Data supplements
Supplemental Data R-script to plot recombination fraction and logarithm of odds (LOD) threshold. ##Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: quantitative trait locus (QTL) mapping in experimental crosses. Bioinformatics 19:889-890.
Supplemental Figure 1 Leaf disk assay based on OIV descriptors 452-1 (International Organization of Vine and Wine). Panels A, B, C, D, and E show examples of very low, low, medium, high, and very high level of resistance, where 50% or more, ~20%, 10%, >5%, and none of the leaf disk area was covered by sporangiophores, respectively, seven days postinoculation. Scores assigned to the levels of resistance depicted in panels A, B, C, D, and E were 1, 3, 5, 7, and 9, respectively.Supplemental Figure 2 Integrated linkage map.
Supplemental Figure 3 Synteny between genetic distance and physical distance in Vitis rupestris, Vitis riparia, and integrated maps.
Supplemental Figure 4 Pairwise recombination fractions and logarithm of odds (LOD) plots for parental maps. Pairwise recombination fractions and LOD scores in (A) Vitis rupestris and (B) Vitis riparia linkage groups. Yellow and blue coloring below the identity line represent low and high crossover frequency regions, respectively. Yellow and blue coloring above the identity line represent high and low LOD values, respectively. The top X- and right Y-axes are numbered according to linkage groups; the bottom X- and left Y-axes indicate the position of markers in the 19 linkage groups.
Supplemental Figure 5 Flower sex-determining quantitative trait locus (QTL) on chromosome 2. Maleness-determining locus on chromosome 2 in the integrated map. Right panel shows a significant logarithm of odds (LOD) peak (p < 0.05) with corresponding tightly linked marker within the maleness-determining QTL region (QTL.Sex) on chromosome 2. The horizontal black dashed-dotted line represents genome-wide LOD threshold (number of permutations = 1000) at p = 0.05. Marker in red color represents a marker with the largest LOD value.
Supplemental Figure 6 Phylogenetic relatedness of downy mildew strain MO-1. Position of Plasmopara viticola strain MO-1 in the phylogeny of P. viticola cryptic species. Phylogenetic tree was constructed with the 235-bp long internal transcribed spacer-1 (ITS-1) nucleotide sequence of the 5.8S ribosomal RNA gene (GeneBank accession: JF897779; Rouxel et al. 2014).
Supplemental Figure 7 Frequency distribution of F1 progeny for disease resistance trait. Disease resistance as measured by leaf area covered by sporangiophores under (A) greenhouse and (B) in vitro conditions.Supplemental Table 1 Vitis rupestris map: Markers, ID and its segregation type, phase information, classification, genetic position, corresponding linkage group and genotypes across individuals. Number of markers = 1177; number of F1 individuals = 294.
Supplemental Table 2 Vitis riparia map: Markers, ID and its segregation type, phase information, classification, genetic position, corresponding linkage group and genotypes across individuals. Number of markers = 1115; number of F1 individuals = 294.
Supplemental Table 3 Integrated map: Markers, ID and its segregation type, phase information, classification, genetic position, corresponding linkage group and genotypes across individuals. Number of markers = 2583; number of F1 individuals = 294.
Supplemental Table 4 In vitro disease coverage. Mean and standard deviation of scores for leaf disks calculated for each genotype.
Supplemental Table 5 Logarithm of odds (LOD) values from interval mapping across Vitis rupestris chromosome 10 for downy mildew resistance under greenhouse and in vitro conditions (LOD Threshold: 4.8) and the list genotyping-by-sequencing (GBS) markers, genetic positions, and corresponding Vitis vinifera RefSeq (12X.v3 assembly, Canaguier et al. 2017) coordinates within the 2-LOD interval of Rpv28.1 (dark gray highlight) and Rpv28.2 (light gray highlight).Supplemental Table 6 Predicted genes within the 2-LOD interval of Rpv28.1 as inferred from the corresponding Vitis vinifera RefSeq (12X.v3 assembly, Canaguier et al 2017).
Supplemental Table 7 SSR markers within the 2-LOD interval of Rpv28.2.
