Supplemental figures and files for "Assessment of genetic differentiation and linkage disequilibrium in Solanum pimpinellifolium using genome-wide high-density SNP markers."
Figure S1. The cross-validation error of K value in ADMIXTURE. This figure shows the cross-validation of ADMIXTURE for the 98 S. pimpinellifolium accessions. The lowest cross-validation error is best K = 3.
Figure S2. LD decay of the whole
genome. The pairwise LD through the
whole genome was plotted. The red curve indicates non-linear regression. The
dotted line indicates the fixed r2 on 0.1.
Figure S3. 50 kb interval LD decay of each chromosome. 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 r2 on 0.1.
Figure S4. The local LD of each chromosome. The LD of paired flanking sequencing units were plotted along each chromosome. The red dotted line indicates the baseline of r2, and the orange line indicates the heterochromatic region.
Figure S5. Pairwise isolation by distance of 98 accessions. This plot presents the correlation between pairwise genetic distance and geographic distance.
Figure S6. Pairwise isolation by distance of SolCAP meta-analysis. This plot presents the correlation between pairwise genetic distance and geographic distance for the collection of 214 samples from the previous studies (Blanca et al. 2012, 2015; Sim et al. 2012a).
Figure S7. The cross-validation error of SolCAP meta-analysis. This figure shows the cross-validation of ADMIXTURE analysis for the SolCAP genotypes of the 214 S. pimpinellifolium accessions in the previous studies (Blanca et al. 2012, 2015; Sim et al. 2012a). The lowest cross-validation error shows best K = 15.
Figure S8. The genome patterns of 214 samples in SolCAP meta-analysis. The labels on the top indicate accessions; the labels on the bottom indicate sample ID in this meta-analysis.
Figure S9. The PCA of SolCAP meta-analysis. A) The PCA plot of bi-allelic SNPs. B) The PCA plot after removing those SNPs of reverse-complement allele designation.
File S1. The analysis of isolation by distance. The isolation by distance was performed for the 98 S. pimpinellifolium accessions with the RAD SNP dataset.
File S2. The meta-analysis of S. pimpinellifolium SolCAP genotyping data. We performed a meta-analysis of 214 S. pimpinellifolium accessions using SolCAP genotyping data downloaded from previous studies Sim et al. 2012a, Blanca et al. 2012, and Blanca et al. 2015.
