 cw |
2.3 |
| GCF08.Ib |
Ib |
XVI_18_sa |
80.1 |
12.5 |
7.28 |
0.001 cw |
6.1 |
| GCF08.II |
II♂-2 |
II_35_sa |
84.8 |
8 |
10.54 |
0.002 gw |
16.7 |
| GCF08.III |
III |
III_8om_sa |
24.8 |
36 |
2.91 |
0.045 cw |
1.7 |
| GCF08.V |
V♂ |
V-5_sa |
52.8 |
16 |
5.93 |
0.001 cw |
5.5 |
| GCF08.X |
X |
X-4 |
90.4 |
5.5 |
16.31 |
0.001 gw |
2.3 |
| GCF08.XIV |
XIV♂ |
XIV-4_sa |
82.3 |
14 |
4.42 |
0.005 cw |
2.8 |
| GCF08.XVIII |
XVIII |
XVII_9om_sa_pI |
43.9 |
47 |
2.83 |
0.043 cw |
3.5 |
| GCF08 total sum of explained variance |
40.9 |
||||||
|
Growth cessation in field conditions year 2009 (GCF09) | |||||||
| GCF09.Ib |
Ib |
XVI_18_sa |
80.2 |
14.5 |
4.75 |
0.004 cw |
4.9 |
| GCF09.II.1 |
II♂-1 |
II-Ib_pI |
11.0 |
26 |
4.02 |
0.001 cw |
7.0 |
| GCF09.II.2 |
II♂-2 |
II_33_sa |
43.1 |
17 |
4.82 |
0.004 cw |
2.4 |
| GCF09.II.3 |
II♂-2 |
II_35_sa |
84.8 |
13 |
6.15 |
0.001 cw |
6.2 |
| GCF09.III |
III |
III-4_sa |
23.8 |
29 |
2.95 |
0.047 cw |
3.2 |
| GCF09.V |
V♂ |
V_5_sa |
52.8 |
55 |
3.15 |
0.032 cw |
1.2 |
| GCF09.IX |
IX |
IX_8_sa |
75.2 |
22.9 |
3.82 |
0.007 cw |
4.2 |
| GCF09.X |
X |
X-4 |
91.4 |
5.5 |
8.55 |
0.002 gw |
10.7 |
| GCF09.XIV |
XIV♂ |
XIV-4_sa |
82.3 |
7.5 |
5.50 |
0.001 cw |
1.4 |
| GCF09.XVIII |
XVIII |
XVIII_8_sa |
39.7 |
51.5 |
2.88 |
0.042 cw |
2.1 |
| GCF09.Ib × GCF09.XVIII |
|
|
|
|
|
5.8 |
|
| GCF total sum of explained variance |
49.1 |
||||||
|
Leaf senescence in field conditions year 2009 (LSF09) | |||||||
| LSF09.Ib |
Ib |
SB265 |
219.5 |
23 |
4.34 |
0.007 cw |
1.6 |
| LSF09.II |
II♂-2 |
II_35_sa |
84.8 |
4 |
32.11 |
0.001 gw |
34.2 |
| LSF09.III |
III |
III-14_sa |
87.1 |
36 |
3.57 |
0.018 cw |
excl |
| LSF09.IV |
IV |
Ro11 |
21.6 |
38 |
3.0 |
0.030 cw |
excl |
| LSF09.VI.1 |
VI-1 |
VI-3d |
4.3 |
10.5 |
3.32 |
0.023 cw |
1.2 |
| LSF09.VI.2 |
VI-2 |
Sa_con27_PopI |
8.4 |
10.5 |
8.11 |
0.001 gw |
3.7 |
| LSF09.VII |
VII |
VII_1_sa |
1.0 |
6 |
6.18 |
0.001 gw |
4.3 |
| LSF09.VIII.1 |
VIII-2 |
VIII_3_sa |
27.7 |
23 |
3.30 |
0.005 cw |
1.6 |
| LSF09.VIII.2 |
VIII-3 |
VIII_5_sa |
4.0 |
15.5 |
7.55 |
0.001 gw |
5.6 |
| LSF09.X |
X |
X-4 |
88.4 |
6.5 |
20.49 |
0.001 gw |
2.2 |
| LSF09.XI |
XI |
R_52_sa |
4.5 |
91 |
3.14 |
0.021 cw |
1.1 |
| LSF09.XIV |
XIV ♀ |
XIV-12_sa |
30.0 |
34.7 |
2.47 |
0.030 cw |
1.0 |
| LSF09 total sum of explained variance |
56.5 |
||||||
|
Leaf senescence in field conditions year 2010 (LSF 2010) | |||||||
| LSF10.II |
II♂-2 |
II-12_sa |
89.6 |
5.5 |
16.89 |
0.001gw |
19.3 |
| LSF10.III |
III |
III-18_sa |
118.6 |
15.5 |
6.35 |
0.003 gw |
6.0 |
| LSF10.IV |
IV |
Ph30 |
95.3 |
30.9 |
2.88 |
0.034 cw |
2.3 |
| LSF10.V |
V♂ |
V_10_sa |
59.4 |
28.5 |
3.64 |
0.005 cw |
5.0 |
| LSF10.VI |
VI-1 |
VI-3d |
4.3 |
12.5 |
2.94 |
0.049 cw |
1.8 |
| LSF10.VII |
VII |
VII_1_sa |
1.0 |
26 |
2.73 |
0.047 cw |
1.4 |
| LSF10.VIII |
VIII-3 |
VIII_5_sa |
4.0 |
45.5 |
2.91 |
0.002 cw |
1.8 |
| LSF10.X |
X |
X-4 |
88.4 |
8.5 |
10.49 |
0.001 gw |
1.8 |
| LSF10.XII |
XII |
XII-4d |
63.7 |
45.5 |
3.22 |
0.016 cw |
1.2 |
| LSF10.XIV.1 |
XIV♀ |
XIV-9_sa |
22.8 |
20 |
6.73 |
0.001 gw |
3.2 |
| LSF10.XIV.2 |
XIV♂ |
XIV-14_sa |
135.8 |
45.3 |
4.60 |
0.030 gw |
excl |
| LSF10.B |
B |
VI_22_sa |
12.0 |
41.5 |
4.51 |
0.037 gw |
excl |
| LSF10 total sum of explained variance | 43.8 | ||||||
aThe closest SNP marker to the QTL peak position, also used in multiple QTL mapping, and in mixed model and variance components analyses. When the closest marker to peak position was not a SNP, the AFLP marker is reported in brackets. bQTL position on the S1 linkage map [35]. cHeuristic support interval determined as a 1.5-unit drop off on either side of the local LOD score peak. dProbability for the null hypothesis of no QTL obtained after 5,000 permutations. ePercentage of variance explained by the QTL or by the QTL × QTL interaction estimated by variance components analysis. gw Genome-wide, significant QTL. cw Chromosome-wide, suggestive QTL. excl QTL excluded from the complete model following a backward selection procedure at a test level of 0.05 (see Methods for details).