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Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays
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 ma...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566846/ https://www.ncbi.nlm.nih.gov/pubmed/26357913 http://dx.doi.org/10.1186/s13059-015-0716-z |
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author | Dell’Acqua, Matteo Gatti, Daniel M. Pea, Giorgio Cattonaro, Federica Coppens, Frederik Magris, Gabriele Hlaing, Aye L. Aung, Htay H. Nelissen, Hilde Baute, Joke Frascaroli, Elisabetta Churchill, Gary A. Inzé, Dirk Morgante, Michele Pè, Mario Enrico |
author_facet | Dell’Acqua, Matteo Gatti, Daniel M. Pea, Giorgio Cattonaro, Federica Coppens, Frederik Magris, Gabriele Hlaing, Aye L. Aung, Htay H. Nelissen, Hilde Baute, Joke Frascaroli, Elisabetta Churchill, Gary A. Inzé, Dirk Morgante, Michele Pè, Mario Enrico |
author_sort | Dell’Acqua, Matteo |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0716-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4566846 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-45668462015-09-12 Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays Dell’Acqua, Matteo Gatti, Daniel M. Pea, Giorgio Cattonaro, Federica Coppens, Frederik Magris, Gabriele Hlaing, Aye L. Aung, Htay H. Nelissen, Hilde Baute, Joke Frascaroli, Elisabetta Churchill, Gary A. Inzé, Dirk Morgante, Michele Pè, Mario Enrico Genome Biol Research 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0716-z) contains supplementary material, which is available to authorized users. BioMed Central 2015-09-11 2015 /pmc/articles/PMC4566846/ /pubmed/26357913 http://dx.doi.org/10.1186/s13059-015-0716-z Text en © Dell’Acqua et al. 2015 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Dell’Acqua, Matteo Gatti, Daniel M. Pea, Giorgio Cattonaro, Federica Coppens, Frederik Magris, Gabriele Hlaing, Aye L. Aung, Htay H. Nelissen, Hilde Baute, Joke Frascaroli, Elisabetta Churchill, Gary A. Inzé, Dirk Morgante, Michele Pè, Mario Enrico Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays |
title | Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays |
title_full | Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays |
title_fullStr | Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays |
title_full_unstemmed | Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays |
title_short | Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays |
title_sort | genetic properties of the magic maize population: a new platform for high definition qtl mapping in zea mays |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566846/ https://www.ncbi.nlm.nih.gov/pubmed/26357913 http://dx.doi.org/10.1186/s13059-015-0716-z |
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