Figure S1. Rust disease responses of parents of the mapping populations, ICSV745 (a), R890562-1-2 (b), IS8525 (c), R931945-2-2 (d) and S. bicolor subsp. verticilliflorum (e). The number in each figure indicated the predicated mean values of rust infection score. S. bicolor subsp. verticilliflorum could not be grown in the field due to its weedy nature, hence its disease score was not provided.

Two distinct classes of QTL determine rust resistance in sorghum

Additional File 23.50 8.00

7.75 4.00

0.0 0.2 0.4 0.6 0.8 1.0

-0.4

-0.2

0.0

0.2

0.4

0.6

rust loading

En

viro

nm

en

t lo

ad

ing

DalBox.R986087-2-4-1

DalBox.R993396

DalBox.R995248

LivPl1.R986087-2-4-1

LivPl1.R993396

LivPl1.R995248

Sitemale Relationships for 2012 aytfemale rust

Da

lBo

x.R

99

33

96

Da

lBo

x.R

98

60

87

-2-4

-1

Liv

Pl1

.R9

86

08

7-2

-4-1

Da

lBo

x.R

99

52

48

Liv

Pl1

.R9

93

39

6

Liv

Pl1

.R9

95

24

8

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

Cluster Dendrogram

hclust (*, "complete")dist(correls)

He

igh

t

Figure S2. Site relationships in AYT trials across 3 male tester genotypes. Second order factor analytic site by male loadings are represented using A: segment plot of the 2 sets of loadings; B: Dendrogram

A

B

Figure S3. Localisation of QTL for rust resistance, day to flower (DTF) and height (HGT) identified in the S2 population. Length of each chromosome (in cM) is indicated by the left-most ruler. QTL are represented by bars (1-LOD interval) and extended lines (2-LOD interval), and colour-coded per trait as indicated. QTL names and significance levels are detailed where * indicates suggestive QTL (LOD≥2); ** indicates significant QTL (LOD≥3); *** indicates highly significant QTL (LOD≥5). Graphs to the right of each LG represent the LOD value, colour-coded per trait as previously.

