Figure 1
Figure 1

Minor allele frequency distribution across 414 single nucleotide polymorphism (SNP) loci as determined within the full panel of grain amaranth and Amaranthus hybridus accessions.

 


Figure 2.
Figure 2.

Unrooted neighbor joining tree showing the genetic relationship among accessions of the Amaranthus hybridus complex (A. caudatus, A. cruentus, A. hypochondriacus, and A. hybridus) genotypes based on single nucleotide polymorphism (SNP) marker data. Bootstrap support values are given at each node. Individuals in the tree are identified by their abbreviated species. Amaranthus hybridus accessions are identified with stars (*). The boxed accession, PI 481125, was originally classified as A. caudatus.

 


Figure 3.
Figure 3.

Example of single nucleotide polymorphism (SNP) assays using the KASPar genotyping chemistry on the Fluidigm access array in the F2 mapping population. Panels A and B show codominant SNP loci AM19584 and AM18604 while panels C and D show dominant SNP loci AM27609 and AM19502. No template controls (NTC) are identified at the origin of each Cartesian graph.

 


Figure 4.
Figure 4.

A 16 group linkage map constructed from an interspecific Amaranthus hypochondriacus × A. caudatus F2 population (2n = 32). Distances are shown in centiMorgans (cM) corrected with the Kosambi mapping function. Single nucleotide polymorphism (SNP) loci showing segregation distortion (p < 0.001) to PI 642741 or PI 481125 are identified with blackened or shaded boxes, respectively.