Additional file 2 Title: Composite map – component map marker ...

Additional file 2 Title: Composite map – component map marker colinearity

Description: Marker colinearity between all six component maps and the Eucalyptus composite map. For each LG, three LG ‘triplets’ show marker colinearity between two component maps (outside) and the composite map (centre). Horizontal lines on LG bars indicate marker positions and lines between LGs indicate the position of common markers. The scale bar shown is in Kosambi’s centiMorgans. Component map names (abbreviations; see Table 1) are given above each LG. LGs excluded from composite map construction are

indicated in parentheses following the component map name. An asterisk indicates whether marker-order information from the component map was incorporated during composite map construction (see Methods). For the GU-Emb component map, superscript letters indicates whether the framework (f) or comprehensive (c) linkage group from this pedigree was used in composite map construction.

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

Linkage group 1

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

1_Con

1_CC_1032

GU-Embf

GLOB-F2-1*

GLOB-F1-5*

Composite

1_JF2

Composite

mock GLOB-F1-4*

1_JF1 GLOB-F1-1*

1_Con

Composite

GLOB-LH*

1_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

Linkage group 2

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

2_CC_2484

GU-Embc*

Composite

GLOB-F2-1*

2_JFAM5 2_JF2 Mock22_Con GLOB-F1-5

Composite

GLOB-F1-4*

2_JFAM1 2_JF4 mock 2_Con GLOB-F1-1*

2_Con

Composite

GLOB-LH*

2_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

Linkage group 3

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

3_CC_1032

GU-Embf*

1_Con

Composite

mock 1_JF2 GLOB-F2-1*

3_JF5 GLOB-F1-5*

3_Con

Composite

mock 3_JF4 GLOB-F1-4*

3_JF1 GLOB-F1-1*

3_Con

Composite

GLOB-LH

3_Cor

0

0

0

5

5

5

10

10

10

15

15

15

20

20

20

25

25

25

30

30

30

35

35

35

40

40

40

45

45

45

50

50

50

55

55

55

60

60

60

65

65

65

70

70

70

75

75

75

80

80

80

85

85

85

90

90

90

95

95

95

100

100

100

Linkage group 4

4_CC_2484

GU-Embc

4_Con

Composite

GLOB-F2-1*

4_JF2

GLOB-F1-5 (excluded)

GLOB-F1-4 (excluded)

mock

Composite

4_JF1 GLOB-F1-1*

4_Con

Composite

GLOB-LH

4_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

Linkage group 5

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

5_CC_1032

GU-Embf

GLOB-F2-1* 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

Composite

5_J_FAM55_JF2 mock2 5_Con GLOB-F1-5*

Composite

GLOB-F1-4*

5_J_FAM1 5_JF4 mock 5_Con GLOB-F1-1*

5_Con

Composite

GLOB-LH*

5_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150 155

Linkage group 6

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150 155

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150 155

GU-Embc*

Composite

GLOB-F1-5

GLOB-F2-1*

mock

Composite

GLOB-F1-4*

6_J_FAM1

GLOB-F1-1 (excluded)

6_Con

Composite

GLOB-LH*

6_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

Linkage group 7

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

7_CC_1032

GU-Embf

GLOB-F2-1*

GLOB-F1-5* 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130

7_Con

Composite

7_JF2

mock

Composite

GLOB-F1-4*

7_J_FAM1 GLOB-F1-1*

7_Con

Composite

GLOB-LH*

7_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150

Linkage group 8

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150

8_Con

8_CC_2484

GU-Embc*

GLOB-F2-1*

GLOB-F1-5*

8_JF2

Composite

mock

Composite

GLOB-F1-4*

8_J_FAM1

GLOB-F1-1

8_Con

Composite

GLOB-LH*

8_Cor

0

0

0

5

5

5

10

10

10

15

15

15

20

20

20

25

25

25

30

30

30

35

35

35

40

40

40

45

45

45

50

50

50

55

55

55

60

60

60

65

65

65

70

70

70

75

75

75

80

80

80

85

85

85

90

90

90

95

95

95

100

100

100

105

105

105

110

110

110

Linkage group 9

9_CC_1032

GU-Embf*

9_Con

Composite

GLOB-F2-1*

9_JF2

GLOB-F1-5

GLOB-F1-4 (excluded)

mock

Composite

9_JF1 GLOB-F1-1*

9_Con

Composite

GLOB-LH*

9_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

Linkage group 10

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

10_CC_2484

GU-Embc*

10_Con

Composite

mock 10_F2 GLOB-F2-1*

10_JF5 GLOB-F1-5*

GLOB-F1-4 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120

10_Con

Composite

10_JF1 10_JF4 mock GLOB-F1-1 (excluded)

10_Con

Composite

GLOB-LH*

10_Cor

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125

Linkage group 11

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 125

11_CC_2484

GU-Embc*

11_Con

Composite

GLOB-F2-1*

11_JF2 GLOB-F1-5*

GLOB-F1-4

mock

Composite

11_JF1 GLOB-F1-1*

11_Con

Composite

GLOB-LH*

11_Cor