Two major loci located on chromosomes 15 and 7 from the V. cinerea B9 and ‘Horizon’ parents, respectively, showed dominant effects and significantly predicted both the severity and incidence of cane and cluster symptoms, respectively, for all years and families tested (Table 3). Here, we refer to these V. cinerea B9 and ‘Horizon’ loci as Rda1 and Rda2, respectively. For all crosses used in this study, vines with either the Rda1 or Rda2 resistance allele had either no symptoms or small, discrete lesions (scores 0 or 1), while vines with both susceptible alleles showed moderate to severe symptoms (scores 2–3). On the Illinois 547-1 map, two other minor QTL were significant only in the 2011 evaluation of dormant canes and explained much less of the phenotypic variance (3.2 and 3.5%) than Rda1 or Rda2 (28.4 and 24.8%) (Table 3). No QTL was identified from ‘Chardonnay’.Table 3QTL mapping statisticsFamilyParentChraPhenotypeYearPeak Markera (cM)Left Markera (cM)Right Markera (cM)LODPVEc (%)‘Chardonnay’ × V. cinerea B9V. cinerea B915Cane2012S15_19560016 (62.2)S15_19299979 (61.4)S15_19591520 (63.7)51.479.82013S15_19560016 (62.2)S15_19299979 (61.4)S15_19591520 (63.7)44.275.2Cluster2013S15_19591520 (63.7)S15_18780806 (57.1)S15_20031941 (66.8)*16.573.02014S15_19560016 (62.2)S15_18780806 (57.1)S15_20031941 (66.8)*10.560.7‘Horizon’ × V. cinerea B9‘Horizon’7Cane2012S7_2768585 (15.2)S7_1087848 (10.0)S7_3855744 (19.1)50.441.12013S7_3127568 (15.5)S7_1087848 (10.0)S7_3855744 (19.1)29.148.0Cluster2013S7_3127568 (15.5)S7_1087848 (10.0)S7_4952429 (24.7)30.622.82014S7_1860119 (13.9)S7_1087848 (10.0)S7_4952429 (24.7)25.111.2V. cinerea B915Cane2012S15_19591538 (51.4)S15_19560016 (50.6)S15_19637245 (53.1)*56.151.02013S15_19591538 (51.4)S15_19560016 (50.6)S15_19637245 (53.1)*32.256.3Cluster2013S15_19591538 (51.4)S15_19560016 (50.6)S15_19637245 (53.1)*30.120.02014S15_19637245 (53.1)S15_19560016 (50.6)S15_19637245 (53.1)*26.520.4‘Horizon’ × Illinois 547-1‘Horizon’7Cane2011S7_2000903 (6.5)S7_1459378 (4.5)S7_2409624 (7.7)30.324.82012S7_1912889 (5.6)S7_1459378 (4.5)S7_2409624 (7.7)58.445.5Illinois 547-11Cane2011S1_3046182 (11.3)S1_1170106 (3.8)S1_4279265 (14.5)3.63.222011S2_5852870 (34.5)S2_2340804 (12.0)S2_7231845 (40.5)4.73.4152011S15_19300044 (49.2)S15_19053446 (46.1)S15_19591538 (54.7)34.228.42012S15_19300044 (49.2)S15_19300044 (49.2)S15_19591538 (54.7)58.646.1Loci associated with Phomopsis cane and berry symptoms were identified by multiple QTL mapping on parental maps for three familiesaChromosome (Chr) and marker positions correspond to the physical location in the 12X.0 PN40024 Vitis vinifera reference genome. Markers are reported in the format S(chromosome)_(position in bp). Left and right markers correspond to the closest marker to the borders of a 1.5 LOD interval. An asterisk (*) indicates the last marker of the mapbLOD threshold was determined by permutation test (1000), at α = 0.05, and ranged from 2.90 to 3.14cPVE refers to the percentage of variance explained by the locus