Table 1.
Targets for SureSelect bait library development.
Figure 1.
Mapping of resequencing targets onto the potato genome.
Physical position of the approximately 800 target genes scattered across the 12 potato chromosomes. Physical positions are ordered according to the latest pseudomolecule order (v.3 beta). The distribution of the ∼800 genes reflect the physical proportions of gene rich chromosome arms and gene poor heterochromatic regions.
Table 2.
Summary of target enrichment sequence coverage for 84 potato cultivars.
Table 3.
Overview of DNA variants observed across 84 cultivars in the accessible potato genome.
Figure 2.
Sequence variant density as the number of randomly-added cultivars increases.
The bars show variant density (primary Y-axis), and the black line shows the number of newly-identified variants (secondary Y-axis) as a function of the number of sequenced cultivars. Data is not shown after the 25th cultivar, but continues to drop to a variant density of 1/16.4 bp and an average of 116 novel variants at the 84th cultivar.
Figure 3.
Distribution of minor allele frequencies (MAF) of all 129,156 genotyped sequence variants.
Figure 4.
Distribution of nucleotide diversity across sequenced contigs for coding and non-coding regions.
Figure 5.
Mean nucleotide diversity across sequenced contigs per chromosome.
Dashed line represents genome wide nucleotide diversity (both coding and noncoding sequences), and error bars represent 95% confidence intervals.
Table 4.
Nucleotide diversity in potato (mean value and standard deviation across contigs).
Figure 6.
First and second components from principal component analysis of potato sequence variant genotypes.
Population structure was analysed using ∼43 K sequence variants genotyped in all 84 cultivars. The first three components describe 14.7% of the variance. Based on these three components, the cultivars were clustered into five groups. The most distant cultivar is the monoploid S. tuberosum Group Phureja clone. In the centre of the PCA plot cultivars of diverse, world-wide origins are observed. Three additional divergent groups can be observed, consisting of heirloom cultivars, frying cultivars from continental Europe and cultivars and germplasm used in starch industry.
Figure 7.
Manhattan plots of p values for associations between DNA sequence variants and two phenotypic traits in potato: (A) plant maturity and (B) tuber flesh colour.
The FDR corrected −log10(p) values from GWAS analysis are plotted relative to the physical position on each of 12 potato chromosomes. The horizontal dashed line is plotted at the FDR-corrected significance threshold of α = 0.001 (−log10(p) = 3).
Table 5.
Concordance between genotyping-by-sequencing and KASP genotyping calls.
Figure 8.
Neighbour-Joining tree of chloroplast haplotypes.
The distances of 241 sequence variants for the 84 cultivars were computed using the Jukes-Cantor method and the tree inferred using the Neighbor-joining method.