Supporting Information (SI) Appendix - Proceedings of the National ...

Figure S4: GWA result for grape color and the associated signals of selection for lighter
pigmentation. A) P values for association between SNPs and grape color across the 19
assembled chromosomes of the grape. The horizontal dashed line corresponds to a 5%
significance threshold with Bonferroni correction for 5110 tests. B) Magnification of the
association result on chromosome 2. The location of the known causal alleles for grape color in
the VvMybA1 and VvMybA2 genes, which were not genotyped in the present study, is indicated
by the vertical line. C) Average Fst is shown for 10-SNP windows with a 5-SNP overlap across
chromosome 2. The horizontal dashed line represents the top 1% Fst threshold from windows
genome-wide. D) Haplotype diversity in white cultivars relative to red cultivars in sliding
windows as above. Values below the horizontal dashed line represent windows within the 1%
most extreme reductions in haplotype diversity in white cultivars from windows genome-wide.
The elevated LD generated by selection for white grapes has generated a diffuse association peak
covering 5Mb and several hundred genes. The observation that the strongest signals of
association and selection are not found directly at the causal locus has been seen in other plants,
for example in Arabadopsis [1] and maize [2].