Genome-based prediction of testcross values in maize

  • Theresa Albrecht
  • Valentin Wimmer
  • Hans-Jürgen Auinger
  • Malena Erbe
  • Carsten Knaak
  • Milena Ouzunova
  • Henner Simianer
  • Chris-Carolin Schön
Original Paper


This is the first large-scale experimental study on genome-based prediction of testcross values in an advanced cycle breeding population of maize. The study comprised testcross progenies of 1,380 doubled haploid lines of maize derived from 36 crosses and phenotyped for grain yield and grain dry matter content in seven locations. The lines were genotyped with 1,152 single nucleotide polymorphism markers. Pedigree data were available for three generations. We used best linear unbiased prediction and stratified cross-validation to evaluate the performance of prediction models differing in the modeling of relatedness between inbred lines and in the calculation of genome-based coefficients of similarity. The choice of similarity coefficient did not affect prediction accuracies. Models including genomic information yielded significantly higher prediction accuracies than the model based on pedigree information alone. Average prediction accuracies based on genomic data were high even for a complex trait like grain yield (0.72–0.74) when the cross-validation scheme allowed for a high degree of relatedness between the estimation and the test set. When predictions were performed across distantly related families, prediction accuracies decreased significantly (0.47–0.48). Prediction accuracies decreased with decreasing sample size but were still high when the population size was halved (0.67–0.69). The results from this study are encouraging with respect to genome-based prediction of the genetic value of untested lines in advanced cycle breeding populations and the implementation of genomic selection in the breeding process.



This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr “Synbreed—Synergistic plant and animal breeding” (FKZ: 0315528A).

Supplementary material

122_2011_1587_MOESM1_ESM.doc (540 kb)
Supplemental Fig. 1 Linkage disequilibrium between pairs of marker loci within the same linkage group as a function of physical distance on the reference map for 31 parental inbred lines (DOC 540 kb)


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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Theresa Albrecht
    • 1
  • Valentin Wimmer
    • 1
  • Hans-Jürgen Auinger
    • 1
  • Malena Erbe
    • 2
  • Carsten Knaak
    • 3
  • Milena Ouzunova
    • 3
  • Henner Simianer
    • 2
  • Chris-Carolin Schön
    • 1
  1. 1.Plant BreedingTechnische Universität MünchenFreisingGermany
  2. 2.Department of Animal SciencesGeorg-August-Universität GöttingenGöttingenGermany
  3. 3.KWS SAAT AGEinbeckGermany

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