Success of marker-assisted breeding (MAB) largely depends on the availability of cost-effective genotyping platforms. Single nucleotide polymorphisms (SNPs) are the choice of molecular markers for establishment of such a platform. The resolution of SNP markers available in maize is now high enough for genomewide linkage disequilibrium mapping. Several strategies have been developed to facilitate large-scale MAB, including the use of seed DNA-based genotyping to replace leaf DNA-based genotyping and the combination of selective genotyping and pooled DNA analysis to replace the entire population genotyping for genetic mapping of quantitative trait loci (QTL) with relatively small effects as well as for linked and interacting QTL. The use of pooled DNA analysis with Illumina?s Golden Gate/Bead Station platform has been successfully applied to genetic mapping of kernel hardness and maize steak virus resistance. For various purposes of MAB, platforms should be developed that function well at three different scales, i.e., major gene introgression (target genes only) for a few markers per trait and for multiple traits; marker-assisted backcrossing for a few target markers plus genomewide markers (a few hundreds to thousands) for background selection; and genomewide assay including marker-assisted recurrent selection using several hundreds to millions of markers for hundreds or thousands of plants. Data management and decision-support tools should be developed to replace time consuming manual data manipulation and analysis processes. All these new methodologies offer solutions to increasing the scale and power of molecular breeding while decreasing unit costs and in some cases reducing overall project costs.

Global Maize Program

English

Lucia Segura

INT2735

CIMMYT Staff Publications Collection