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PMID: 22246502 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Genomic and metabolic prediction of complex heterotic traits in hybrid maize.

Nature genetics ·Vol. 44 ·No. 2 ·2012-01-15 ·Pages 217-20

Riedelsheimer C, Czedik-Eysenberg A, Grieder C, Lisec J, Technow F, Sulpice R, Altmann T, Stitt M, Willmitzer L, Melchinger AE

Abstract

Maize is both an exciting model organism in plant genetics and also the most important crop worldwide for food, animal feed and bioenergy production. Recent genome-wide association and metabolic profiling studies aimed to resolve quantitative traits to their causal genetic loci and key metabolic regulators. Here we present a complementary approach that exploits large-scale genomic and metabolic information to predict complex, highly polygenic traits in hybrid testcrosses. We crossed 285 diverse Dent inbred lines from worldwide sources with two testers and predicted their combining abilities for seven biomass- and bioenergy-related traits using 56,110 SNPs and 130 metabolites. Whole-genome and metabolic prediction models were built by fitting effects for all SNPs or metabolites. Prediction accuracies ranged from 0.72 to 0.81 for SNPs and from 0.60 to 0.80 for metabolites, allowing a reliable screening of large collections of diverse inbred lines for their potential to create superior hybrids.

MeSH Terms
Chimera/genetics,metabolism Energy Metabolism/genetics Genetic Markers Genome-Wide Association Study Genomics Hybrid Vigor/genetics Metabolomics Polymorphism, Single Nucleotide Zea mays/genetics,metabolism
Chemicals
Genetic Markers
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Riedelsheimer Christian
Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany.
Czedik-Eysenberg Angelika
Grieder Christoph
Lisec Jan
Technow Frank
Sulpice Ronan
Altmann Thomas
Stitt Mark
Willmitzer Lothar
Melchinger Albrecht E
References (43)
43 references, click to expand
  1. Genome-based prediction of testcross values in maize.
    Theor Appl Genet. 2011 Jul;123(2):339-50 PMID: 21505832
  2. Metabolomics for functional genomics, systems biology, and biotechnology.
    Annu Rev Plant Biol. 2010;61:463-89 PMID: 19152489
  3. The B73 maize genome: complexity, diversity, and dynamics.
    Science. 2009 Nov 20;326(5956):1112-5 PMID: 19965430
  4. Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.
    PLoS One. 2009 Dec 24;4(12):e8451 PMID: 20041112
  5. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement.
    Nat Biotechnol. 2006 Apr;24(4):447-54 PMID: 16531992
  6. GCTA: a tool for genome-wide complex trait analysis.
    Am J Hum Genet. 2011 Jan 7;88(1):76-82 PMID: 21167468
  7. Starch as a major integrator in the regulation of plant growth.
    Proc Natl Acad Sci U S A. 2009 Jun 23;106(25):10348-53 PMID: 19506259
  8. Performance of genomic selection in mice.
    Genetics. 2008 Sep;180(1):611-8 PMID: 18757934
  9. Prediction of total genetic value using genome-wide dense marker maps.
    Genetics. 2001 Apr;157(4):1819-29 PMID: 11290733
  10. Genomic selection in plant breeding: from theory to practice.
    Brief Funct Genomics. 2010 Mar;9(2):166-77 PMID: 20156985
  11. Gas chromatography mass spectrometry-based metabolite profiling in plants.
    Nat Protoc. 2006;1(1):387-96 PMID: 17406261
  12. Genomic selection: prediction of accuracy and maximisation of long term response.
    Genetica. 2009 Jun;136(2):245-57 PMID: 18704696
  13. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness.
    Nat Genet. 2006 Feb;38(2):203-8 PMID: 16380716
  14. Family-based association tests for genomewide association scans.
    Am J Hum Genet. 2007 Nov;81(5):913-26 PMID: 17924335
  15. Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm.
    Theor Appl Genet. 2011 Jun;123(1):11-20 PMID: 21404061
  16. Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach.
    Plant Biotechnol J. 2010 Oct;8(8):900-11 PMID: 20353402
  17. Metabolic networks: how to identify key components in the regulation of metabolism and growth.
