1. Title: Genetic analysis of Soil-borne cereal mosaic virus response in durum wheat: Evidence for the role of the major QTL QSbm.ubo-2BS and of minor QTLs. Journal: Molecular Breeding Author’s names: Marco Maccaferri 1, Rossella Francia 1, Claudio Ratti 1, Concepcion Rubies-Autonell 1, Chiara Colalongo 1, Gianluca Ferrazzano 2, Roberto Tuberosa 1, Maria Corinna Sanguineti 1 Affiliations and addresses: 1 Department of Agroenvironmental Science and Technology, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy 2 Società Produttori Sementi Bologna S.p.A., Divisione Ricerca, Via Macero 1, 40050 Argelato (BO), Italy corresponding author: marco.maccaferri@unibo.itmarco.maccaferri@unibo.it Phone:+39 051 2096645 Fax:+39 051 2096241

2. Supplementary material Figure 1. Frequency distributions of the phenotypic traits recorded for the Simeto × Levante (SxL) recombinant inbred line population (180 F 6:7 RILs) in two field trials carried out in Cadriano (44°35’N 11°27’E), Northern Italy (Po valley), under high SBCMV-disease pressure during two seasons (2008 and 2009). The following SBCMV-response traits were measured at the plant growth stages showing the maximum disease symptom intensity, i.e. from mid-end of tillering (Z25 in the Zadoks scale, Zadoks et al., 1974) to first (Z31) and second (Z32) node appearance stages (corresponding to a period from the end of February to April): symptom severity (SS), visually scored following a 0-4 scale at three and five scoring/sampling dates in 2008 and 2009, respectively; leaf virus concentration (ELISA), determined using DAS-ELISA (reported as absorbance units at 405 nm) on samples collected at two scoring/sampling dates in both 2008 and 2009. Frequency distributions were obtained using the mean values across scoring/sampling dates of each year for SS, ELISA values, leaf greenness (SPAD) and Normalized Difference Vegetation Index (NDVI). Grain yield (GY) was also considered. Mean values for the RILs (S×L), Simeto (S), Levante (L) and for the highly susceptible check cv. Grazia (G) are indicated with arrows and reported together with the corresponding standard deviation in parenthesis.

3. Symptom severity (SS), score unit: scale 0-4 RIL number SxL RIL SS-2008 0 1 2 34 5 10 15 20 25 Virus concentration (ELISA values), A 405 nm 21 0.51.50 10 20 30 SxL RIL ELISA-2008 G (3.42 ± 0.29) L (0.13 ± 0.10) S (2.78 ± 0.17) G (1.41 ± 0.16) L (0.02 ± 0.01) S (1.78 ± 0.12)

4. Leaf greenness (SPAD), SPAD units 45 405035 10 20 30 40 50 64 352 7 8 9 10 20 30 0.50 0.450.550.40 10 20 30 40 50 Spectral reflectance (NDVI), NDVI units 0.600.650.70 SxL RIL SPAD-2008SxL RIL SR-2008 SxL RIL GY-2008 Grain yield (GY), t ha -1 G (43.0 ± 2.58) L (52.2 ± 0.10) S (43.7 ± 1.62) G (0.58 ± 0.07) L (0.61 ± 0.10) S (0.54 ± 0.06) S (5.41 ± 0.18) L (7.74 ± 0.11) G (2.17 ± 0.50) 55

5. RIL number SxL RIL SS-2009 0 1 2 34 5 10 15 20 25 21 0.51.50 10 20 30 SxL RIL ELISA-2009 G (3.81 ± 0.25) L (0.65 ± 0.35) S (2.88 ± 0.17) G (1.62 ± 0.08) L (0.17 ± 0.06) S (1.50 ± 0.15) Symptom severity (SS), score unit: scale 0-4 Virus concentration (ELISA values), A 405 nm

6. Leaf greenness (SPAD), SPAD units 35 304025 10 20 30 40 50 64 352 7 8 9 10 20 30 0.35 0.300.40 10 20 30 Spectral reflectance (NDVI), NDVI units 0.45 0.500.55 SxL RIL SPAD-2009SxL RIL NDVI-2009 SxL RIL GY-2009 Grain yield (GY), t ha -1 45 50 0.60 G (30.2 ± 2.60) L (43.4 ± 2.00) S (32.6 ± 2.21) G (0.38 ± 0.06) L (0.59 ± 0.04) S (0.47 ± 0.03) G (3.67 ± 0.33) L (7.40 ± 1.46) S (5.00 ± 0.75)

7. Supplementary material Figure 2. Location of the QTLs controlling the SBCMV response in the Simeto × Levante recombinant inbred line (RIL) population, as evaluated in two field trials carried out in 2008 and in 2009. The location of the chromosome regions that were found significant on the basis of the composite interval mapping (CIM) is reported on the right side of the chromosome bars for each trait and for each scoring/sampling date. QTLs for the following traits are reported: visually estimated symptom severity (SS), virus concentration in the leaves (ELISA) and grain yield (GY). QTLs for GY were reported only when their positions overlapped with those of QTLs for direct SBCMV-response traits. The QTLs are indicated with acronyms including the trait acronym and the scoring/sampling date (indicated with a progressive number from 1 to 5, see materials and methods section for the corresponding dates). QTLs are indicated with vertical lines spanning the significance intervals (LOD = 2) and with triangles pointing to the QTL peak position. At each QTL region, the parent contributing the favorable allele has been reported within curly brackets (S = Simeto or L = Levante).

8. SS-1-08 SS-2-08 SS-3-08 SS-2-09 SS-1-09 SS-3-09 SS-4-09 SS-5-09 ELISA-4-09 ELISA-2-09 GY-09 L Chr. 2A

9. SS-1-08 SS-2-08 SS-3-08 SS-2-09 SS-1-09 ELISA-3-08 ELISA-2-08 GY-08 SS-3-09 SS-4-09SS-5-09 ELISA-2-09ELISA-4-09 GY-09 L Chr. 2B

10. SS-1-08 SS-2-08 SS-3-08 SS-2-09 GY-08 SS-3-09 ELISA-4-09 SS-1-09 SS-4-09 SS-5-09 ELISA-2-09 S Chr. 3A

11. SS-2-08 ELISA-4-08 GY-08ELISA-4-09 GY-08 SS-1-09 L L Chr. 4B Chr. 5A

12. SS-3-09 SS-4-09 SS-3-08 GY-08 L S Chr. 6B Chr. 7A

13. ELISA-2-08 GY-08 L Chr. 7B