Figure 1.
Figure 1.

A) The distribution of the number of single nucleotide polymorphisms (SNPs) by the number of contigs. B) The distribution of coverage depth by the number of SNPs. The average depth of coverage at a SNP was 7.8x.

 


Figure 2.
Figure 2.

Example single nucleotide polymorphism (SNP) assays using the KASPar genotyping chemistry on the Fluidigm access array. Panels A and B show SNP loci Cq05798_991 and Cq08757_1585, respectively. No template controls (NTC), synthetic heterozygous controls, and heterozygous samples are identified in each graph. Pop, population.

 


Figure 3.
Figure 3.

A) Principle coordinate analysis of the entire Chenopodium diversity panel, including the eight related Chenopodium taxa. Principle coordinate 1 and 2 explain 72.3 and 7.3% of the total variance, respectively. B) Unrooted NeighborNet (Bryant and Moulton, 2002) analysis using the 113 C. quinoa accessions. Accessions in the NeighborNet analysis are coded as given in Table 1.

 


Figure 4.
Figure 4.

Integrated linkage map constructed from a cross of KU-2 × 0654 and NL-6 × 0654. single nucleotide polymorphism (SNP) loci showing segregation distortion (P < 0.01) are identified with asterisks. Asterisks to the left of the linkage group (LG) identify marker loci that are skewed toward the coastal parent (KU-2 or NL-6) while asterisks to the right identify markers skewed toward the 0654 paternal parental. Exact map positions for each SNP marker are provided in Supplemental Table S2.