Abstract
BackgroundMaize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. New tools that improve our understanding of the genetic basis of quantitative traits are needed to guide predictive crop breeding. We have produced the first balanced multi-parental population in maize, a tool that provides high diversity and dense recombination events to allow routine quantitative trait loci (QTL) mapping in maize.ResultsWe produced 1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines. The characterization of 529 MAGIC maize lines shows that the population is a balanced, evenly differentiated mosaic of the eight founders, with mapping power and resolution strengthened by high minor allele frequencies and a fast decay of linkage disequilibrium. We show how MAGIC maize may find strong candidate genes by incorporating genome sequencing and transcriptomics data. We discuss three QTL for grain yield and three for flowering time, reporting candidate genes. Power simulations show that subsets of MAGIC maize might achieve high-power and high-definition QTL mapping.ConclusionsWe demonstrate MAGIC maize’s value in identifying the genetic bases of complex traits of agronomic relevance. The design of MAGIC maize allows the accumulation of sequencing and transcriptomics layers to guide the identification of candidate genes for a number of maize traits at different developmental stages. The characterization of the full MAGIC maize population will lead to higher power and definition in QTL mapping, and lay the basis for improved understanding of maize phenotypes, heterosis included. MAGIC maize is available to researchers.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0716-z) contains supplementary material, which is available to authorized users.
Highlights
Maize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation
We provide the first description of the Multi-parent advanced intercrosses (MAGIC) maize (MM) population, the first balanced Multi-parent cross designs (MpCD) developed in maize that integrates the diversity of eight diverse inbred founder lines into 1,636 recombinant inbred lines (RIL)-F6 made available to researchers
Multi-parent crosses are the future of complex trait genetics [4]: here we have shown that the MM population contains roughly equal proportions of the founder genomes, that the genetic distance between the lines is evenly distributed and that the linkage disequilibrium (LD) decays sharply
Summary
Maize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. MpCD are produced by crossing more than two inbred founder lines in one of three ways: (1) by creating panels of recombinant inbred lines (RIL) that are mosaics of the founder genomes (for example, mouse Collaborative Cross (CC) [5] or Multi-parent Advanced Generation InterCrosses (MAGIC) populations [6,7,8]); (2) by breeding a single reference inbred line to many inbred lines and creating multiple bi-parent RIL (for example, Nested Association Mapping (NAM) panel [9], Dent and Flint panels [10]); or (3) by crossing n founders and maintaining an outbred population (for example, Diversity Outbred (DO) in mice [11, 12] and Heterogenous Stock (NIH-HS) in rat [13]). Combined with founder expression data, these populations can lead to the discovery of variants associated with both expression and structural variation
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