An F8:9 recombinant inbred line (RIL) population including 188 lines derived from a cross between Kenong 9204 (KN9204) and Jing 411 (J411) (denoted as KJ-RILs), 65 KN9204-derived advanced lines/authorized varieties, three parental lines of KN9204, three control varieties from the Winter Wheat Performance Trial of the Northern Huang-Huai Regional Nursery of China, and Chinese Spring (CS) were genotyped using the 630517 SNPs on the Wheat660K SNP array as probes. The sample call rates ranged from 18.6% to 100.0%, with an average of 98.9% for the 265 accessions (data not shown). The scores for the probes were classified into one of the following six categories according to the cluster patterns produced by the Affymetrix software (Table S1): (i) Poly High Resolution (PHR) (188040; 29.8%); (ii) No Minor Homozygote (NMH) (133246; 21.1%); (iii) Off-Target Variant (OTV) (18471; 3.0%); (iv) Mono High Resolution (MHR) (163308; 25.9%); (v) Call Rate Below Threshold (CRBT) (22635; 3.6%); and (vi) Other (91425, 14.5%). Only the first three groups (PHR, NMH and OTV) were considered useful, and they accounted for 53.9% of the Wheat660K SNP array probes.