Linkage maps for the 4 homoeologues of linkage groups 2 and 6 from the Holiday x Korona mapping population. Allele sizes are given in the boxes next to the names of the SSR primer pairs. “X” signifies that no allele could be assigned, as some of the observed alleles could not be reliably scored. In the figure, “0” stands for a null allele. H1 indicates Holiday haplotype 1, K1 indicates Korona haplotype 1, etc. Regions highlighted in the same colour (within a homoeologue) indicate identical haplotypes. Dark grey lines connect homoeologous loci that segregated for both neighbouring homoeologues. For light grey lines, one or both of the homoeologous loci had its position imputed. An asterisk (*) indicates that the allelic composition can be switched between homoeologues due to multiple occurrences of homozygosity. A dagger (†) indicates a primer pair that amplifies on multiple heterologous chromosomes. The minimum resolution that still represents a single recombination event is 0.6 cM for regions in which both parents segregate and 1.2 cM where only one parent segregates. Any unit that is smaller occurred due to technical issues such as missing values, uninformative individuals and integration between parents. All LGs are available in Additional file 2: Figure S1.