Figure 1

Summary of re-sequencing panel. (a) Evolution of the hexaploid wheat genome. The tetraploid wheat T. turgidum (AABB) originated by the hybridization of T. urartu with the close unidentified relative of Ae. speltoides occurred about 0.58 to 0.82 million years ago according to the genome-wide divergence time estimate [10]. The origin of hexaploid wheat occurred about 10,000 years ago [11] by the hybridization of T. turgidum with Ae. tauschii (DD) [12]. Marcussen et al. [10] suggested that Ae. tauschii might have originated by homoploid hybrid speciation (shown by dashed arrows). (b) Geographic distribution of 62 accessions of wheat accessions. Pie charts indicate the proportion of genetic ancestry for K = 4 inferred using Structure. (c) Efficiency of homoeologous gene capture. The depth of read coverage was extracted for each of the three copies of 47,739 homoeologous gene sets. The histogram of the log₂ transformed ratio of read coverage between A and B (red), A and D (blue), and B and D (green) genomes was plotted. Each plot shows a normal distribution with the overall mean at 0. (d) Overlap between the SNP and indel datasets generated by WEC and GBS. (e) Minor allele frequency of different functional classes of SNPs as a proportion of total SNPs within each genome and class. PTC: premature termination codons; SSD: splice-site disruptions.