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KEY MESSAGE : Wheat yellow mosaic virus resistance of Madsen is governed by two complementary QTLs, Qym1 and Qym2 , located on chromosome arms 2DL and 3BS. Wheat yellow mosaic, caused by Wheat yellow mosaic virus (WYMV), is one of the most serious wheat diseases in East Asia. In this study, recombinant inbred lines (RILs, F₉) from a cross between cultivars Madsen (resistant) and Hokushin (susceptible) grown in a WYMV-infected nursery field were tested for the presence of WYMV in leaves by enzyme-linked immunosorbent assay (ELISA) and genotyped by using genome-wide molecular markers. Two major QTLs were detected: Qym1 located between Xgwm539 and Xgwm349 on chromosome 2DL and Qym2 located between Xbarc147 and Xwmc623 on chromosome 3BS. The resistance alleles for both QTLs originated from Madsen. The third QTL Qym3 located near Xwmc457 on chromosome 4D, where the resistant allele for this QTL originated from Hokushin. Although the Qym3 was rather minor, it was essential to complement Qym1 and Qym2 for complete avoidance of WYMV infection. Near-isogenic lines carrying the resistance QTLs were developed by repeated backcrosses using Madsen as the donor parent and Hokushin as the recurrent parent. The lines that were resistant to WYMV (as tested by ELISA) were homozygous for the Madsen alleles at both Qym1 and Qym2. Qym1 dominance was partial, whereas that of Qym2 was nearly complete. Qym1 was closely linked to Xwmc41; Qym2 was closely linked to Xwmc754. These markers will be useful in marker-assisted selection in wheat breeding for WYMV resistance; this study will facilitate cloning the WYMV resistance genes.