Molecular Breeding
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.
Marco Maccaferri1, Rossella Francia1, Claudio Ratti1, Concepcion Rubies-Autonell1, Chiara Colalongo1, Gianluca Ferrazzano2, Roberto Tuberosa1, Maria Corinna Sanguineti1
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:
Phone: +39 051 2096645
Fax: +39 051 2096241
Supplemental Table 1a. Mean SBCMV-symptom severity (SS) and virus concentration (ELISA absorbance values) of each scoring/sampling date for Simeto (S) and Levante (L), i.e. the parents of the RIL population, Grazia (susceptible check) and for the 180 F6:7 S×L recombinant inbred lines RILs evaluated in the 2008 field trial. Range (minimum and maximum), coefficient of variation (CV) and heritability values (h2) of the S×L RILs are also reported.
SS-1 / SS-2 / SS-3 / ELISA-1 / ELISA-3
(score) / (A 405 nm)
Simeto / 3.02 / 2.41 / 2.91 / 1.88 / 1.68
Levante / 0.10 / 0.19 / 0.11 / 0.02 / 0.02
Grazia / 3.20 / 3.34 / 3.71 / 1.52 / 1.29
RILs
Mean / 1.79 / 1.69 / 1.76 / 1.18 / 0.68
Min / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
Max / 3.88 / 3.75 / 3.70 / 1.97 / 1.79
CV / 30.9 / 31.1 / 25.3 / 38.1 / 57.5
h2 (%) / 90.0 / 91.6 / 94.4 / 72.7 / 71.0
a The date of each scoring/sampling is reported in the materials and methods section
b Visual score from 0 (no symptoms) to 4 (severe mottling and stunting, with dead plants)
Supplemental Table 1b. Mean SBCMV-symptom severity (SS) and virus concentration (ELISA absorbance values) of each scoring/sampling date for Simeto (S) and Levante (L), i.e. the parents of the RILs), for Grazia (susceptible check) and for the 180 F6:7 S×L RILs evaluated in the 2009 field trial. Range (minimum and maximum), coefficient of variation (CV) and heritability values (h2) of the S×L RILs are also reported.
SS-1 / SS-2 / SS-3 / SS-4 / SS-5 / ELISA-1 / ELISA-3
(score) / (A 405 nm)
Simeto / 2.62 / 3.12 / 2.84 / 3.12 / 2.66 / 1.75 / 1.23
Levante / 0.09 / 0.46 / 0.74 / 1.43 / 0.54 / 0.27 / 0.10
Grazia / 3.18 / 3.64 / 3.70 / 4.73 / 3.82 / 1.83 / 1.41
RILs
Mean / 1.93 / 2.67 / 2.76 / 3.11 / 2.44 / 1.23 / 0.92
Min / 0.00 / 0.25 / 0.50 / 0.23 / 0.13 / 0.00 / 0.00
Max / 3.63 / 4.00 / 4.00 / 4.00 / 4.00 / 2.01 / 1.67
CV / 35.9 / 20.9 / 21.2 / 17.6 / 24.9 / 30.1 / 31.3
h2 (%) / 78.9 / 83.8 / 73.3 / 84.8 / 79.9 / 79.1 / 81.6
a The date of each scoring/sampling is reported in the materials and methods section
b Visual score from 0 (no symptoms) to 4 (severe mottling and stunting, with dead plants
Supplemental Table 2. Features of the main QTL (QSbm.ubo-2BS) that has been identified based on the analysis of the 180 F6:7 Simeto × Levante recombinant inbred lines (RILs). QTL results for symptom severity (SS), virus concentration in the leaves (ELISA) and grain yield (GY) are reported for each consecutive scoring/sampling date of the two years (2008 and 2009) of field trials.