QR

ustR_S

2_2.1*

0 1 2

SBI-02

QD

TF

_S2_3.1*

QH

GT

_S2_3.1*

QD

TF

_S2_3.2*

0 1 2 3

SBI-03

QD

TF

_S2_4.1*

0 1 2

SBI-04

QR

ustR_S

2_5.1***

QD

TF

_S2_5.1*

0 1 2 3 4 5

SBI-05Q

RustR

_S2_6.1*

QH

GT

_S2_6.1*

0 1 2 3

SBI-06-I

0102030405060708090100110120130140150160170180190200210220230240

QH

GT

_S2_7.1*

0.0

0.5

1.0

1.5

2.0

SBI-07

QR

ustR_S

2_8.1*

0 1 2 3

QR

ustR_S

2_8.2***

0 1 2 3 4 5 6

SBI-08

QH

GT

_S2_9.1**

0 2 4 6

SBI-09

QD

TF

_S2_10.1*

0.0

0.5

1.0

1.5

2.0

SBI-10

rust_LOD

DTF_LOD

HGT_LOD

0102030405060708090100110120130140150160170180190200210220230240

0.0

0.5

1.0

1.5

2.0

SBI-07

0 1 2 3

0 1 2 3 4 5 6

SBI-08

0 2 4 6

SBI-09

0.0

0.5

1.0

1.5

2.0

SBI-10

rust_LOD

DTF_LOD

HGT_LOD

0102030405060708090100110120130140150160170180190200210220230240

QD

TF

_S

4_1

.1*

QH

GT

_S

4_1

.1*

QR

ustR

_S

4_1

.1*

QR

ustR

_S

4_1

.2***

0

2

4

6

SBI-01

QR

ustR

_S

4_2

.1*

QR

ustR

_S

4_2

.2*

QD

TF

_S

4_2

.1*

0.0

0.5

1.0

1.5

2.0

SBI-02

QR

ustR

_S

4_3

.1**

QD

TF

_S

4_3

.1*

0

1

2

3

4

SBI-03

QR

ustR

_S

4_4

.1**

QR

ustR

_S

4_4

.2*

QH

GT

_S

4_4

.1*

0

1

2

3

4

SBI-04

QH

GT

_S

4_5

.1*

0

1

2

3

SBI-05

0

10

20

30

40

50

60

70

80

90

100

110

120

130

140

150

160

170

180

190

200

210

220

230

QD

TF

_S

4_6

.1***

QH

GT

_S

4_6

.1***

0

2

4

6

8

SBI-06

QH

GT

_S

4_7

.1***

0

2

4

6

SBI-07

QR

ustR

_S

4_9

.1*

QH

GT

_S

4_9

.1***

0

2

4

6

8

SBI-09

QD

TF

_S

4_1

0.1***

QR

ustR

_S

4_1

0.1

**

0

1

2

3

4

5

6

SBI-10

rust_LOD

DTF_LOD

HGT_LOD

0

10

20

30

40

50

60

70

80

90

100

110

120

130

140

150

160

170

180

190

200

210

220

230

0

2

4

6

8

SBI-06

0

2

4

6

SBI-07

0

2

4

6

8

SBI-09

0

1

2

3

4

5

6

SBI-10

rust_LOD

DTF_LOD

HGT_LOD

0

10

20

30

40

50

60

70

80

90

100

110

120

130

140

150

160

170

180

190

200

210

220

230

Figure S4. Localisation of QTL for rust resistance, day to flower (DTF) and height (HGT) identified in the S4 population. Length of each chromosome (in cM) is indicated by the left-most ruler. QTL are represented by bars (1-LOD interval) and extended lines (2-LOD interval), and colour-coded per trait as indicated. QTL names and significance levels are detailed where * indicates suggestive QTL (LOD≥2); ** indicates significant QTL (LOD≥3.4); *** indicates highly significant QTL (LOD≥5). Graphs to the right of each LG represent the LOD value, colour-coded per trait as previously.

QD

TF

_S7_1.1

QD

TF

_S7_1.2

SBI-01

QD

TF

_S7_2.1

SBI-02

QD

TF

_S7_3.1

QD

TF

_S7_3.2

QH

GT

_S7_3.1

SBI-03

QH

GT

_S7_4.1

QR

ustR_S

7_4.1

SBI-04

QR

ustR_S

7_5.1

SBI-05

QD

TF

_S7_6.1

QH

GT

_S7_6.1

QD

TF

_S7_6.2

QH

GT

_S7_6.2

SBI-06

QD

TF

_S7_7.1

SBI-07Q

DT

F_S

7_8.1Q

RustR

_S7_8.1

QD

TF

_S7_8.2

QD

TF

_S7_8.4

QD

TF

_S7_8.3

SBI-08

QD

TF

_S7_9.1

QD

TF

_S7_9.2

QH

GT

_S7_9.1

SBI-09

QD

TF

_S7_10.1

QD

TF

_S7_10.2

QD

TF

_S7_10.3

QD

TF

_S7_10.4

QH

GT

_S7_10.1

QR

ustR_S

7_10.1

SBI-10

0

10

20

30

40

50

60

70

80

90

100

110

120

130

140

150

160

170

180

190

200

210

220

Figure S5. Localisation of QTL for rust resistance, day to flower (DTF) and height (HGT) identified in the S7 population. Length of each chromosome (in cM) is indicated by the left-most ruler. QTL are represented by bars and colour-coded per trait as indicated. A minimum CI of 3cM has been used for visualisation purposes.

Figure S6. QTL for days to flower (DTF) from the current study projected onto the sorghum consensus map and comparison with DTF QTL identified in previous studies.

