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

Supplementary Methods
Genotype data quality filters
To verify genotypes, we compared genotype calls from the BeadStudio software to Illumina GA
sequence data from 17 accessions of diverse origin for which a strict set of rules were used to
call genotypes [3]. We only considered genotypes above the following SNP quality thresholds:
GenTrain Score ≥ 0.3 and GenCall ≥ 0.2. At these thresholds, we observe 93.18% concordance
for 60411 genotypes called on both platforms, which is an underestimate of genotyping accuracy
as reduced representation libraries (RRLs) were sequenced with the Illumina GA, which results
in heterozygotes being called homozygotes at an unknown rate. In addition, lower concordance
rates are expected in highly diverse species, where numerous unknown flanking polymorphisms
cause hybridization issues on the genotyping arrays. Based on 145 pairwise comparisons
between replicate samples genotyped with the Vitis9KSNP array, we discarded SNPs with
replication rates < 97%. The mean replication rate for the remaining 6507 SNPs was 0.9981. We
discarded 307 excessively heterozygous SNPs with HWE p-values < 1e-4 within a group of
vinifera that was pruned so that no two accessions had an Identity-by-State (IBS) > 0.95. SNPs
with significant excess homozygosity were left in after visual inspection of cluster plots. An
additional 727 SNPs were removed because they were monomorphic in the sample analysed here
and 86 poor quality SNPs were removed after visual inspection of cluster plots. The total number
of SNPs remaining for analysis was 5387.
The species, cultivar name and cultivar type (wine or table grape) of each sample was obtained
from the Germplasm Resources Information Network (GRIN) database of the USDA
(http://www.ars-grin.gov/). Twenty-three samples labeled as vinifera in GRIN were excluded
from analysis because they were identified as wild Vitis species or wild/vinifera hybrids based on
multi-dimensional scaling (MDS) plots of an IBS matrix that included hundreds of samples from
numerous wild Vitis species and wild/vinifera hybrids. A geographic region of origin was
assigned to 811 vinifera accessions based on mostly on information from GRIN and the
geographic origin of each sylvestris accession was assigned based on its collection location
(Table S1). Samples with genotype call rates < 0.7 were excluded. In total, 950 vinifera and 59
sylvestris remained for analysis.