Figure 5

Effect of excluding 51 “non-ananassa” octoploid accessions from genotyping co-cluster runs for two SNPs. The cluster plots in the left column are for 310 strawberry samples. The cluster plots in the right column are for 284 strawberry samples, excluding the non-ananassa samples (F. chiloensis and F. virginiana). SNP A is a robust diploid-like SNP site that produces only three genotype clusters in the presence as well in the absence of the wild progenitor samples, and thus is genotyped correctly in both circumstances. SNP B is a more challenging SNP site at which the genomes of the divergent non-ananassa form a 4th genotype cluster (arrow). This 4th cluster causes the samples in the BB homozygous genotype cluster to be incorrectly called as heterozygous (colored gold). When the non-ananassa samples are excluded (bottom right), the software correctly calls the samples in the homozygous BB cluster as “BB” (colored blue).