1.1. Chromosome 1 1.2. Chromosome 2 1.3. Chromosome 3 1.4. Chromosome 4 1.5. Chromosome 5

Supplementary Figure 1: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. The color legend is given under each figure but the trait colors, automatically determined by the software, may change from one figure to the other.

1.1. Chromosome 1

1.2. Chromosome 2

1.3. Chromosome 3

1.4. Chromosome 4

1.5. Chromosome 5

1.6. Chromosome 6

1.7. Chromosome 7

1.8. Chromosome 8

1.9. Chromosome 9

1.10. Chromosome 10

1.11. Chromosome 11

1.12. Chromosome 12

Supplementary Figure 1.1: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 1QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.2: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 2QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.3: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 3QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.4: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 4QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.5: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 5QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.6: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 6QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Chromosome 7

Supplementary Figure 1.7: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 7QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.8: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 8QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.9: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 9QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Chromosome 10

Supplemental Figure 1.10: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 10QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.11: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 11QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)

Supplementary Figure 1.12: Position of the QTLs involved in the study for the 11 traits with more than 20 QTLs each. Distances on the map are in Mb. Chromosome 12QTL are named according to the study in which they were detected followed by their ID number in TropgeneDB and a letter indicating under which conditions they were detected (w = well watered; s = water stress; c = compaction stress)