Trait / QTL position(cM)a / Most associated marker / LOD peak
(LOD unit) / R2
(%) / Additive effect b
SS-1-08 / 16-22-24 / wPt-2106 / 47.43 / 71.24 / + 1.07
SS-2-08 / 16-22-24 / wPt-2106 / 43.31 / 66.29 / + 1.07
SS-3-08 / 15-19-23 / wPt-0100 / 51.84 / 80.45 / + 1.25
ELISA-2-08 / 14-22-24 / wPt-2106 / 25.48 / 44.32 / + 0.41
ELISA-3-08 / 16-24-28 / wPt-2106 / 22.86 / 44.01 / + 0.35
GY-08 / 16-22-24 / wPt-2106 / 18.11 / 30.38 / – 0.76
SS-1-09 / 16-24-26 / wPt-2106 / 36.10 / 56.61 / + 0.83
SS-2-09 / 18-22-25 / wPt-2106 / 36.38 / 58.90 / + 0.77
SS-3-09 / 16-22-24 / wPt-2106 / 34.23 / 52.12 / + 0.60
SS-4-09 / 18-22-24 / wPt-2106 / 29.07 / 47.06 / + 0.71
SS-5-09 / 18-22-24 / wPt-2106 / 28.08 / 46.73 / + 0.67
ELISA-2-09 / 20-23-26 / wPt-2106 / 29.33 / 50.81 / + 0.42
ELISA-4-09 / 16-23-32 / wPt-2106 / 30.62 / 50.13 / + 0.35
GY-09 / 14-21-26 / wPt-2106 / 8.66 / 16.77 / – 0.48
Supplemental Table 3. Main features of the QTLs for symptom severity (SS), virus concentration in the leaves (ELISA) and grain yield (GY) for each consecutive scoring/sampling date of the two years (2008 and 2009) of field trials. Scoring/sampling dates are indicated in the materials and methods section.
Composite interval mapping (CIM) analysis has been carried out with a common LOD threshold of 2. QTLs with LOD peak comprised between 2 and 3 were considered as low confidence ones. QTLs for GY are reported only when their position overlap with that of QTLs for direct SBCMV-response traits.
Trait / QTL position(cM)a / Most associated marker / LOD peak
(LOD unit) / R2
(%) / Additive effect b
QSbm.ubo-2AS
SS-1-08 c / 0-12-24 / wPt-0102 / 3.8 / 3.5 / + 0.24
SS-2-08 / 0-10-25 / wPt-0102 / 3.6 / 3.2 / + 0.24
SS-3-08 / 0-15-26 / wPt-0102 / 3.2 / 2.7 / + 0.23
SS-1-09 / 0-16-30 / wPt-0102 / 3.9 / 3.9 / + 0.22
SS-2-09 / 0-12-24 / wPt-0102 / 3.0 / 2.9 / + 0.17
SS-3-09 / 0-10-26 / wPt-0102 / 4.2 / 4.6 / + 0.18
SS-4-09 / 0-12-26 / wPt-0102 / 4.6 / 5.1 / + 0.23
SS-5-09 / 0-14-24 / wPt-0102 / 3.2 / 3.9 / + 0.19
ELISA-2-09 d / 2- 8-20 / wPt-0102 / 7.2 / 10.1 / + 0.20
ELISA-4-09 / 0-12-23 / wPt-0102 / 2.4 / 2.5 / + 0.07
GY-09 e / 0-12-30 / wPt-0102 / 2.4 / 4.1 / – 0.24
QSbm.ubo-3AL
SS-1-08 c / 0-12-27 / cfa2234 / 2.4 / 2.1 / – 0.19
SS-2-08 / 0-10-26 / barc45 / 4.4 / 4.5 / – 0.27
SS-3-08 / 0-14-30 / cfa2234 / 4.2 / 4.2 / – 0.28
GY-08 / 10-26-48 / wPt-5886 / 2.4 / 4.3 / + 0.28
SS-1-09 / 0-12-30 / cfa2234 / 3.4 / 3.4 / – 0.21
SS-2-09 / 0-16-32 / cfa2234 / 4.2 / 5.5 / – 0.24
SS-3-09 / 0-14-28 / cfa2234 / 5.0 / 6.1 / – 0.20
SS-4-09 / 0-18-32 / cfa2234 / 3.4 / 5.9 / – 0.25
SS-5-09 / 0-10-30 / cfa2234 / 4.8 / 6.5 / – 0.25
ELISA-2-09 d / 0-18-32 / cfa2234 / 3.8 / 6.4 / – 0.15
ELISA-4-09 / 4-12-23 / cfa2234 / 6.2 / 7.2 / – 0.13
QSbm.ubo-4BS
ELISA-3-08 / 0-8-22 / wPt-4931 / 2.7 / 3.7 / + 0.10
GY-08 e / 2-8-18 / wPt-4931 / 4.9 / 6.7 / – 0.35
ELISA-4-09 / 0-2-12 / wmc89 / 3.0 / 3.3 / + 0.10
(continued)
Supplemental Table 3 (continued).
