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

Table S1. The detail information of each accession. This table lists the RAD sequencing summary, mating type and collection location of the 99 S. pimpinellifolium in this study. The RAD sequencing summary includes the reads, the missing proportion and the heterozygous proportion. FSC and ASC indicate facultative self-compatible and autogamous self-compatible mating type, respectively.

Table S2. The statistical summaries of expected sites and sequenced sites of PstI, the sites targeted by SNP and the sequenced genes. This table contains the numbers of expected cutting sites and the actually sequenced sites of PstI 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 summarized to reveal the capability of capturing genes in this RAD sequencing strategy. Also, the sequenced genes are summarized.

Table S3. The information of 24,330 SNPs. We list all the genotypes of the 98 S. pimpinellifolium. Each row indicates a SNP and each column indicates an individual.

Table S4. Pairwise F_st of seven subpopulations. This table is the pairwise F_st of seven subpopulations for 98 S. pimpinellifolium. The names of subpopulations are stated in Table 2.

Table S5. The locations and genotypes of 214 samples of SolCAP genotyping array. This table contains the 2,307 consistent allele calling markers of SolCAP array for 214 samples in the three previous studies (Blanca et al. 2012, 2015; Sim et al. 2012a). The gathering locations are also provided.

Table S6. The removed 627 SNPs with reverse-complement allele designation. This list includes the SNPs we removed in SolCAP meta-analysis due to reverse-complement allele designation

Table S7. The identity of 2,307 SNP markers within accessions. For the 214 S. pimpinellifolium, we listed all the accessions that contain more than one individual to count monomorphic SNP. The identity is the percentage of monomorphic SNP for the same accession excluding missing values.