The 5175 bin markers were used for linkage analysis based on their scores in the 188 KJ-RILs. In total, 4959 bin markers were mapped to the wheat genetic map. The co-segregated markers (redundant markers) were then added to the high-density genetic map based on information of bin serial number and the genetic information of the corresponding bin markers. A high-density genetic map with 119566 loci spanning 4424.4 cM was constructed (Table S2). Of these loci, 119001 were SNP markers derived from the Wheat660K SNP array, and the remaining 565 markers were reported previously by Cui et al.3. Of the 119001 SNPs, 83953 (70.5%) were transitions, and 35048 (29.5%) were transversions (data not shown). Most markers were mapped to the B (44.6%) and A genomes (43.7%), and only 11.7% markers were mapped to the D genome. For the map lengths, the A, B, and D genomes covered 36.4%, 27.7%, and 35.8% of the total map length, respectively. The chromosome sizes ranged from 84.4 cM (chromosome 1BL) to 289.1 cM (chromosome 5D), averaging 210.7 cM per chromosome. The number of markers on each chromosome ranged from 78 (chromosome 1BL) to 13898 (chromosome 3B), with a mean of 5693.6 loci per chromosome. Due to the 1BL/1RS translocation of KN9204, the 1RS- or 1BS-specific markers not only showed co-segregation but also exhibited distorted segregation in the KJ-RILs as shown by Cui et al.3. These markers were excluded from the linkage analysis and map construction, which reduced the genetic maps for analysis to 1BL only. In addition, no markers on chromosome 5BS were polymorphic between KN9204 and J411, resulting in the release of the 5BL genetic map only. Of the 119566 loci, 33598 (28.1%) were distributed on chromosomal regions near the centromeres. Marker density per genetic distance unit peaked at the centromeric regions, possibly due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes (Fig. 1). The 4 959 bin markers are shown in the genetic map (Fig. 2). The following mapping-bin sets were observed: approximately 3.7% and 3.2% of the markers were unique for genomes A and B, respectively, and approximately 9.6% of the markers for the D genome showed unique segregation patterns.Figure 1Distribution of the 119 566 loci on the 21 wheat chromosomes. The 21 circles indicate the 21 wheat chromosomes, with 7D to 1D, 7B to 1B, and 7A to 1A from inside to outside, respectively. Each chromosome was evenly divided into 100 segments based on the map length, which are shown with different colours. The arc lengths indicate the percentage of markers on each segment (The total number of markers on the corresponding chromosome divided by the number of markers on the segments). The arc in red colour indicates the chromosomal bins near the centromere. The upper left histogram in the circle indicates the distribution of markers on each chromosome; the upper right histogram in the circle indicates the distribution of markers near the centromere on each chromosome; the bottom right histogram in the circle indicates the distribution of map length on each chromosome; the bottom left histogram in the circle indicates the distribution of markers in/near the coding sequences. Figure 2The high-density genetic map of wheat developed using an RIL population derived from the cross of cultivars KN9204 and J411. For the redundant loci that showed co-segregation in the 188 KJ-RILs, only one unique informative marker is shown in this figure. The approximate positions of the centromeres are indicated by pink. Short arms are at the top. The positions of the marker loci are indicated using a ruler on the left side of this figure. The names of the marker loci are listed to the right of the corresponding chromosomes. Loci in red were best hits to Chinese Spring (CS) contigs of the short arm of the corresponding chromosomes. Loci in green were best hits to CS contigs of the long arm of the corresponding chromosomes. Loci in black were unknown. Contigs from chromosome 3B were not separated into short/long arm bins, as individual arm datasets were not generated for this chromosome in the Chromosome Survey Sequence (CSS) project.