Trait / QTL position(cM)a / Most associated marker / LOD peak
(LOD unit) / R2
(%) / Additive effect b
QSbm.ubo-5AL
SS-2-08 / 40-70-96 / wPt-7201 / 2.8 / 4.9 / + 0.29
GY-08 / 36-55-85 / barc197 / 4.1 / 12.2 / – 0.49
SS-1-09 / 39-55-83 / barc197 / 2.6 / 6.1 / + 0.28
QSbm.ubo-6BL
SS-3-09 / 48-58-70 / wPt-3309 / 3.4 / 3.3 / + 0.15
SS-4-09 / 48-58-69 / wPt-3309 / 2.4 / 2.6 / + 0.16
QSbm.ubo-7AL
SS-3-08 / 15-28-42 / wPt-5949 / 2.3 / 2.1 / – 0.21
GY-08 / 11-25-43 / wPt-5949 / 2.8 / 4.1 / + 0.28
QSbm.ubo-7BS
ELISA-1-08 / 0-6-12 / gwm400 / 2.7 / 4.2 / + 0.13
GY-08 / 0-4-12 / gwm400 / 4.1 / 6.7 / – 0.35
a The central value indicates the QTL peak position; flanking values indicate the LOD-2 confidence interval
b Calculated as half of the difference between the mean value of the RILs homozygous for the Simeto allele and the mean value of the RILs homozygous for the Levante allele. Allelic effects positive in sign indicate that the allele increasing the trait originates from Simeto (susceptible parent)
c SS as visual score from 0 (no symptoms) to 4 (severe mottling and stunting, with dead plants). Scoring/sampling dates are indicated in the materials and methods section
d ELISA as absorbance units at 405 nm
e GY reported as t ha-1
Supplemental Table 4. SSR- and DArT-based haplotype comparison among the eight T. durum parents of the four mapping populations considered in this study. Meridiano, Levante, Lloyd, Kofa and Svevo are known to carry resistant alleles at QSbm.ubo-2BS while Claudio, Colosseo and Simeto are known to be either moderately susceptible or susceptible based on the characterization of the RIL populations obtained from Meridiano (resistant) × Claudio (medium susceptible) and Simeto (susceptible) × Levante (resistant) while the response of cv. Colosseo, Lloyd, Kofa and Svevo has been described by Ratti et al. (2006). The allelic state of the SSRs is reported as the molecular size (base pairs) of the amplicons corresponding to the marker loci mapped on chr. 2BS. Null alleles are reported as null. The allelic state of the DArT markers is indicated as either 0 (absence of hybridization signal) or 1 (high hybridization signal). Alleles common to those carried by the resistant cv. Meridiano are highlighted with grey shadow. The markers tagging the most probable interval harboring QSbm.ubo-2BS based on the confidence interval obtained from the meta-QTL analysis are highlighted with grey shadows. Marker order and genetic distances are from a T. durum consensus map obtained from the merged analysis of the genotypic data from four T. durum RIL populations (see materials and methods).
0.0b / 9.8 / 12.4 / 13.5 / 14.0 / 16.9 / 16.9 / 17.8 / 20.4 / 21.3 / 21.6 / 23.2 / 23.5 / 37.0 / 40.7 / 43.7
Meridiano / R / null / 141 / 184 / 179 / 271 / 0 / 0 / 348 / 0 / 0 / 0 / 0 / 0 / 220 / 153 / 176
Claudio / MS / null / 141 / 198 / 191 / null / 1 / 1 / 342 / 1 / 0 / 1 / 1 / 0 / 226 / 149 / 172
Simeto / S / null / 137 / null / 185 / null / 1 / 1 / 354 / 1 / 0 / 0 / 0 / 0 / 224 / 151 / 174
Levante / R / 116 / 137 / null / 185 / null / 1 / 1 / 354 / 0 / 0 / 0 / 0 / 0 / 220 / 149 / 170
Colosseo / MS / 116 / 147 / 198 / 191 / null / 1 / 1 / 342 / 0 / 1 / 0 / 0 / 0 / 220 / 153 / 174
Lloyd / R / null / 141 / 184 / 179 / 271 / 0 / 0 / 348 / 0 / 0 / 0 / 0 / 0 / 220 / 155 / 176
Kofa / R / null / 141 / 184 / 179 / 271 / 0 / 0 / 348 / 0 / 0 / 0 / 0 / 0 / 220 / 155 / 176
Svevo / R / null / 141 / 184 / 179 / 271 / 0 / 0 / 348 / 0 / 0 / 0 / 0 / 0 / 220 / 153 / 176
a The SBCMV response of the T. durum cultivars is reported using the following categories: resistant (R), moderately resistant (MR), moderately susceptible (MS), susceptible (S)
b The genetic distances are reported in cM; molecular marker orders and genetic distances are from a T. durum consensus map based on four different RIL populations.