The 188 KJ-RILs and their parental lines were genotyped with the Wheat660K SNP array. SNPs were rejected if they showed minor allele frequency (defined as frequency <0.3) or contained >10% missing data. Markers were binned based on their segregation patterns in the KJ-RIL population using the BIN function in IciMapping 4.1 (http://www.isbreeding.net/) according to Winfield et al.18. Markers that shared their segregation pattern with at least one other marker were retained. One marker was chosen to represent each bin on the basis of the least amount of missing data or, when the percentage of missing data was equal, at random. Markers were tested for significant segregation distortion using a chi-square test. SNPs were sorted into groups using the MAP function in IciMapping 4.1, with the previously mapped 591 loci serving as anchored markers3. A logarithm of the odds (LOD) score of 3.5 and a recombination fraction of 0.3 were used to sort the SNPs with the Kosambi mapping function70. Groups were ordered with the Kosambi mapping function within the JoinMap v. 4.0, using a LOD score ≥3 after preliminary analysis of SNPs with LOD scores ranging from 2 to 10. The long and short arms of each chromosome were identified from the IWGSC wheat survey sequence (http://www.wheatgenome.org/), and groups were orientated to have the short arm above the long arm. MapChart 2.2 (http://www.biometris.nl/uk/Software/MapChart/) was used to draw the genetic map.