## 5 Conclusions  
This study constructed a high-density, integrated VRS-F\({}_{2}\) GBS-rhAmpSeq genetic map with 2519 markers across the 19 grapevine chromosomes. Natural segregation distortion was identified on chromosomes 5, 7, 11, and 15 during map development and marker testing. The inclusion of many markers that were identified as distorted at the standard 0.05 \(p\)-value provided a VRS-F\({}_{2}\) GBS-rhAmpSeq map that was truer to the genetic structure of the inbred population. The greater marker density and rhAmpSeq markers provided greater opportunity to map traits and make comparisons with other interspecific populations. The map presented here identified remarkably narrow confidence intervals and candidate for qualitative traits, such as berry skin color (6.5 Mb) and flower type (0.2 Mb). Two transferable marker pairs ((one pistillate (rh_2_4497054 or rh_2_4599939) and one hermaphroditic (rh_2_4703733 or rh_2_4825658)) were identified to predict flower type in VRS-F\({}_{2}\). Total anthocyanin and monoglucoside QTL occur on chromosome 2, with the monoglucoside peak marker located upstream of the berry color and total anthocyanins QTL peak positions. Total and individual diglucosides QTL were located on chromosome 9 with 5-O-GLUCOSYLTRANSFERASE candidate gene (Vitvi09g00582) in repeat years. Our findings confirmed the presence of multiple acidity-related (malic acid and TA) QTL in one growing season. The malic acid QTL on chromosome 1 in 2016 and 2018 identified two additional malic acid related candidate genes (_MALATE DEHYDROGENASE_, Vitvi01g01744, Vitvi01g02239, Vitvi01g02240). The three seasons also confirmed stable QTL on chromosome 6, and ALMT (Vitvi06g00922, Vitvi01g00928) was the candidate gene in this interval. Modeling the QTL indicated multiple malic acid related genes on chromosome 1, 6, and 8 and explained >50% of the variation in 2016 and 2018. This study provides the first report of a volatile QTL and candidate gene _PHOSPHOLIPID HYDROFOXIDE GLUTATHIONE PEROXIDASE_ for (E)-2-hexenal, a grassy-smelling volatile that can have a negative herbaceous aroma at high concentrations. **Supplementary Materials:** The following are available online at [[https://www.mdpi.com/article/10.3390/plants11050696/s1](https://www.mdpi.com/article/10.3390/plants11050696/s1)]([https://www.mdpi.com/article/10.3390/plants11050696/s1](https://www.mdpi.com/article/10.3390/plants11050696/s1)) Table S1. VRS-F\({}_{2}\) GBS-rhAmpseq genetic map coverage relative to _V. vinifera_ PN40024 12X V2 reference genome. Table S2. Predicted pistillate (ff), homozygous hermaphroditic (HH) and heterozygous hermaphroditic (Hf) flower phenotype for VRS-F\({}_{2}\) subset using linked markers. Table S3. Descriptive trait data for grandparents, parent, and VRS-F\({}_{2}\) population. Table S4. Pearson correlation coefficient for malic acid and tittatable acidity (TA) trait pairs. Table S5. Modeling of malic acid QTL increases explained variation for 2016 and 2018. Table S6. Growing degree days (GDD) from June through August in 2013, 2016, and 2018. Table S7. Individual mono- and diglucoside anthocyanins QTL Figure S1. Genotype frequency plots for all markers in 19 chromosomes. Dotted and dotdash lines represent the projected genotype count 128 (for AA and BB) and 256 (for AB) with an expected 1:21 Mendelian ratio. Figure S2. Number of genetic markers included with decreasing level of chi-square adjusted \(p\)-values. Figure S3. Collinearity between _V. vinifera_ PN40024 V2 reference genome physical positions and genetic positions of the VRS-F\({}_{2}\) GBS-rhAmpSeq linkage map. Figure S4. VRS-F\({}_{2}\) GBS-rhAmpSeq genetic map. Chromosome number is at the top and black and red colors indicate GBS and rhAmpSeq markers, respectively (A, chromosome 1-5; B, chromosome 6-10; C, chromosome 11-15; D, Chromosome 16-19). Figure S5. Genotype accuracy relative to flower phenotype for a training set for potential flower type markers (n = 97). **Author Contributions:** Conceptualization, A.F., L.C.-D., B.I.R. and G.S. ; data curation, D.A.