Figure 2

Schematic representation of SNP identification and BSA in polyploid genomes. A) Schematic representation of a homoeologous SNP between the A and B genome (C/T, broken line rectangle) and of an inter-varietal SNP (or hemi-SNP) between LDN and RSL65 (C/G, full line rectangle). The homoeologous SNP generates the same Maq ambiguity code in both parents (C/T = Y), whereas the hemi-SNP generates a unique ambiguity code (S) in the parental line with the informative base (G in bold red). Figure adapted from [21]. B) Schematic representation of the composition of alleles for a SNP that is closely linked to GPC-B1 in the low and high bulks. The reference A genome is indicated at the top with additional reads aligning below. The homoeologous SNP (C/T) and the hemi-SNP (C/G) are shown. The ratio between LDN and RSL65 plants in each bulk is shown (LDN:RSL65), as is the calculated BFR of the informative base G.