The length of each chromosome (in cM) is indicated by the left-most ruler. QTL colour-coded as follows: red/unfilled: S2 ; black/solid: S4; red/solid: S7; green brown/solid: AYT; black/unfilled: Brown et al. 2006; black/hashed: Chantereau et al. 2001; red/hashed: Alam 2013; dark green/unfilled: Crasta et al. 1999; dark green/hashed: Felderhoff et al. 2012; dark green/hashed: Feltus et al. 2006; dark blue/unfilled: Hart et al. 2001; dark blue/hashed: Kim 2003; dark blue/solid: Kebede et al. 2001; pink/unfilled: Lin et al. 1995; pink/hashed: Parh 2005; pink/solid: Upadhyaya et al. 2013; green/unfilled: Zou et al. 2012; green/hashed: Ritter et al. 2008; green/solid: Mace, Hunt & Jordan 2013; brown/unfilled: Srinivas et al. 2009; brown/hashed: Takai et al. 2012; brown/solid: Upadhyaya et al 2012; blue/hashed: Shiringani et al. 2010; blue/hashed: Mannai et al. 2011. Additionally, the map locations of the 4 targeted major effect genes of maturity and stem height are included in italics; the degree of confidence of the location is indicated by the suffix; *** equates to greater than a 10

cM location range (Mace and Jordan 2010).

