Chromosomal distributions of dosage variation and parent-informative markers in the dihaploid population. (A) Read depth standardized to tetraploid Alca Tarma in nonoverlapping 250-kb bins of chromosome 1. Each individual in the dihaploid population is represented by a single line. Dihaploids that are trisomic for any chromosome are represented by colored lines. For example, chromosome 1 trisomic LOP868.238 is displayed as a green line. The plot also displays unique segmental dosage variants, one starting at 24 Mb and involving a trisomic of eight (pink line), a second one at 67 Mb and involving two trisomics of two (overlapping magenta and blue lines), and a terminal deletion of the short arm in an otherwise euploid line (gray line). (B–F) Circos plots for the 12 chromosomes. For each chromosome, 167 lines are shown. Aneuploids of any chromosome are uniquely colored and all other individuals are colored gray. (B) Standardized read-depth plots of all chromosomes smoothed to 1-Mb bins. (C) Percent haploid inducer allele at all parent-informative marker loci in nonoverlapping 1-Mb bins. Refer to Figure S3 for expected haploid inducer allele percentages derived from simulated hybrid analyses. (D) Log10-scaled counts of parent-informative markers in nonoverlapping 1-Mb bins. (E) Genes per 1-Mb sliding window and 200-kb step. (F) Percent repeat sequence per 1-Mb sliding window and 200-kb step. Chr, chromosome.
