Allelic configurations of SNP (di-allelic and multi-allelic) and indel markers in an octoploid. Panel A) Di-allelic SNPs: To qualify as di-allelic, only two alleles can be detected at the site. The “marker allele” is present only in one subgenome (the marker subgenome), within which it can be homozygous present, heterozygous, or homozygous absent. In case 1 a single probe can be used to interrogate the marker because the indicated polymorphism is neither A/T nor G/C. In case 2 two probes must be used because the indicated polymorphism is an A/T (also true for a G/C polymorphism). Panels B and C) Multi-allelic SNPs: More than two alleles are represented at the site. Three distinctive cases are shown for tri-allelic (Panel B) and for tetra-allelic sites (Panel C). In tri-allelic case 1 the marker polymorphism is G/T, while there is a C at the same site in the background subgenomes. Genotyping of this marker would require two probes. In case 2 the marker polymorphism is G/T, with a background G in one subgenome and a background C in the others. Genotyping of this marker would require two probes. In case 3 there are two marker polymorphisms, a G/T in one subgenome and a G/C in another, while there is a C at the site in the background subgenomes. Three probes and a non-standard analysis algorithm are needed for this polymorphism. Genotyping of case 3 tri-allelic markers, and of tetra-allelic markers (Panel C) is currently not possible. Panel D) Di-allelic indels: Only two alleles are represented at the site. Although they are genomic insertions and deletions, the indel polymorphisms are genotyped as SNPs, and various probing strategies may be employed depending upon the sequence characteristics within and immediately adjacent to the indel.