Ma3***

QD

TF

_NA

M_1_10

QD

TF

_S7_1.1

QD

TF

L14_1Q

DT

FL17_1

QD

TF

L1_1Q

DT

FL4_1

QD

TF

L6_1Q

DT

F_S

7_1.2

QD

TF

_S4_1.1

QD

TF

_NA

M_1_112

QF

l_HR

S09_S

2_1_1

QD

TF

L10_1Q

DT

FL11_1

QD

TF

L18_1

QP

PS

1_1Q

DT

FL16_1

QD

TF

_NA

M_1_182

QP

PS

2_1Q

DT

FL15_1

QD

TF

_AY

T_1.1

QD

TF

L2_1Q

DT

FL7_1

QD

TF

L13_1Q

DT

FL8_1

QD

TF

_NA

M_1_53

QD

TF

L12_1

QD

TF

_NA

M_1_66

QD

TF

L9_1

QD

TF

L5_1

QD

TF

L3_1

SBI-01

Ma5***

QD

TF

_NA

M_2_23

QD

TF

L4_2Q

DV

S1_2

QD

TF

_S7_2.1

QD

VS

2_2

QD

TF

_NA

M_2_123

QD

VS

3_2

QD

TF

_AY

T_2.1

QD

TF

_AY

T_2.2

QD

TF

L8_2Q

DT

FL9_2

QD

TF

L7_2

QF

l_HR

S09_S

2_2_1Q

DT

F_N

AM

_2_147

QD

TF

L2_2Q

DT

FL10_2

QD

TF

L3_2Q

DT

F_S

4_2.1

QD

TF

L5_2

QD

TF

L6_2

QD

TF

L11_2

SBI-02

QD

TF

_NA

M_3_21

QD

TF

L4_3

QD

TF

_NA

M_3_34

QD

TF

_NA

M_3_133

QD

TF

_NA

M_3_47

QD

TF

_S2_3.2

QD

TF

L1_3Q

DT

F_N

AM

_3_57Q

DT

F_S

4_3.1

QD

TF

L2_3Q

DT

F_N

AM

_3_68Q

DT

F_S

7_3.2

QD

TF

_S2_3.1

QD

TF

L3_3Q

DT

FL5_3

QD

TF

_S7_3.1

QD

TF

L6_3Q

DT

F_A

YT

_3.1

SBI-03

QD

TF

L6_4Q

DT

FL9_4

QD

TF

L5_4

QD

TF

L7_4Q

DT

F_N

AM

_4_87

QD

TF

L8_4Q

DT

F_N

AM

_4_98

QD

TF

_NA

M_4_15

QD

TF

L2_4Q

DT

FL4_4

QD

TF

_NA

M_4_43

QD

TF

_AY

T_4.1

QD

TF

_NA

M_4_58

QD

TF

_NA

M_4_74

QD

TF

_S2_4.1

QD

TF

L3_4

QD

TF

L1_4

SBI-04

0

20

40

60

80

100

120

140

160

180

200

220

QF

l_HR

S10_S

2_5_1

QF

l_HR

S09_S

2_5_1

QD

TF

_NA

M_5_10

QD

TF

_NA

M_5_67

QD

TF

_NA

M_5_27

QD

TF

L2_5

QD

TF

_NA

M_5_4

QD

TF

L1_5

QD

TF

_S2_5.1

SBI-05

Ma1***

QF

l_HR

S10_S

4_6_1Q

DT

FL8_6

QD

TF

_S7_6.2

QD

TF

_NA

M_6_10

QD

TF

L5_6Q

DT

FL14_6

QD

TF

L11_6Q

DT

FL10_6

QD

TF

L7_6

QF

l_HR

S10_S

4_6_2Q

DT

FL6_6

QD

TF

L4_6

QD

TF

L9_6

QD

TF

L3_6

QD

TF

L1_6

QF

l_HR

S09_S

4_6_1

QF

l_HR

S09_S

4_6_2

QF

l_HR

S09_S

4_6_3

QD

TF

_NA

M_6_23

QD

TF

_NA

M_6_83

QD

TF

_NA

M_6_32

QD

TF

_NA

M_6_43

QD

TF

_S4_6.1

QD

TF

L12_6Q

DT

FL16_6

QD

TF

_S7_6.1

QD

TF

L15_6Q

DT

FL13_6

QD

TF

L2_6

QD

TF

L8_6

QD

TF

L9_6

SBI-06

QD

TF

_NA

M_7_5

QD

TF

_NA

M_7_73

QF

l_HR

S09_S

5_7_1

QD

TF

_NA

M_7_59

QD

TF

_S7_7.1

QD

TF

L3_7

QD

TF

L1_7

QD

TF

L2_7

QD

TF

L4_7

SBI-07

QD

TF

_NA

M_8_30

QD

TF

_NA

M_8_115

QD

TF

_S7_8.1

QD

TF

_NA

M_8_66

QD

TF

_S7_8.3

QD

TF

L5_8

QD

TF

_S7_8.2

QD

TF

_S7_8.4

QD

TF

_AY

T_8.1

QD

TF

L4_8

QF

l_HR

S10_S

5_8_1

QD

TF

L3_8

QD

TF

L1_8

QD

TF

L2_8

SBI-08

0

20

40

60

80

100

120

140

160

180

200

220

QD

TF

L2_9Q

DT

FL4_9

QD

TF

L1_9Q

DT

F_S

7_9.2Q

DT

FL6_9

QD

TF

_NA

M_9_25

QD

TF

L7_9

QD

TF

_S7_9.1

QD

TF

_NA

M_9_75

QD

TF

_AY

T_9.1

QD

TF

L8_9

QD

TF

_AY

T_9.2

QD

TF

L5_9

QD

TF

_AY

T_9.3

QD

TF

_NA

M_9_136

SBI-09

Ma4***

QD

VS

1_10Q

DT

FL5_10

QD

VS

2_10Q

DT

FL6_10

QP

PS

1_10Q

DT

F_S

7_10.4

QP

PS

2_10Q

DT

FL11_10

QP

PS

3_10

QD

TF

_AY

T_10.1

QD

TF

L3_10

QD

TF

L7_10

QF

l_HR

S10_S

5_10_1

QF

l_DB

10_S5_10_1

QF

l_HR

S10_S

5_10_2

QF

l_HR

S09_S

5_10_1

QF

l_HR

S09_S

4_10_1

QF

l_HR

S09_S

5_10_2

QD

TF

_NA

M_10_44

QD

TF

_NA

M_10_61

QD

TF

L1_10

QD

TF

L4_10

QD

TF

L2_10

QD

TF

_S2_10.1

QD

TF

_S4_10.1

QD

TF

_S7_10.1

QD

TF

_S7_10.2

QD

TF

_S7_10.3

QD

TF

L9_10

QD

TF

L8_10

QD

TF

L10_10

SBI-10

0

20

40

60

80

100

120

140

160

180

200

220

Figure S7. QTL for height (HGT) from the current study projected onto the sorghum consensus map and comparison with HGT QTL identified in previous studies.

