Genotype calling using the Miscanthus GoldenGate™ array. The graphs in panels A-F plot normalized theta (ratio of signal intensities assayed for A and B SNP alleles) against normalized R (signal intensity) for each individual represented as a colored square. Panels A, C, and E illustrate markers that cluster as predicted for a biallelic SNP, which segregate as AA (red), AB (yellow), or BB (blue). Panels B, D, and F illustrate markers that cluster as predicted for a SNP distinguishing alleles for one of two duplicated and unlinked loci, where theta is skewed by the relative dosage of A and B SNPs. In all panels, clusters are defined as sharing alleles with either the Grosse Fontaine (green circles) or Undine (pink circles) parents, individuals that fall outside the cluster are marked as "no calls" (NC, grey), and the doubled haploid genotype is indicated by the black arrow. Panel G reports the relative fraction of genotyped segregating SNPs within each clustering type among the Grosse Fontaine and Undine parents, the population of their F1 progeny, as well as the two doubled haploids and their respective parents. Single cluster markers (fixed differences between paralogs) behave similarly in diploids and doubled haploids. In contrast, while diploid accessions show extensive heterozygosity at segregating loci (two- and three-cluster markers), doubled haploids show no heterozygosity.