AX: Axillary (High-Order) Branches;

Supplementary Table 1: QTL affecting vegetative branching in the S. bicolor and S. propinquum RILs in three specific environments. QTL names in bold indicate environment-specific QTLs (09, 10 and 11) that elude detection by using the overall BLUP values in Table 4.

Trait / QTL Name / Chr / Position / Lod / Additive / R2 / Start(Mp) / End(Mp)
TL11 / qTL11_1.1 / 1 / 25.0 / 4.1 / -1.73 / 9.2% / 5.4 / 7.4
TL09 / qTL09_1.1 / 1 / 54.8 / 3.2 / -2.42 / 6.3% / 28.2 / 61.6
TL10 / qTL10_1.1 / 1 / 52.8 / 7.6 / -4.76 / 15.9% / 28.2 / 60.8
TL10†a / qTL10_3.1 / 3 / 50.2 / 2.3 / -2.49 / 4.5% / 3.5 / 18.2
TL10 / qTL10_3.2 / 3 / 84.3 / 4.2 / 3.32 / 8.1% / 52.3 / End
TL_09† / qTL09_4.1 / 4 / 36.9 / 2.3 / 1.89 / 4.8% / 5.1 / 10.0
TL09† / qTL09_6.1 / 6 / 46.6 / 2.7 / -1.88 / 4.9% / 60.8 / 62.1
TL09 / qTL09_7.1 / 7 / 18.9 / 4.1 / -2.70 / 9.7% / 0.9 / 8.4
TL10† / qTL10_7.1 / 7 / 24.3 / 2.5 / -2.25 / 4.6% / 0.9 / 37.7
TL09 / qTL09_7.2 / 7 / 30.9 / 5.7 / -2.88 / 10.9% / 8.4 / 57.4
TL09† / qTL09_8.1 / 8 / 51.2 / 2.0 / -1.79 / 3.4% / 4.5 / 51.5
TL09 / qTL09_8.2 / 8 / 57.9 / 3.6 / -2.56 / 8.7% / 49.1 / 51.5
TL11† / qTL11_9.1 / 9 / 31.9 / 2.2 / -1.07 / 4.6% / 31.7 / 54.5
AX11 / qAX11_1.1 / 1 / 39.3 / 15.5 / -46.35 / 35.7% / 28.2 / 57.5
AX10 / qAX10_1.1 / 1 / 67.9 / 2.8 / -9.47 / 8.4% / 64.0 / 70.0
AX09 / qAX09_2.1 / 2 / 58.9 / 4.9 / -7.05 / 16.8% / 60.5 / 63.2
AX10 / qAX10_3.1 / 3 / 51.2 / 6.2 / -12.58 / 15.5% / 6.2 / 7.8
AX09 / qAX09_4.1 / 4 / 56.5 / 3.6 / 4.08 / 7.8% / 51.2 / 58.8
AX09† / qAX09_8.1 / 8 / 0.0 / 2.1 / -6.19 / 4.5% / 0.2 / 3.0
MA09 / qMA09_1.1 / 1 / 39.3 / 6.9 / -4.17 / 34.0% / 28.2 / 57.5
MA10 / qMA10_1.1 / 1 / 39.3 / 9.1 / -7.96 / 39.8% / 28.2 / 57.5
MA11 / qMA11_1.1 / 1 / 38.3 / 5.1 / -7.24 / 22.3% / 28.2 / 57.5
MA10 / qMA10_8.1 / 8 / 0.0 / 3.8 / -1.63 / 10.4% / 0.2 / 3.0
MA11 / qMA11_8.1 / 8 / 4.0 / 4.4 / -1.49 / 12.0% / 0.2 / 3.0
IM11 / qIM11_1.1 / 1 / 39.3 / 15.3 / -36.99 / 36.7% / 28.2 / 57.5
IM10 / qIM10_1.1 / 1 / 67.9 / 3.2 / -9.96 / 9.3% / 61.6 / 70.0
IM11 / qIM11_1.2 / 1 / 70.4 / 2.6 / -6.35 / 6.3% / 64.0 / 70.0
IM09 / qIM09_2.1 / 2 / 58.9 / 5.4 / -6.65 / 17.1% / 59.1 / 63.2
IM10 / qIM10_3.1 / 3 / 50.2 / 4.3 / -10.08 / 9.7% / 6.2 / 7.8
IM09 / qIM09_4.1 / 4 / 52.0 / 3.5 / 4.12 / 9.3% / 12.5 / 58.8
IM10† / qIM10_8.1 / 8 / 0.0 / 2.41 / -6.65 / 5.1% / 0.2 / 3.0
