Resistance gene deployment strategies in cereal hybrids using marker-assisted selection: Gene pyramiding, three-way hybrids, and synthetic parent populations

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 s ingle host genotype. However, this may not provide durable genetic resistan ce because the pathogen is exposed to a full homozygous pyramid during hybr id seed production and to a full heterozygous pyramid in the resultant hybr id. Alternative gene deployment strategies that generate genetic variabilit y were analysed, for hybrid cereal cultivars of pearl millet, maize, sorghu m and rice, using maintainer lines (B-lines) with two smaller complementary pyramids. An F-1 seed parent, produced on two such B-lines, can be used to produce a three-way hybrid. All target loci are heterozygous for resistanc e alleles in the F-1 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 c an be made on seed parents that are maintained by two B-lines that differ f or 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 i nbreeding crop, the B-lines are equivalent to a two-component multiline var iety. In inbreeding crops, because there is no intermating between the B-li ne components, the resultant synthetic seed parents have a higher frequency of genotypes with resistance alleles (R-alleles) at several resistance loc i. However, in both cross-pollinated and inbreeding crops the genotypic str ucture in the hybrids is almost the same. All alternatives to a single-cros s hybrid having a full pyramid produce hybrid cultivars having lower freque ncies of resistance alleles. The frequency of genotypes having R-alleles at several loci increases greatly in both seed parent and hybrid when the ove rall frequency of R-alleles in the maintainer lines increases. This is simp ly done by adding a maintainer line that has a full pyramid or by the compo nent lines having overlapping pyramids.