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Genetic analysis using quality protein maize (QPM) recombinant inbred lines derived from K0326Y QPM and W64Ao2 identified three quantitative trait loci (QTL) in bins 1.06, 7.02 and 9.03 associated with opaque2 endosperm modification. We evaluated the effects of these QTLs on protein accumulation and starch physicochemical properties. The QTL in bin 1.06 is close to α-zein genes, and vitreous individuals with this QTL had increased accumulation of 19-kDa α-zein, 27-kDa γ-zein and legumin-1. The QTL in bin 7.02 corresponds to the γ-zein locus, and greater accumulation of this protein was found in vitreous individuals. The QTL in bin 9.03 is close to starch biosynthetic genes; greater accumulation of granule-bound starch synthase and amylose was observed in vitreous kernel samples with this locus and that in bin 1.06, as well as less gelatinization enthalpy and crystallinity. Vitreous kernels contained …