Speeding up QTL Cloning in Maize: Power and Prospects of the MAGIC Maize Population

The first step to QTL cloning is the discovery of genetic loci linked to phenotypes of interest. Increasing the power, definition and speed by which such genetic loci are pinpointed on the genome is crucial for the success of this challenging task. New breeding designs emerged to address this need by increasing diversity and recombination events in QTL mapping panels. We discuss the MAGIC maize, a 1,636 recombinant inbred lines mapping panel we developed by intercrossing eight diverse Zea mays inbred lines in a balanced scheme. Each MAGIC recombinant inbred line is a unique mosaic of the diversity of the original founders, the population altogether collecting more than a hundred thousand recombination events. The increased diversity in elevated minor allele frequency permits the MAGIC maize to bridge the flexibility of association mapping approaches to the power of linkage mapping, speeding up the discovery of candidates for cloning. The MAGIC maize leverages transcriptomics data and full sequencing of the founder lines to reach single-gene definition. We genotyped and phenotyped a subset of the MAGIC maize and used it to show the general features of the population, identifying candidate genes for complex phenotypes. Mapping power simulations showed that the MAGIC maize may allow efficient QTL mapping even when few hundred lines are phenotyped, favoring its use in controlled conditions experiments. We discuss the perspectives that the MAGIC maize discloses in maize QTL mapping and cloning, and the further steps to exploit this resource, including the production of recombinant intercrosses for the study of heterosis.