    Plant Physiol. 2010 Feb;152(2):428-44 PMID: 20018593
  18. Different models of genetic variation and their effect on genomic evaluation.
    Genet Sel Evol. 2011 May 17;43:18 PMID: 21575265
  19. Accuracy of genotypic value predictions for marker-based selection in biparental plant populations.
    Theor Appl Genet. 2009 Dec;120(1):151-61 PMID: 19841887
  20. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species.
    PLoS One. 2011 May 04;6(5):e19379 PMID: 21573248
  21. The metabolic signature related to high plant growth rate in Arabidopsis thaliana.
    Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4759-64 PMID: 17360597
  22. Genome-wide association study of leaf architecture in the maize nested association mapping population.
    Nat Genet. 2011 Feb;43(2):159-62 PMID: 21217756
  23. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize.
    Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):6893-8 PMID: 21482771
  24. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population.
    Nat Genet. 2011 Feb;43(2):163-8 PMID: 21217757
  25. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines.
    BMC Genet. 2002 Oct 7;3:19 PMID: 12366868
  26. Novel throughput phenotyping platforms in plant genetic studies.
    Trends Plant Sci. 2007 Oct;12(10):433-6 PMID: 17719833
  27. Invited review: Genomic selection in dairy cattle: progress and challenges.
    J Dairy Sci. 2009 Feb;92(2):433-43 PMID: 19164653
  28. Plant genetic resources: what can they contribute toward increased crop productivity?
    Proc Natl Acad Sci U S A. 1999 May 25;96(11):5937-43 PMID: 10339521
  29. Metabolomics-assisted breeding: a viable option for crop improvement?
    Trends Genet. 2009 Jan;25(1):39-48 PMID: 19027981
  30. Predicting genetic predisposition in humans: the promise of whole-genome markers.
    Nat Rev Genet. 2010 Dec;11(12):880-6 PMID: 21045869
  31. Linkage disequilibrium--understanding the evolutionary past and mapping the medical future.
    Nat Rev Genet. 2008 Jun;9(6):477-85 PMID: 18427557
  32. Genome partitioning of genetic variation for complex traits using common SNPs.
    Nat Genet. 2011 Jun;43(6):519-25 PMID: 21552263
  33. Prediction of testcross means and variances among F3 progenies of F1 crosses from testcross means and genetic distances of their parents in maize.
    Theor Appl Genet. 1998 Mar;96(3-4):503-12 PMID: 24710890
  34. Increased accuracy of artificial selection by using the realized relationship matrix.
    Genet Res (Camb). 2009 Feb;91(1):47-60 PMID: 19220931
  35. Extension of the bayesian alphabet for genomic selection.
    BMC Bioinformatics. 2011 May 23;12:186 PMID: 21605355
  36. Accurate prediction of genetic values for complex traits by whole-genome resequencing.
    Genetics. 2010 Jun;185(2):623-31 PMID: 20308278
  37. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
    J Comput Biol. 2002;9(5):687-705 PMID: 12487758
  38. Variation of enzyme activities and metabolite levels in 24 Arabidopsis accessions growing in carbon-limited conditions.
    Plant Physiol. 2006 Dec;142(4):1574-88 PMID: 17085515
  39. Investigation of the bottleneck leading to the domestication of maize.
    Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4441-6 PMID: 9539756
  40. TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.
    BMC Bioinformatics. 2009 Dec 16;10:428 PMID: 20015393
  41. Heterosis: revisiting the magic.
    Trends Genet. 2007 Feb;23(2):60-6 PMID: 17188398
  42. Common SNPs explain a large proportion of the heritability for human height.
    Nat Genet. 2010 Jul;42(7):565-9 PMID: 20562875
  43. The genetics of plant metabolism.
    Nat Genet. 2006 Jul;38(7):842-9 PMID: 16751770
Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.1033
Published
2012-01-15
Epub
2012-00-15
Pages
217-20
Language
English
Region
United States
NLM ID
9216904
Subset
IM
External Links
PubMed source DOI: 10.1038/ng.1033 View journal details
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