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

<b>Table S1. The detail information of each accession. </b> This table lists the RAD sequencing summary, mating type and collection location of the 99 <i>S. pimpinellifolium</i> 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.<br> <b>Table S2. The expected sites and sequenced sites of <i>Pst</i>I as well as the sites with SNP. </b> This table contains the numbers of expected cutting sites and the actually sequenced sites of <i>Pst</i>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.<br> <b>Table S3. The information of 24,330 SNPs. </b> We list all the genotypes of the 98 <i>S. pimpinellifolium</i>. Each row indicates a single SNP and each column indicates an individual.<br> <b>Table S4. The list of InDel markers. </b>The putative InDel markers are summarized in this table, including the physical positions, reference alleles and Insertion/Deletion alleles.<br> <b>Table S5. The list of SSR markers. </b>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.<br> <b>Table S6. Pair-wise F_st of subpopulations. </b>This table is the pair-wise F_st result of seven subpopulations of 98 <i>S. pimpinellifolium</i>. 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.<br> <b>Table S7. The genotypes of 4,326 SNPs of 214 samples. </b>This table contains the bi-allelic genotypes of SolCAP array of 214 <i>S. pimpinellifolium</i> 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.<br> <b>Table S8. The identity of 4,326 SNPs within accessions. </b>For the 214 <i>S. pimpinellifolium</i>, 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.

**表S1 各种质材料详细信息**
本表格汇总了本研究中99份醋栗番茄（*Solanum pimpinellifolium*）的RAD测序（限制性酶切位点相关DNA测序，Restriction-site Associated DNA sequencing）统计数据、交配型及采集地点。该统计数据包含测序读段、缺失率与杂合率。其中FSC与ASC分别代表兼性自交亲和型与专性自花授粉自交亲和型交配型。

**表S2 *Pst*I酶切预期位点、测序实际位点及含单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的位点**
本表格统计了各染色体上*Pst*I酶的预期酶切位点数量与实际测序位点数量，并核查了测序位点是否存在SNP。同时列出了预期测序区域内的预期基因数量，以体现本次RAD测序策略的基因捕获能力。

**表S3 24330个SNP位点信息**
本表格汇总了98份醋栗番茄的全部基因型数据。表格中每一行代表一个SNP位点，每一列代表一份个体材料。

**表S4 插入缺失（Insertion/Deletion, InDel）标记列表**
本表格汇总了推定的InDel标记信息，包含其物理位置、参考等位基因与插入/缺失等位基因。

**表S5 简单重复序列（Simple Sequence Repeat, SSR）标记列表**
本表格汇总了推定的SSR标记信息：若插入缺失标记存在串联重复单元，则可将其转化为SSR标记。表格中列出了标记的物理位置、重复单元与InDel片段长度。

**表S6 亚群间的成对F_st值**
本表格呈现了98份醋栗番茄分为7个亚群的成对F_st分析结果。其中蓝色、红色与绿色组为ADMIXTURE群体结构分析得到的三个纯合祖先类群；蓝-绿、红-蓝与红-绿组为两类祖先混合形成的混合类群；三混合组则指同时包含三类祖先的类群。

**表S7 214份样本的4326个SNP位点基因型数据**
本表格包含了三项既往研究中214份醋栗番茄的SolCAP芯片双等位基因分型结果（Sim等，2012；Blanca等，2012；Blanca等，2015）。样本ID由其对应种质材料与原始研究标注。表格中每一行代表一个SNP位点，每一列代表一份个体材料。

**表S8 种质材料内4326个SNP位点的一致性率**
针对214份醋栗番茄，本表格列出了样本量大于1的所有种质材料，并统计了其单态SNP位点数量。一致性率指剔除缺失值后，同一种质材料内单态SNP位点所占的百分比。