The left-most rule indicates the length of each chromosome in cM. QTL colour-coded as follows: red/unfilled: S2 ; black/solid: S4; red/solid: S7; green brown/solid: AYT; black/unfilled: Brown et al. 2006; black/hashed: Murray et al. 2008a; red/hashed: Alam 2013; dark green/unfilled: Pereira et al. 1995; dark green/hashed: Felderhoff et al. 2012; dark green/solid: Feltus et al. 2006; dark blue/unfilled: Hart et al. 2001; dark blue/hashed: Pereira and Lee 1995; dark blue/solid: Kebede et al. 2001; pink/unfilled: Lin et al. 1995; pink/hashed: Parh 2005; pink/solid: Upadhyaya et al 2013; green/unfilled: Zou et al. 2012; green/hashed: Ritter et al. 2008; green/solid: Klein et al. 2001; brown/unfilled: Srinivas et al. 2009; brown/hashed: Takai et al. 2012; brown/solid: Upadhyaya et al 2012; blue/unfilled: Brown et al. 2008; blue/hashed: Shiringani et al. 2010; blue/solid: Rami et al. 1998; green brown/unfilled: Guan et al. 2011.Additionally, the map locations of the 3 targeted major effect genes of maturity and stem height are included in italics; the degree of confidence of the location is indicated by the suffix; no asterisk equates to a precise location and * equates to less than a 5 cM location range. (Mace and Jordan 2010).

