Theoretical and Applied Genetics

, Volume 120, Issue 2, pp 451–461 | Cite as

Prediction of hybrid performance in maize using molecular markers and joint analyses of hybrids and parental inbreds

  • Tobias A. Schrag
  • Jens Möhring
  • Albrecht E. MelchingerEmail author
  • Barbara Kusterer
  • Baldev S. Dhillon
  • Hans-Peter Piepho
  • Matthias Frisch
Original Paper


The identification of superior hybrids is important for the success of a hybrid breeding program. However, field evaluation of all possible crosses among inbred lines requires extremely large resources. Therefore, efforts have been made to predict hybrid performance (HP) by using field data of related genotypes and molecular markers. In the present study, the main objective was to assess the usefulness of pedigree information in combination with the covariance between general combining ability (GCA) and per se performance of parental lines for HP prediction. In addition, we compared the prediction efficiency of AFLP and SSR marker data, estimated marker effects separately for reciprocal allelic configurations (among heterotic groups) of heterozygous marker loci in hybrids, and imputed missing AFLP marker data for marker-based HP prediction. Unbalanced field data of 400 maize dent × flint hybrids from 9 factorials and of 79 inbred parents were subjected to joint analyses with mixed linear models. The inbreds were genotyped with 910 AFLP and 256 SSR markers. Efficiency of prediction (R 2) was estimated by cross-validation for hybrids having no or one parent evaluated in testcrosses. Best linear unbiased prediction of GCA and specific combining ability resulted in the highest efficiencies for HP prediction for both traits (R 2 = 0.6–0.9), if pedigree and line per se data were used. However, without such data, HP for grain yield was more efficiently predicted using molecular markers. The additional modifications of the marker-based approaches had no clear effect. Our study showed the high potential of joint analyses of hybrids and parental inbred lines for the prediction of performance of untested hybrids.


Amplify Fragment Length Polymorphism Simple Sequence Repeat Marker General Combine Ability Amplify Fragment Length Polymorphism Marker Grain Yield 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This article is dedicated to Prof. Dr. H. F. Utz on the occasion of his 70th birthday. The project was supported by the German Research Foundation DFG in the framework program ‘Heterosis in Plants’ (research grants FR 1615/3-1 and 3-3). We gratefully acknowledge the staff at the Plant Breeding Research Station at Eckartsweier and Hohenheim for conducting the field experiments and Christine Beuter for skilled technical assistance in the SSR marker lab. We thank Keygene N.V. for providing the AFLP marker data and mapping information. We thank the anonymous reviewers for their helpful comments and suggestions.


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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Tobias A. Schrag
    • 1
  • Jens Möhring
    • 2
  • Albrecht E. Melchinger
    • 1
    Email author
  • Barbara Kusterer
    • 3
  • Baldev S. Dhillon
    • 1
  • Hans-Peter Piepho
    • 2
  • Matthias Frisch
    • 4
  1. 1.Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
  2. 2.Bioinformatics Unit, Institute for Crop Production and Grassland ResearchUniversity of HohenheimStuttgartGermany
  3. 3.HYBRO Saatzucht GmbH & Co. KGSchenkenbergGermany
  4. 4.Institute of Agronomy and Plant Breeding IIJustus-Liebig-University GiessenGiessenGermany

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