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

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east Azerbaijan Fabrizio Grassi east Pakistan DVIT 2263 Austin Goheen east Georgia DVIT 3349 41°48' 43°20' Ed Stover 828 east Turkmenistan Fabrizio Grassi east Pakistan DVIT 2262.1 Austin Goheen west Tunisia DVIT 2426 Harold Olmo east Turkey 38°03' 26°95' Fabrizio Grassi west Spain 37°55' 05°42' Raffael Ocete west Spain 36°49' 05°29' Raffael Ocete west Spain 37°08' 06°32' Raffael Ocete west Spain 36°49' 05°29' Raffael Ocete west Spain 38°01' 06 47' Raffael Ocete west Spain 37°55' 05°42' Raffael Ocete west Spain 36°07' 06 30' Raffael Ocete west Spain Raffael Ocete west Spain 36°22' 05 38' Raffael Ocete west Spain 36°46' 05°33' Raffael Ocete west Spain 36°20' 05 37' Raffael Ocete Table S6: Details of the sylvestris samples used in the present study. See the section “Supplementary Text: Authenticity of Vitis vinifera subsp. sylvestris” for a discussion of authenticity of these sylvestris samples.
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.
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Supporting Information (SI) Appendi
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Authenticity of Vitis vinifera subs
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Figure S2: Evalution of domesticati
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Figure S4: GWA result for grape col
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Figure S6: The inter-SNP distance d
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Figure S8: Evaluation of authentici
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Supplementary Tables Vitis vinifera
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Sovrana (DVIT 525) Delizia Di Vapri
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382) Corniola (DVIT 3162) Muscat of
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2684) (DVIT 1326) Ribier (DVIT 503)
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Cultivar Clones 030-33 (DVIT 1796)
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Argant (DVIT 2305) Arhaniotico Koki
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Barmak Isium (DVIT 310) Barone Dell
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Blauer Spatburgunder (DVIT 661) Blu
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Cardinal (DVIT 370) Carignane (DVIT
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Chasselas Dore (DVIT 689) Chasselas
Page 33 and 34: Chasselas Tokay (DVIT 377) Chassela
Page 35 and 36: Dermatas (DVIT 572) Diamente Nero (
Page 37 and 38: Folle Noire (DVIT 725) Fort Ross Vi
Page 39 and 40: Gewurztraminer (DVIT 740) Ghlicopat
Page 41 and 42: Hunisa (DVIT 418) Husseine (DVIT 42
Page 43 and 44: Karadzhandal (DVIT 2323) Karistino
Page 45 and 46: Kleinberger (DVIT 776) Klusaine Red
Page 47 and 48: Late Blue Burgundy (DVIT 793) Pinot
Page 49 and 50: Maria Pirovano (DVIT 588) Markandi
Page 51 and 52: Moscato Jesus (DVIT 2062) Moscato M
Page 53 and 54: Muscat Galego (DVIT 859) Muscat Gro
Page 55 and 56: Muscat of Alexandria (DVIT 841) Ivi
Page 57 and 58: NA (PI 588326.03) NA (PI 588425.02)
Page 59 and 60: Olivette Noir (DVIT 1306) Olivette
Page 61 and 62: Petrolianos (DVIT 899) Peverella (D
Page 63 and 64: Pinot Noir (DVIT 914) Pinot Noir (D
Page 65 and 66: Poet Matabon (DVIT 1597) Poet Matab
Page 67 and 68: Red Veltliner (DVIT 928) Ree (DVIT
Page 69 and 70: Royal E (DVIT 506) Royal Thompson (
Page 71 and 72: Sciacarello (DVIT 1125) Montanaccio
Page 73 and 74: Smederevka (DVIT 1074) Prokupac (DV
Page 75 and 76: Tabyrn (DVIT 969) Tadone (DVIT 970)
Page 77 and 78: Tokay (DVIT 2157) Tokay (DVIT 540)
Page 79 and 80: Van Der Laan (DVIT 543) Velana (DVI
Page 81 and 82: White Riesling (DVIT 1015) White Ri
Page 83: egion country USDA ID latitude long
Page 87 and 88: in cultivar naming. The present dat
Page 89 and 90: Figure S8, which includes only west
Page 91 and 92: the eastern sylvestris is more ques
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