Marker-assisted selection (MAS) for resistance genes (R-genes), identified using molecular markers and quantitative trait loci (QTL) analysis, is now possible in many crops. MAS can be used to pyramid several R-genes into a single host genotype. However, this may not provide durable genetic resistance because the pathogen is exposed to a full homozygous pyramid during hybrid seed production and to a full heterozygous pyramid in the resultant hybrid. Alternative gene deployment strategies that generate genetic variability were analysed, for hybrid cereal cultivars of pearl millet, maize, sorghum and rice, using maintainer lines (B-lines) with two smaller complementary pyramids. An F1 seed parent, produced on two such B-lines, can be used to produce a three-way hybrid. All target loci are heterozygous for resistance alleles in the F1 seed parent, and the pathogen is exposed in the hybrid to a host population that is heterogeneous and heterozygous for alleles at the resistance loci targeted by MAS. Alternatively, single-cross hybrids can be made on seed parents that are maintained by two B-lines that differ for the complementary resistance gene pyramids. In a cross-pollinated crop, the B-lines are allowed to intermate to produce a synthetic B-line. In an inbreeding crop, the B-lines are equivalent to a two-component multiline variety. In inbreeding crops, because there is no intermating between the B-line components, the resultant synthetic seed parents have a higher frequency of genotypes with resistance alleles (R-alleles) at several resistance loci. However, in both cross-pollinated and inbreeding crops the genotypic structure in the hybrids is almost the same. All alternatives to a single-cross hybrid having a full pyramid produce hybrid cultivars having lower frequencies of resistance alleles. The frequency of genotypes having R-alleles at several loci increases greatly in both seed parent and hybrid when the overall frequency of R-alleles in the maintainer lines increases. This is simply done by adding a maintainer line that has a full pyramid or by the component lines having overlapping pyramids.