VG10 / qVG10_1.1 / 1 / 40.3 / 7.1 / -8.02 / 27.6% / 28.2 / 57.5
VG11 / qVG11_1.1 / 1 / 40.3 / 9.0 / -4.46 / 31.0% / 28.2 / 57.5
VG09† / qVG09_2.1 / 2 / 56.9 / 2.8 / -2.29 / 6.0% / 59.1 / 63.2
VG11 / qVG11_2.1 / 2 / 50.6 / 3.7 / -1.46 / 6.8% / 4.7 / 63.2
VG10 / qVG10_3.1 / 3 / 50.2 / 3.9 / -2.30 / 9.1% / 6.2 / 7.8
VG09† / qVG09_3.1 / 3 / 79.1 / 2.3 / -1.87 / 6.1% / 51.2 / 55.9
VG11 / qVG11_5.1 / 5 / 50.9 / 4.6 / 1.46 / 8.7% / 4.8 / 54.3
VG09 / qVG09_7.1 / 7 / 35.7 / 3.6 / -2.20 / 8.6% / 37.7 / 57.4
VG09 / qVG09_8.1 / 8 / 68.1 / 2.9 / -1.99 / 6.6% / 49.1 / 51.9
VG10† / qVG10_8.1 / 8 / 46.5 / 2.7 / -2.04 / 7.2% / 4.5 / 5.3
SR10 / qSR10_2.1 / 2 / 53.6 / 5.0 / -0.03 / 14.5% / 4.7 / 63.2
SR09† / qSR09_6.1 / 6 / 42.6 / 2.2 / 0.01 / 4.7% / 57.4 / 61.4
SR09 / qSR09_7.1 / 7 / 27.3 / 8.5 / 0.03 / 20.4% / 0.9 / 37.7
SR11† / qSR11_7.1 / 7 / 14.9 / 2.6 / 0.03 / 8.7% / 0.9 / 8.4
SR11 / qSR11_8.1 / 8 / 7.5 / 3.6 / -0.03 / 9.0% / 0.2 / 3.0
TR09† / qTR09_1.1 / 1 / 11.4 / 2.2 / 0.16 / 5.4% / 1.8 / 5.4
TR10 / qTR10_1.1 / 1 / 12.4 / 2.4 / 0.12 / 5.8% / 1.8 / 5.4
TR09 / qTR09_3.1 / 3 / 50.2 / 3.5 / -0.19 / 7.2% / 6.2 / 18.2
TR10 / qTR10_3.1 / 3 / 51.2 / 7.2 / -0.23 / 19.2% / 6.2 / 7.8
TR11 / qTR11_3.1 / 3 / 50.2 / 4.3 / -0.24 / 9.9% / 6.2 / 7.8
TR09 / qTR09_4.1 / 4 / 52.0 / 4.0 / 0.22 / 12.1% / 12.5 / 58.8
TR11† / qTR11_4.1 / 4 / 56.5 / 2.9 / 0.19 / 6.2% / 51.2 / 58.8
TR09 / qTR09_9.1 / 9 / 32.9 / 4.2 / -0.22 / 9.7% / 31.7 / 54.5
M1_10 / qM1_10_2.1 / 2 / 55.9 / 2.6 / -1.06 / 6.1% / 59.1 / 63.2
M1_10† / qM1_10_6.1 / 6 / 15.7 / 2.1 / -1.09 / 7.8% / 57.4 / 60.8
M1_11 / qM1_11_8.1 / 8 / 54.2 / 2.6 / -0.74 / 6.4% / 4.5 / 51.5
IM2_09† / qIM2_09_2.1 / 2 / 55.9 / 2.6 / -1.91 / 4.9% / 59.1 / 63.2
IM2_10† / qIM2_10_3.1 / 3 / 66.1 / 2.3 / -3.16 / 4.6% / 11.9 / 52.3
IM2_10† / qIM2_10_7.1 / 7 / 41.4 / 3.0 / -3.43 / 6.4% / 37.7 / 58.3

a †: Significant at a LOD score of 2.0

TL: Tillers;

AX: Axillary (high-order) branches;

MA: Mature branches;

IM: Immature branches (with floral induction);

VG: Vegetative branches (without floral induction);

SR: Secondary ratio (potential of forming secondary branches);

TR: Tertiary ratio (potential of forming tertiary branches);

M1: Mature primary branches;

IM2: Immature secondary branches.

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