Supplemental tables for "Assessment of population differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers"

The expected sites and sequenced sites of Pst I as well as the sites with SNP. This table contains the numbers of expected cutting sites and the actually sequenced sites of Pst I of each chromosome in this study. The sequenced sites are also checked if they contained any SNP.

The number of expected genes in the expected sequencing regions is listed to reveal the capability of capturing genes in this RAD sequencing strategy. Table S3. The information of 24,330 SNPs.

We list all the genotypes of the 98 S. pimpinellifolium . Each row indicates a single SNP and each column indicates an individual. Table S4.

The list of InDel markers. The putative InDel markers are summarized in this table, including the physical positions, reference alleles and Insertion/Deletion alleles. Table S5.

The list of SSR markers. The putative SSR markers are summarized in this table. The SSR markers were obtained from the InDel markers if the InDels show tandem repeat units.

The physical positions, repeat units and the InDel length are listed. Table S6. Pair-wise F st of subpopulations.

This table is the pair-wise F st result of seven subpopulations of 98 S. pimpinellifolium . The blue, red and green groups are the three pure ancestries in ADMIXTURE result. The blue-green, red-blue and red-green groups are the admixture groups of pair ancestries.

Three-mixture indicates the group contains the three ancestries. Table S7. The genotypes of 4,326 SNPs of 214 samples.

This table contains the bi-allelic genotypes of SolCAP array of 214 S. pimpinellifolium in the three previous studies (Sim et al., 2012; Blanca et al., 2012; Blanca et al., 2015). The ID was labelled by the accession and its original study. Each row indicates a single SNP and each column indicates an individual.

Table S8. The identity of 4,326 SNPs within accessions. For the 214 S. pimpinellifolium , we listed all the accessions whose sample size is more than one individual and checked the number of monomorphic SNP.

The identity is the percentage of monomorphic SNP within the same accession excluding missing values.