Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

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.

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

“…We previously reported similar result based on 1582 SSR markers [4]. Our results are also comparable with the genetic studies using MAGIC populations developed in other crops such as maize [43], rice [28] and wheat [44]. Thus, we believe that our Upland cotton MAGIC population is an excellent resource for GWAS as well as other genetic studies.…”

“…In this study, the LD blocks are more or less uniform across the genome except on a few chromosomes (Additional file 8). This uniformity may also be due to the lack of selection during population development, since human selection inflates LD [43]. …”

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

“…Multi-parent crosses have become increasingly popular for QTL studies (Gnan et al 2014; Huang et al 2014; Tsaih et al 2014; Dell’Acqua et al 2015) due to the idiosyncratic histories of existing reference populations and the desire to meet ideal properties of uniform allele frequencies, randomized assortment, and recombination. Here, we demonstrate the need for proactive monitoring and potential corrective measures to maintain the utility of populations like the DO.…”

Genome‐wide dissection of the maize ear genetic architecture using multiple populations

“…Conversely, the multi-parent advanced generation intercross (MAGIC) population has a balanced contribution from all founders (Kover et al, 2009;Bandillo et al, 2013). Recently, a maize MAGIC population was established with eight diverse founder lines that provided a useful resource for an understanding of the genetic basis of quantitative traits (Dell'Acqua et al, 2015). Unfortunately, the development of NAM and MAGIC populations requires extensive field and laboratory effort, which greatly limits the application of the multi-parent population design to other plant species or for traits that have shown little variation in the currently available NAM and MAGIC populations.…”