The genetic map is built . Genetic distances ranged from 999.2 to 1350.1 cM (Table 1). The average Pearson’s correlation (r) between physical and genetic positions ranged from 0.86 to 0.95 genome-wide, and genetic maps covered 94.3% to 99.1% of the reference genome (supplementary file 1-4).  Each parental genetic map was similar within each chromosome, but there were some regions that failed to recombine in a specific parent. This might due to structural variation in the genome, for example region on chromosome 1 between 4 - 12 Mbp for the female parental map of the MN family (Figure 4).
We analyzed markers that failed to map, to determine whether these represented poor markers in all families.  The vast majority of these problematic markers were either monomorphic (Provided no information of recombination in either parent, i.e. homozygous) or distorted at P<1e-03 (Table 2); in total these two categories represented 811 to 924 markers in each family. Few markers (3 to 19) were in three other categories: mapped to the wrong linkage group (LG), did not map to any LG, or disproportionately inflated genetic distances. Only 8.4% of the monomorphic markers and 3.4% of the distorted markers were problematic in three or four families; most (65.0% and 67.8%) were problematic in only one family (Figure 3).  We compared the distance between distorted markers and a random sampling of the same number of markers from the entire set, and the distance between distorted markers was significantly smaller than the random expectation (supplemental figure S6, Mann-Whitney test, P<1E-13).[CL1]  Thus, the distorted markers are linked and may reflect differences in genome biology among taxa. While these and monomorphic markers might be problematic for a specific genetic background, over 83% [CL2] of the markers in this panel should provide useful information in genetic map construction  in most Vitis taxa. [based on the mata
meta-consus useful --> return data, polymorphic  and  segregated follow  expected medienial segregation ratio.  ]

Consensus genetic map

A consensus genetic map was constructed using 600 vines (150 vines from each family) and 1,969 markers, of which 83% mapped (Table 2).  The total sex-averaged genetic distance of the consensus map was 1,198.1 cM, about 0.38 Mb/cM. Markers in the consensus map provided genome coverage of 99.1%, with the largest gap being 9.28 cM or ~3.5 Mb. The average Pearson’s correlation (r) between physical and genetic positions was 0.95 across all chromosomes (supplementary file 5).

 GWAS for flower sex

A total of 1,712 and 1,784 post-imputed and filtered markers were analyzed for association with flower sex trait measured in 157 and 509 vines from the HC and RS families, respectively. Trait segregation ratios of 71:76 and 86:18 matched expectations of 1:1 for HC and 3:1 for RS, respectively, based on non-significance in a chi-squared test. Thirteen and seventeen markers, respectively, significantly predicted flower sex after Bonferroni multiple comparisons correction. Marker chr2_4825658 (chromosome 2 at position 4,825,658 bp) was the most significant marker in both HC (P < 9.6E-17) and RS (P < 2.8E-09) family, explaining 82.0% and 50.4% of the phenotypic variation, respectively (Figure 5).
 [CL1]This is a result, moved from discussion.
 [CL2]I think this is the right place for this sentence from above, but I am not sure where the 99% number comes from – it seems high.  I revised based on the previous sentence and markers that fail to return data.