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

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Biotechnology for a sustainable economy (Bio-Economy)
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.
Keywords
ARABIDOPSIS-THALIANA, COMPLEX TRAITS, COLLABORATIVE CROSS, FLOWERING-TIME, DNA-SEQUENCING DATA, LONG NONCODING RNAS, INTER-CROSS POPULATION, RECOMBINANT INBRED LINES, GENOME-WIDE ASSOCIATION, QUANTITATIVE TRAIT LOCI

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Chicago
Dell’Acqua, Matteo, Daniel M Gatti, Giorgio Pea, Federica Cattonaro, Frederik Coppens, Gabriele Magris, Aye L Hlaing, et al. 2015. “Genetic Properties of the MAGIC Maize Population: a New Platform for High Definition QTL Mapping in Zea Mays.” Genome Biology 16.
APA
Dell’Acqua, M., Gatti, D. M., Pea, G., Cattonaro, F., Coppens, F., Magris, G., Hlaing, A. L., et al. (2015). Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. GENOME BIOLOGY, 16.
Vancouver
1.
Dell’Acqua M, Gatti DM, Pea G, Cattonaro F, Coppens F, Magris G, et al. Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. GENOME BIOLOGY. 2015;16.
MLA
Dell’Acqua, Matteo, Daniel M Gatti, Giorgio Pea, et al. “Genetic Properties of the MAGIC Maize Population: a New Platform for High Definition QTL Mapping in Zea Mays.” GENOME BIOLOGY 16 (2015): n. pag. Print.
@article{6951208,
  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.},
  articleno    = {167},
  author       = {Dell'Acqua, Matteo and Gatti, Daniel M and Pea, Giorgio and Cattonaro, Federica and Coppens, Frederik and Magris, Gabriele and Hlaing, Aye L and Aung, Htay H and Nelissen, Hilde and Baute, Joke and Frascaroli, Elisabetta and Churchill, Gary A and Inz{\'e}, Dirk and Morgante, Michele and P{\`e}, Mario Enrico},
  issn         = {1465-6906},
  journal      = {GENOME BIOLOGY},
  keyword      = {ARABIDOPSIS-THALIANA,COMPLEX TRAITS,COLLABORATIVE CROSS,FLOWERING-TIME,DNA-SEQUENCING DATA,LONG NONCODING RNAS,INTER-CROSS POPULATION,RECOMBINANT INBRED LINES,GENOME-WIDE ASSOCIATION,QUANTITATIVE TRAIT LOCI},
  language     = {eng},
  pages        = {23},
  title        = {Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays},
  url          = {http://dx.doi.org/10.1186/s13059-015-0716-z},
  volume       = {16},
  year         = {2015},
}

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