QP

AN

LG1_8

QH

GT

1_8

SBI-08

Dw1*

QH

GT

1_9Q

PF

gLfHG

T1_9

QP

AN

LG1_9

QH

GT

6_9

QC

L1_9Q

HG

T2_9

QH

GT

7_9

QH

GT

_AY

T_9.1

QH

GT

8_9

QH

GT

9_9

QH

GT

10_9

QH

GT

11_9

QH

GT

12_9

QH

GT

13_9

QH

GT

14_9

QH

GT

U1_9

QC

L2_9

QH

GT

5_9

QC

L3_9

QH

GT

_HR

S09_S

2_9_1

QH

GT

_HR

S10_S

2_9_1

QH

GT

4_9

QH

GT

_S2_9.1

QH

GT

_S4_9.1

QH

GT

_S7_9.1

QH

GT

3_9

QC

L4_9

QC

L5_9

QC

L6_9

QH

GT

15_9

SBI-09

QH

GT

U1_10

QC

L1_10

QC

L2_10

QH

GT

_HR

S09_S

5_10_1

QH

GT

_HR

S10_S

5_10_1

QH

GT

_HR

S10_S

5_10_2

QP

ED

LG1_10

QH

GT

1_10

QP

AN

LG1_10

QP

AN

LG2_10

QH

GT

_S7_10.1

QH

GT

2_10

QH

GT

3_10Q

HG

T4_10

SBI-10

0

20

40

60

80

100

120

140

160

180

200

220

dw2*

QC

L4_6Q

HG

T1_6

QH

GT

3_6Q

HG

T7_6

QC

W1_6

QH

GT

10_6Q

HG

T4_6

QP

AN

LG6_6

QH

GT

11_6Q

HG

T5_6

QC

L1_6Q

PA

NLG

5_6

QH

GT

U1_6

QP

AN

LG4_6

QH

GT

6_6

QC

L3_6Q

HG

T_S

7_6.2Q

HG

T9_6

QC

L2_6Q

HG

T_S

7_6.1Q

HG

T8_6

QH

GT

_HR

S09_S

4_6_1Q

HG

T14_6

QP

AN

LG2_6

QH

GT

2_6

QH

GT

_S2_6.1

QP

AN

LG3_6

QP

AN

LG7_6

QH

GT

_S4_6.1

QP

AN

LG1_6

QP

AN

LG8_6

QC

L5_6

QC

W2_6

QC

W3_6

QH

GT

13_6

QH

GT

12_6

QH

GT

12_6

SBI-06

dw3

QH

GT

_HR

S10_S

4_7_1Q

FgLfH

GT

1_7Q

CL4_7

QH

GT

_S2_7.1

QH

GT

9_7

QH

GT

1_7Q

CL2_7

QH

GT

13_7

QP

AN

LG1_7

QC

L3_7

QC

L6_7 QP

AN

LG4_7

QP

ED

LG1_7

QC

L1_7Q

HG

T12_7

QH

GT

14_7

QH

GT

_HR

S10_S

4_7_2

QH

GT

7_7

QH

GT

5_7Q

FgLfH

GT

2_7

QH

GT

3_7Q

HG

T10_7

QH

GT

4_7 QP

AN

LG3_7

QH

GT

_S4_7.1

QH

GT

2_7Q

HG

T16_7

QH

GT

6_7

QH

GT

8_7

QP

AN

LG2_7

QC

L5_7

QH

GT

15_7

QC

L7_7

QP

AN

LG5_7

QP

AN

LG6_7

QP

AN

LG7_7

QH

GT

U1_7

SBI-07

0

20

40

60

80

100

120

140

160

180

200

220

QH

GT

1_1Q

HG

T7_1

QC

L3_1Q

CL4_1

QC

L1_1Q

PE

DLG

2_1Q

HG

T5_1

QP

ED

LG1_1

QC

L2_1Q

FgLfH

GT

1_1

QK

FL1_1

QP

AN

LG1_1

QP

AN

LG3_1

QH

GT

8_1Q

HG

T2_1

QH

GT

4_1Q

HG

T6_1

QP

AN

LG4_1

QH

GT

3_1Q

PE

DLG

3_1

QP

AN

LG2_1

QC

W1_1

QH

GT

_S4_1.1

QC

W3_1

QC

W2_1

QP

AN

LG5_1

QP

AN

LG6_1

QP

AN

LG7_1

SBI-01

QP

AN

LG1_2

QH

GT

2_2

QP

AN

LG2_2

QP

AN

LG4_2

QH

GT

1_2

QP

AN

LG3_2

SBI-02

QH

GT

1_3Q

HG

T2_3

QC

L3_3

QC

L1_3Q

HG

T3_3

QH

GT

_HR

S09_S

2_3_1

QC

L2_3Q

HG

T_H

RS

10_S2_3_1

QH

GT

4_3Q

PA

NLG

2_3

QP

ED

LG1_3

QP

AN

LG1_3

QH

GT

_S2_3.1

QH

GT

_S7_3.1

SBI-03

QH

GT

4_4

QH

GT

5_4

QH

GT

_HR

S09_S

5_4_1Q

HG

T1_4

QH

GT

3_4

QH

GT

_HR

S10_S

5_4_1Q

HG

T2_4

QP

ED

LG1_4

QH

GT

_HR

S09_S

2_4_1

QH

GT

_HR

S09_S

4_4_1

QH

GT

_HR

S10_S

4_4_1

QH

GT

_S4_4.1

QH

GT

_S7_4.1

SBI-04

QH

GT

_HR

S09_S

4_5_1

QH

GT

_HR

S09_S

4_5_2

QH

GT

_S4_5.1

QH

GT

1_5

SBI-05

0

20

40

60

80

100

120

140

160

180

200

220

Zm

_L

ub

b_

5.0

1Z

m_

Lu

bb

_1

.08

-10

Zm

_L

ub

b_

1.0

5-0

6Z

m_

Lu

bb

_1

.03

Zm

_K

ern

s_9

.07

Zm

_K

ern

s_1

.08

Zm

_K

ern

s_1

.02

Zm

_B

row

n_

5.0

2Z

m_

Bro

wn

_1

.03

SBI-01

Zm

_L

ub

b_

