Legends for Supplemental Figures
Supplemental Figure 1. Randomly amplified polymorphic DNA (RAPD) analysis of the O37
series plants. ‘M’ indicates DNA size marker lanes. Lanes 1-6 are RAPD amplicons from
primer pair #1, and lanes 7-12 are RAPD amplicons from primer pair #2. Template genomic
DNA: Lanes 1 and 7: O37 1x; Lanes 2 and 8: O37 2xR3; Lanes 3 and 9: O37 2xR5; Lanes 4 and
10: 4x; Lanes 5 and 11: S. tuberosum cv. Katahdin; Lanes 6 and 12: Solanum bulbocastanum.
The S. tuberosum and S. bulbocastanum lanes show polymorphic bands compared to the O37
series, but the genotypes within O37 are monomorphic.
Supplemental Figure 2. Box charts displaying the distribution of leaflet (A) and root tip (B)
expression levels for different gene lists. The root tip data exhibit higher expression signals due
to the amplification of RNA. The boxes define the 25th and 75th percentiles, with the 50th
percentile indicated by the horizontal line within the box. The whiskers define the 5th and 95th
percentiles. The expression level (Y-axis) was determined by averaging the normalized
microarray signal intensities for a given gene across all leaflet and root tip data points,
respectively. The gene lists were derived from the MAANOVA statistical tests of the ploidy
microarray data: ‘Leaf Sig.’ includes the data from the 948 genes that had Q-value < 0.10 for the
leaflet data; ‘Leaf Not Sig.’ includes the data from the 8,081 genes that had Q-value > 0.10 for
the leaflet data; ‘Root Sig.’ includes the 955 genes that had Q-value < 0.10 for the root tip data;
‘Root Not Sig.’ includes the 8,074 genes that had Q-value > 0.10 for the root tip data. The
leaflet (A) and root tip (B) data show similar relative distributions across gene lists. The 948
genes that were significant in leaflet tissue displayed greater average expression in both leaflet
and root tip tissues. The 955 genes that were significant in root tip tissue displayed no change in
distribution compared to non-significant genes.
Supplemental Figure 3. M-value plot for the 91 ribosomal protein encoding genes that were
found significant in the leaflet data (ANOVA Q < 0.10). The plot format is described in the
Figure 5 legend in the main text. (A) Plot for leaflet data. (B) Plot for root tip data. The leaflet
expression for these genes cluster into the upper-right quadrant of the plot, indicating a ploidyupregulation. The root tip distribution of these genes cluster around the center of the plot,
indicating no consistent trend relative to ploidy.