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Figure Captions
16
17
Fig. 1
18
Directed acyclic graph (DAG), with variables (nodes) connected by directed edges
19
(arrows). Trait and QTL nodes are indicated by white and gray circles, respectively.
20
Traits abbreviations are shown in the footnote of Table 1.
Causal phenotype networks for 24 egg traits in chickens
20
Table 1. Summary of differences of results between QDG and traditional QTL mapping
Trait1
AFE
EPR02
EPR03
EPR09
E_EW
E_LLE
E_LSE
E_SW
E_SS
E_STN
E_STB
E_STE
Chromosome
11
12
10
12
17
17
17
17
QTL position2
ADL0188
ADL0188
ADL0188
MCW0112
MCW0095
MCW0095
MCW0258
MCW0095
MCW0095
ABR0289
ABR0289
ABR0530
ABR0289
ABR0530
ABR0289
Indirect path3
Difference4
Non-effect
Non-effect
E-LSE <- E-EW <- E-LLE <- MCW0258
E-SW <- E-STE <- ABR0530
E-SW <- E-STE <- ABR0289
E-STN <- E-STE <- ABR0530
Direct QTL effect
Non-effect
Direct QTL effect
Direct QTL effect
Non-effect
Non-effect
Indirect QTL effect
Direct QTL effect
Indirect QTL effect
Indirect QTL effect
Non-effect
Direct QTL effect
Non-effect
Indirect QTL effect
Reference5
[1]
[1]
[1]
[1]
[1]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
Direct QTL effect
[2]
[2]
[2]
21
Table 1
(continued)
E_SCR
E_SCY
E_AW
E_AH
E_LTA
E_STA
E_YW
E_YH
E_YL
E_YS
E_YCL
27
15
MCW0112
ABR0331
ADL0233
MCW0112
ABR0331
ADL0233
MCW0240
MCW0095
LEI0146
MCW0223
MCW0258
MCW0095
MCW0095
MCW0233
MCW0095
ABR0119
MCW0120
MCW0095
ADL0273
MCW0095
MCW0095
ADL0229
Non-effect
Non-effect
Non-effect
E-YH <- E-AH <- E-YCY <- ABR0622
Indirect QTL effect
Non-effect
22
[2]
[2]
[2]
[2]
[2]
[2]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
Table 1
(continued)
E_YCY
MCW0095
ABR0622
MCW0095
[3]
[3]
[3]
AFE = age at first egg, EPR02 = egg production rate during 26 to 30 weeks of age, EPR03 = egg production rate during 30 to 34
weeks of age, EPR09 = egg production rate during 54 to 58 weeks of age, E_: egg collected at early stage (first 10 eggs), EW= egg
weight, LLE = length of the long axis of the egg, LSE = length of the short axis of the egg, SW = eggshell weight, SS = eggshell strength,
STN = eggshell thickness at the narrow end of the egg, STB = eggshell thickness at the blunt end of the egg, STE = eggshell thickness
at the equator of the egg, SCR = redness of the eggshell color, SCY = yellowness of the eggshell color, AW = albumen weight, AH =
albumen height, LTA = length of the long axis of the thick albumen, STA = length of the short axis of the thick albumen, YW = yolk
weight, YH = yolk height, YL = length of the long axis of the yolk, YS = length of the short axis of the yolk, YCL = lightness of the yolk
color, YCY = yellowness of the yolk color.
QTL position was indicated by microsatellite marker name. Hyphen indicate no QTL was detected by QDG mapping.
Indirect path was detected by QDG mapping (Please see Fig. 1). QTL to the trait was indicated from right to left and was connected by
arrows.
4 Difference from previous reports (traditional QTL mappings) was listed. Direct QTL effect: direct effect was newly detected by QDG
mapping, Indirect QTL effect: indirect effect was newly detected by QDG mapping, Non-effect: no effect was detected by QDG mapping.
[1] Goto et al. 2011; [2] Goto et al. 2014a; [3] Goto et al. 2014b.
23
Fig. 1
24
Table S1. LOD score and direction of each edges.
No.
Node1
Direction
Node2
LOD
10
11
12
13
14
15
16
AFE
AFE
E_EW
E_EW
E_EW
E_LLE
E_SCR
E_SS
E_SW
E_SW
E_STN
E_STN
E_STB
E_AW
E_AH
E_AH
<--------->
<--------->
----->
<----<----<----<----<--------->
<--------->
----->
----->
----->
EPR02
EPR03
E_LLE
E_LSA
E_AW
E_LTA
E_SCY
E_STB
E_STE
E_YH
E_STB
E_STE
E_STE
E_STA
E_STA
E_YH
-2.83E-04
2.68E+01
-2.81E+01
8.18E-01
6.24E+01
-9.32E+00
-7.25E-02
-3.10E+01
-3.94E+01
-3.38E+01
4.25E+01
-4.38E+01
4.24E+01
5.55E+01
3.92E+01
1.76E+01
17
18
19
20
21
22
23
E_AH
E_LTA
E_YW
E_YW
E_YW
E_YL
E_YCL
<----<--------->
<--------->
<----<-----
E_YCY
E_STA
E_YH
E_YL
E_YS
E_YS
E_YCY
-6.41E-01
-4.98E+01
2.05E+01
-1.07E+02
1.09E+02
-1.09E+02
-1.20E+00
25
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