7.0

1-0

2Z

m_

Ke

rns_

7.0

2Z

m_

Lu

bb

_7

.04

Zm

_K

ern

s_7

.04

SBI-02

Zm

_B

row

n_

3.0

4Z

m_

Ke

rns_

3.0

5

Zm

_L

ub

b_

3.0

4Z

m_

Bro

wn

_3

.06

rp3

Zm

_K

ern

s_8

.01

Zm

_B

row

n_

18

.06

Zm

_B

row

n_

8.0

1

Zm

_K

ern

s_8

.05

SBI-03

Zm

_L

ub

b_

5.0

4-0

5Z

m_

Ke

rns_

5.0

5Z

m_

Bro

wn

_4

.05

SBI-04

rp5

Zm

_K

ern

s_4

.10

rp4

rp1

Zm

_L

ub

b_

4.0

3-0

4

Zm

_B

row

n_

4.0

3

Zm

_L

ub

b_

4.0

8

SBI-05

Zm

_B

row

n_

2.1

0Z

m_

Bro

wn

_2

.05

Zm

_B

row

n_

2.0

4

Zm

_L

ub

b_

2.0

9Z

m_

Lu

bb

_2

.05

-06

Zm

_L

ub

b_

2.0

8

SBI-06

Zm

_L

ub

b_

6.0

4Z

m_

Lu

bb

_4

.08

Zm

_L

ub

b_

6.0

7

rp8

SBI-07

rp5

Zm

_L

ub

b_

10

.05

-06

rp1

Zm

_L

ub

b_

3.0

7

SBI-08Z

m_

Lu

bb

_6

.07

Zm

_L

ub

b_

8.0

2-0

5

rp8

Zm

_K

ern

s_6

.06

SBI-09

Zm

_L

ub

b_

9.0

6-0

7

Zm

_K

ern

s_9

.04

SBI-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

125

130

135

140

145

150

155

160

165

170

175

180

185

190

195

200

205

210

215

220

Figure S8. Maize rust resistance QTL projected on to the sorghum genetic linkage consensus map, in comparison to sorghum rust resistance QTL.The location and density of the rust resistance QTL from sorghum are indicated by the heat maps (number of QTL/1cM). The maize rust resistance QTL are indicated as bars to the right of each chromosome (based on the projection of the mid-point of the QTL, with 4cM CI for visualisation purposes) and colour-coded as follows; black: Wisser et al 2008; red: Brown et al 2001; dark green: Kerns et al 1999; dark blue: Lubberstedt et al 1998.

G104 G105G106G36G35

G34

G103G102G33G101

G1G2G3G4G5G6G9G7G79G8G10G11G12G13G14G18G17G16G15G80G81G19G82 G84

Zm

_Brow

n_3.04

Zm

_Lubb_3.04

Zm

_Kerns_3.1

Zm-chr3

G1

G2

G3

G4

G5

G6

G37

G7

G79

G8G38G39G40

G9

G10G11G12G13

G14

G41G15G16

G17G18

G42

G43

G80

G81

G44

G45

G46

G19

G82G83

G84

G20G21G47G48G49G50G85

G86

G87

G51G52

G88

G89G22

G23

G24

G53

G54G55

Rp1-D

G25

G56G90G26G27G28

G57G91G29G58

G59G30G92

G93G60

G61

G94G95

G96

G31G97G62

G63G64G65G98

G99

G32G100G66G67

G68

G69

G70G71

G72

G73

G74

G75

G101G33G76

G102G103

G77G34

G78

G35

G36

G104G105

G106

QR

ustR_A

YT

_8.1

QR

ustR_S

2_8.1

QR

US

TR

1_8

SBI-08

G37

G79G38 G39G40

G41

G42

G43

G80G81G44G45

G46

G83

G82 G84

G47

G48G49G50G85 G86G87

G51G52

G88

G89

G53 G54G55

Rp1-D

G56G90

G57G91G58

G92 G93G92 G93

G59

G61G60

G94 G95G94 G95G96

G97G62

G63

G64

G98G65

G99

G100G66G67

G68 G69

G100G70

G71

G72

G73

G74

G75G101G76

G102

G103

G78

G77

G104 G105G106

rp1

rp5

Zm-chr10

Zm chr 3 SBI-08 Zm chr 10

Figure S9. Syntenic regions around major rust resistance gene Rp1-D between maize and sorghum. Rp1-D gene indicated as red horizontal line. Homologous genes are detailed. Rust QTL are detailed to the right of each chromosome and colour coded as follows: Sorghum QTL: green: AYT, dark blue: S2, red: Tao et al 1998; Maize QTL: pink: Brown et al 2001, bright green: Lubberstedt et al 1998; brown: Kerns et al 1999; bright blue: Wisser et al 2008.

