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

<b>Figure S1</b><b>. The cross-validation error
of K value in ADMIXTURE. </b>This figure shows the
cross-validation of ADMIXTURE for the 98 <i>S.
pimpinellifolium</i> accessions. The lowest cross-validation error is best K =
3.

<b>Figure S2.</b><b> LD decay of the whole
genome. </b>The pairwise LD through the
whole genome was plotted. The red curve indicates non-linear regression. The
dotted line indicates the fixed <i>r²</i> on 0.1.<br>

<b>Figure S3. 50 kb interval LD decay of
each chromosome. </b>The pairwise LD of each chromosome
was plotted individually and zoomed in to 50 kb interval to observe the fast LD
decay. The red curves indicate non-linear regression. Black dotted lines
indicate the fixed <i>r²</i> on 0.1.

<b>Figure S4. The local LD of each
chromosome. </b>The LD of paired flanking
sequencing units were plotted along each chromosome. The red dotted line
indicates the baseline of <i>r²</i>,
and the orange line indicates the heterochromatic region.

<b>Figure S5.</b><b> Pairwise isolation by
distance of 98 accessions. </b>This plot presents the
correlation between pairwise genetic distance and geographic distance.

<b>Figure S6.</b><b> Pairwise isolation by
distance of SolCAP meta-analysis. </b>This plot presents the
correlation between pairwise genetic distance and geographic distance for the
collection of 214 samples from the previous studies (Blanca <i>et al.</i>
2012, 2015; Sim <i>et al.</i> 2012a).

<b>Figure S7.</b><b> The cross-validation error
of SolCAP meta-analysis. </b>This figure shows the
cross-validation of ADMIXTURE analysis for the SolCAP genotypes of the 214 <i>S. pimpinellifolium</i> accessions in the
previous studies (Blanca <i>et al.</i> 2012, 2015; Sim <i>et al.</i> 2012a). The lowest cross-validation error
shows best K = 15.

<b>Figure S8. The genome patterns of 214
samples in SolCAP meta-analysis. </b>The labels on the top
indicate accessions; the labels on the bottom indicate sample ID in this
meta-analysis.

<b>Figure S9.</b><b> The PCA of SolCAP
meta-analysis. </b>A) The PCA plot of bi-allelic SNPs. B) The PCA plot after removing those
SNPs of reverse-complement allele designation.<b>File S1. The analysis of
isolation by distance. </b>The isolation
by distance was performed for the 98 <i>S. pimpinellifolium</i> accessions with
the RAD SNP dataset.<b>File S2. </b><b>The meta-analysis of <i>S. pimpinellifolium</i> SolCAP genotyping
data. </b>We
performed a meta-analysis of 214 <i>S.
pimpinellifolium</i> accessions using SolCAP genotyping data downloaded from
previous studies Sim <i>et
al.</i> 2012a, Blanca <i>et al.</i> 2012, and Blanca <i>et al.</i> 2015.<br>