, 214:6 | Cite as

Genomic prediction and GWAS of Gibberella ear rot resistance traits in dent and flint lines of a public maize breeding program

  • Sen Han
  • Thomas Miedaner
  • H. Friedrich Utz
  • Wolfgang Schipprack
  • Tobias A. Schrag
  • Albrecht E. MelchingerEmail author


Gibberella ear rot (GER) is a serious threat to maize cultivation, causing grain yield losses and contamination with mycotoxins. Genomic prediction (GP) has great potential to accelerate resistance breeding against GER. However, small training sets (TS) consisting of both phenotyped and genotyped individuals are a challenge for obtaining high prediction accuracy (ρ) in GP. A potential solution would be combining small-size populations across heterotic pools. However, genetic heterogeneity between populations in terms of segregating QTL, linkage disequilibrium (LD) pattern and genomic relationships can impair ρ of GP. In this study, we investigated the genetic architecture of GER severity, deoxynivalenol concentration (DON) and days to silking with genome-wide association studies within two elite panels of 130 dent and 114 flint lines from the maize breeding program of the University of Hohenheim tested in four environments. We also assessed the consistency of LD pattern and genomic relationships between the two heterotic pools. Furthermore, we compared four GP approaches differing in the composition of the TS with lines from a single or combined pool(s) and statistical models with marker effects identical or different but correlated between pools. We detected two and six QTL for DON within the dent and flint pool, respectively, but no common QTL. The LD pattern was consistent between pools for marker pairs ≤ 10 kb apart. GP across pools yielded low or even negative ρ. Combined-pool GP had no higher ρ than within-pool GP, regardless of the statistical model. Our findings underline the importance of investigating the genetic heterogeneity between populations prior to implementing GP using combined TS.


Maize Fusarium GWAS Genomic prediction Training set Heterotic pools 



Across-pool prediction


Combined-pool prediction, assuming marker effects different but correlated across pools


Combined-pool prediction, assuming identical marker effects across pools




Days to silking


Genomic best linear unbiased prediction


Genomic estimated breeding values


Gibberella ear rot


Genomic prediction


Genome-wide association studies


Linkage disequilibrium


Training set


Validation set


Within-pool prediction



This research was supported by Deutsche Forschungsgemeinschaft (DFG) Grant No. ME 2260/6-1. Part of the SNP genotyping was funded by the German Ministry of Education and Research within the AgroClustEr “Synbreed – Synergistic plant and animal breeding” (FKZ: 0315528d). We are grateful to Vilson Mirdita and the staff of the Agricultural Research Station at Eckartsweier and Hohenheim for conducting the field trials for this study. We acknowledge Christian Riedelsheimer’s documentation on using the GenABEL R package and Haixiao Hu’s suggestions for performing genome-wide association studies. We appreciate advices from Pedro Correa Brauner and Willem Molenaar for improving the text of the manuscript.

Compliance with ethical standards

Ethical approval

The experiments reported in this study comply with the current laws of Germany.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10681_2017_2090_MOESM1_ESM.docx (794 kb)
Supplementary material 1 (DOCX 794 kb)


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Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2017

Authors and Affiliations

  • Sen Han
    • 1
    • 3
  • Thomas Miedaner
    • 2
  • H. Friedrich Utz
    • 1
  • Wolfgang Schipprack
    • 1
  • Tobias A. Schrag
    • 1
  • Albrecht E. Melchinger
    • 1
    Email author
  1. 1.Institute of Plant Breeding, Seed Science and Population Genetics (350a)University of HohenheimStuttgartGermany
  2. 2.State Plant Breeding Institute (720)University of HohenheimStuttgartGermany
  3. 3.Monsanto Holland B.VBergschenhoekThe Netherlands

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