Validation of the POPSEQ genetic map. (A) POPSEQ positions  of barley high-confidence genes  were compared with the genetic positions of their putative orthologs in our wheat POPSEQ map. Assignment of orthologous groups agreed in 87% of the cases. Genetic positions within the orthologous group showed high collinearity (Spearman’s ρ = 0.936). Known translocation events relative to barley involving wheat chromosomes 4A, 5A and 7B  could be traced with high precision. (B) Collinearity with a previous genetic map of the Synthetic × Opata population constructed through genotyping by sequencing . A total of 11,000 out of 20,000 genotyping-by-sequencing tags carrying SNPs could be uniquely mapped to our assembly. Chromosome assignments agreed for 99.5% of the genotyping-by-sequencing tags aligned to anchored sequence scaffolds. Genetic positions within linkage groups were highly correlated (Spearman’s ρ = 0.995). (C) Chromosome shotgun contigs were anchored to the same genetic framework as the meraculous scaffolds of W7984. Genetic positions of contigs and scaffolds matched by sequence alignment differed by less than 5 cM in 99.1% of the cases. Chromosomes are separated by blue lines, subgenomes by red lines.