## 2 Results
### Map Validation with Berry Skin Color and Flower Type  
Two well-studied binary traits were used to validate the VRS-F\({}_{2}\) GBS-rhAmpSeq map: grapevine berry skin color and flower type (pistillate, hermaphroditic). There were 22 white and 78 black fruited genotypes observed in the fruiting field vines. Chi-squared test did not reject the hypothesis of a 3:1 ratio of blackwhite (chi-squared value = 0.56 and \(p\)-value = 0.46) consistent with a single locus and black being dominant over white skin color. Berry skin color mapping identified a significant QTL on chromosome 2 with \begin{table}
\begin{tabular}{c c c} \hline
**Parameter** & **Value** \\ \hline Number of F\({}_{2}\) genotypes & 514 \\ Total (GBS and rhAmpSeq) markers used in map curation & 3428 \\ Markers in LGs & 2519 \\ GBS markers in LGs & 1449 \\ rhAmpSeq markers in LGs & 1070 \\ LGs & 19 \\ Distortion threshold & \(1\times 10^{-21}\) \\ Number of markers that formed different LG & 0 \\ Mismapped markers in LG & 0 \\ Markers not in any LG & 0 \\ Problematic markers in LG & 0 \\ Non-informative marker & 677 \\ Distorted marker numbers & 232 \\ Genetic map size (cM) & 1131.3 \\ Genome-wide recombination rate (cM/Mb) & 2.5 \\ Average distance between markers (cM) & 0.5 \\ Genome coverage (\%) & 96.3 \\ Largest gap (cM) & 11.3 \\ \hline \end{tabular}
\begin{tabular}{c c c c c} \hline
**Chromosome** & **Number of Markers** & **Chromosome Genetic** & **Average Spacing** & **Maximum** & **Correlation** \\  
Overall & 2519 & 1131.3 & 0.5 & \\ \hline \end{tabular}
\end{table} 
Table 2: Chromosome summary of the VRS-F\({}_{2}\) genetic map. \begin{table}
\begin{tabular}{c c c c} \hline
**Chromosome** & **Number of Markers** & **Chromosome Genetic** & **Average Spacing** & **Maximum** & **Correlation** \\
**1** & **1**50 & **6**5.3 & 0.4 & 4.7 & 0.9999 * \\
**2** & **112** & **52.2** & 0.5 & 4.2 & 0.9998 * \\
**3** & **97** & **48.2** & 0.5 & 5.3 & 0.9996 * \\
**4** & **181** & **62.7** & 0.3 & 2.3 & 0.9999 * \\
**5** & **193** & **62.5** & 0.3 & 2.0 & 0.999  
22.8 LOD value and peak position at 13.5 Mb position in the map (Table 3). The QTL confidence interval contained many MYB family genes including the MYBA1 gene associated with berry color. Flower type was mapped to chromosome 2 using 97 genotypes. The VRS-F\({}_{2}\) parent (16\(9\)2) was heterozygous (Hf) for the dominant hermaphroditic flower type and analysis of the F\({}_{2}\) progeny field vines flower type indicated 81:16 hermaphroditic (HH or Hf): pistellate (ff) supporting the expected 3:1 ratio (chi-squared value = 2.61 and \(p\)-value = 0.11). A flower type QTL was detected on chromosome 2 at 4.65 (Mb) with 17.2 LOD and a very narrow 95% Bayesian interval (Table 3). Seven markers including markers within the QTL confidence interval (rh_2_4497054, GBS_2_4567885, rh_2_4599939, GBS_2_4650201), two markers nearby the confidence interval (rh_2_4703733 and GBS_2_5352479), and a previously reported marker (rh_2_4825658) were used to predict flower type phenotype based on genotype. These markers predicted that the 358 unknown individuals were potentially 1:1:2 homozygous pistellate, homozygous hermaphroditic, and heterozygous hermaphroditic, respectively (Table S2). The training set of 97 individuals showed varying marker accuracy depending on flower type. Four markers showed 100% prediction accuracy for the pistellate phenotype and prediction for hermaphroditic types ranged from 96 to 99% accuracy across the seven markers (Figure S5). A test data set of 59 newly identified flower type phenotypes gathered in greenhouse-grown vines was used to validate the accuracy of genotype prediction and a 100% accuracy was obtained for the pistellate phenotype in comparison to the genotype prediction for all seven markers. The accuracy for the hermaphroditic phenotype was similar with 95 to 98% accuracy depending on the marker.