191Mb-229Mb 0Mb-5Mb 0.6Mb-9Mb

Rp1-D

Zm chr 5 SBI-01 Zm chr 117Mb-32Mb 13Mb-24Mb 221Mb-256Mb

G13

G247G8 G9G246G245G5

G1

G248G407

G408 G409G249

G250G29

G30

G251

G354G34 G35

G252G253

G255G256

G43G257

G54G258

G381 G387 G388

G259G260

G261G381 G382 G383 G384 G385

G266G267

G74G268

G270G79

G77

G356 G357G355 G356 G357

G75

G271

G87

G88

G358 G359 G360 G361G358

G94 G102 G103 G104

G105G106

G273

G120

G121

G276G125

G277 G278

G279

G280

Zm

_Lubb_5.01

Zm chr5

G1G2G243

G5

G6G8G9G10G247G11G12G13G14G19G20G21G22G248G407G408G409G410G411G415G416G417G418G419G420G249G23G24G25G421G422G27G28G29G30G251G31G32G33G35G36G252G37G253G38G39G254G255G256GG42G43G44G45G46G47G257G51G52G53G54G381G258G55G259G260G56G57G58G59G261G60G382G383G384G385G386G387G388G64G65G66G67G262G263G68G264G265G72G266G267G73G74G268G75G76G355G356G357G269G82G83G84G85G86G271G87G88G389G390G391G392G89G90G93G94G95G96G97

G98G99G100G272G101G102G103G104G105G106G107

G108

G109

Lr34

G111G112G113G114G273G115G116G117G118G119G274

G124G276G125G277G278G279G280G126G127G128G281G129G130G282G134G284G135G136G137G285G286G138G139G140G141G146G147G148G149G150G151G152G287G288G153

G154G289G155G290G156

G298G157G299G158G300G159G301G160G161G302G162G163G164G303G362

G309G310G311G167G363G364G365G366G367G368G312G369

G168

G313G314G315G169G316G170

G371G173G174G175G319G320G321

G176G323G177G178G179G324G180

G184G327G185

G372G186G328G329G330

G187G188

G189

G190

G191

G331G195G196G197G332G333G334

G335

G198

G199

G200

G204G205G337G338G339

G374G375G376G206G207

G208G340

G379G380G214G215G216G217G218G219G220G342G221G222G393G394G395

G223

G229G230G231G344G232G345G346G396G397G398G399G400

G401

G234

G235G236G348G237G238

G239G349G350

G240G351

G241G352G353G242

QR

ustR_A

YT

_1.3Q

RustR

_S4_1.1

SBI-01

G107

G280

G158G300G159G160G302G162G163G362

G168G316G170

G179G324

G372 G373G328

G332G198G199G336G201G202G203G205

G225G226G227G343G228G230G231G344G232G406G348G237G349 G350G351G241G352G353G242

G101

G73G267G266G72G265G264G71G70G69G68G263G262G67G62G388G65G64G258G48 G53

G2G3G6G7G245G246G10G247G11G19G20G21 G22G407G407G409 G410G251G31G32G37G253G38G39G254G254G255G256

Zm

_Kerns_1.1

Zm

_Lubb_1.05-06

Zm

_Kerns_1.2

Zm chr1

Figure S10. Syntenic regions around the rust resistance gene Lr34 between maize and sorghum. Lr34 gene indicated as red horizontal line. Homologous genes are detailed. Rust QTL are detailed to the right of each chromosome and colour coded as follows: Sorghum QTL: green: AYT, red: S4; Maize QTL: pink: Brown et al 2001, brown: Lubberstedt et al 1998; bright blue: Kerns et al 1999

Lr34

Q3E

Figure S11. Sequence alignment of Lr34 (Sb01g016775), underlying a QTL for rust resistance in the S4 and AYT populations, for the parental genotypes: R931945-2-2 and IS8525 (S4), with missense mutation highlighted.

Figure S12. Linkage Disequilibrium (LD) decay comparisons between the S7 and AYT populations. LD decay plots for the S7 population are detailed in the left-hand column; LD decays plots for the AYT population are detailed in the right-hand column. The red curve corresponds to the 95th percentile of r2 estimates between markers.

Genetic distance (cM) Genetic distance (cM)

SBI-01 SBI-01

SBI-02 SBI-02

SBI-03 SBI-03

SBI-05 SBI-05

SBI-04 SBI-04

Figure S12. Linkage Disequilibrium (LD) decay comparisons between the S7 and AYT populations. LD decay plots for the S7 population are detailed in the left-hand column; LD decays plots for the AYT population are detailed in the right-hand column. The red curve corresponds to the 95th percentile of r2 estimates between markers.

Genetic distance (cM) Genetic distance (cM)

SBI-06 SBI-06

SBI-07 SBI-07

SBI-08 SBI-08

SBI-10 SBI-10

SBI-09 SBI-09