Additional file 1: Table S1.

Groups of accessions with the identical SSR profile that included true-to-type Italian varieties. Names of accessions registered as synonymous to the true-to-type prime name are indicated in bold (Vitis International Variety Catalogue webcite). Table S2. Minimum and maximum dates of the beginning of phenological stages for the “phenological core collection” in the three growing seasons (2008-2010). The E-L numbers indicate major vine growth stages according to the modified Eichhorn-Lorenz system [60]. Table S3. SSR markers and multiplex PCR conditions, allele size range and marker profiles of the grapevine cultivars (Pinot noir and Sangiovese) used as internal control for genotyping. a SSR markers with the same number were amplified in a single PCR mix (all primers pooled in the PCR mix). * Reference set of SSR markers used for cultivar identification. Table S4. A total of 384 SNPs selected for genotyping of the FEM grape germplasm collection. Chr - chromosome carrying the SNP according to the reference grapevine genome (Pinot Noir, 8x); LG – linkage group; MAF – minor allele frequency. Source of markers: No. 1-122: [62]; No. 123-286: [19]; No. 287-374: [63]; 375-383: Zyprian et al. (in preparation); 384: [39]. Table S5. Summary statistics of genetic variation at each of the 22 SSR loci in the FEM grape germplasm collection. Total – pooled sample treated as a single population; N – sample size; n – mean sample size over loci; A – number of different alleles; a – mean number of alleles per locus; AE – effective number of alleles; Apr – number of alleles unique to a single population; HO – observed heterozygosity; HE – unbiased expected heterozygosity; F – fixation index (inbreeding coefficient). Table S6. Percent population assignment based on SSR and SNP marker datasets. Each value gives the percentage of individuals that had ≥0.8 membership in a subpopulation using the STRUCTURE analysis (K=2 to 6, with SSR or SNP dataset). Table S7. Groups of V. vinifera ssp. sativa inferred by hierarchical STRUCTURE using SSR and SNP datasets. Listed are the accessions common in the four clusters distinguished using SSR and SNP datasets (i.e. in VV1 and VV1I, VV2 and VV2I, VV3 and VV3I, VV4 and VV4I). The true-to-type samples from these four groups are indicated in bold. Table S8. Common cluster pairwise FST estimates (P=0.00, 1000 permutations).

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Emanuelli et al. BMC Plant Biology 2013 13:39   doi:10.1186/1471-2229-13-39