For all subjects, leaf tissues were sampled. Genomic DNA was extracted and hybridized on the Wheat660K SNP genotyping array by Compass Biotechnology Company (Beijing, China). The DNA samples were prepared, and the chip genotyping was performed on the Wheat660K SNP array according to the Affymetrix Axiom 2.0 Assay Manual Workflow protocol. DNA integrity was confirmed on agarose gels, and DNA quantity was measured spectrophotometrically. The Wheat660K chip contains 630517 markers (http://wheat.pw.usda.gov/GG2/index.shtml). Variant quality from the Wheat660K chip genotyping was initially assessed according to Affymetrix best practices. The 188 RILs and their parents were aslo assayed using the ‘Wheat PstI (TaqI) 2.3D’ DArT array (the medium density array) (http://www.triticarte.com.au/). The PCR-based markers were genotyped as described in our previous study3.