title: Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays.
abstract: BACKGROUND
  Maize (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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy. m.dellacqua@sssup.it.
authors.forename: Matteo
authors.initials: M
authors.lastname: Dell'Acqua
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine, USA. dan.gatti@jax.com.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Gatti
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy. giorgio.pea@gmail.com.|Current address: Thermo Fisher Scientific, Via G.B Tiepolo 18, 20900, Monza, MB, Italy. giorgio.pea@gmail.com.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Pea
authors.affiliation: Institute of Applied Genomics, Udine, Italy. fcattonaro@igatechnology.com.
authors.forename: Federica
authors.initials: F
authors.lastname: Cattonaro
authors.affiliation: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium. frcop@psb.vib-ugent.be.
authors.forename: Frederik
authors.initials: F
authors.lastname: Coppens
authors.affiliation: Institute of Applied Genomics, Udine, Italy. folegandros89@gmail.com.|Department of Agricultural and Environmental Sciences, University of Udine, Udine, Italy. folegandros89@gmail.com.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Magris
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy. ayelaelae@gmail.com.|Current address: Department of Agricultural Research, Nay Pyi Taw, Myanmar. ayelaelae@gmail.com.
authors.forename: Aye L
authors.initials: AL
authors.lastname: Hlaing
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy. hthtaung@gmail.com.|Current address: Plant Biotechnology Center, Yangon, Myanmar. hthtaung@gmail.com.
authors.forename: Htay H
authors.initials: HH
authors.lastname: Aung
authors.affiliation: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium. hinel@psb.vib-ugent.be.|Department of Plant Systems Biology, VIB, Gent, Belgium. hinel@psb.vib-ugent.be.
authors.forename: Hilde
authors.initials: H
authors.lastname: Nelissen
authors.affiliation: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium. jobau@psb.vib-ugent.be.|Department of Plant Systems Biology, VIB, Gent, Belgium. jobau@psb.vib-ugent.be.
authors.forename: Joke
authors.initials: J
authors.lastname: Baute
authors.affiliation: Department of Agricultural Sciences, University of Bologna, Bologna, Italy. elisabetta.frascaroli@unibo.it.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Frascaroli
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine, USA. gary.churchill@jax.org.
authors.forename: Gary A
authors.initials: GA
authors.lastname: Churchill
authors.affiliation: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium. dirk.inze@psb.vib-ugent.be.|Department of Plant Systems Biology, VIB, Gent, Belgium. dirk.inze@psb.vib-ugent.be.
authors.forename: Dirk
authors.initials: D
authors.lastname: Inzé
authors.affiliation: Institute of Applied Genomics, Udine, Italy. michele.morgante@uniud.it.|Department of Agricultural and Environmental Sciences, University of Udine, Udine, Italy. michele.morgante@uniud.it.
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy. marioenrico.pe@sssup.it.
authors.forename: Mario Enrico
authors.initials: ME
authors.lastname: Pè
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D014644:Genetic Variation; D018745:Genome, Plant; D000069600:Plant Breeding; D040641:Quantitative Trait Loci; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics*