Genomic prediction of single crosses in the early stages of a maize hybrid breeding pipeline

Dnyaneshwar C. Kadam, Sarah M. Potts, Martin O. Bohn, Alexander E. Lipka, Aaron J. Lorenz

Research output: Contribution to journalArticlepeer-review

89 Scopus citations


Prediction of single-cross performance has been a major goal of plant breeders since the beginning of hybrid breeding. Recently, genomic prediction has shown to be a promising approach, but only limited studies have examined the accuracy of predicting single-cross performance. Moreover, no studies have examined the potential of predicting single crosses among random inbreds derived from a series of biparental families, which resembles the structure of germplasm comprising the initial stages of a hybrid maize breeding pipeline. The main objectives of this study were to evaluate the potential of genomic prediction for identifying superior single crosses early in the hybrid breeding pipeline and optimize its application. To accomplish these objectives, we designed and analyzed a novel population of single crosses representing the Iowa Stiff Stalk synthetic/non-Stiff Stalk heterotic pattern commonly used in the development of North American commercial maize hybrids. The performance of single crosses was predicted using parental combining ability and covariance among single crosses. Prediction accuracies were estimated using cross-validation and ranged from 0.28 to 0.77 for grain yield, 0.53 to 0.91 for plant height, and 0.49 to 0.94 for staygreen, depending on the number of tested parents of the single cross and genomic prediction method used. The genomic estimated general and specific combining abilities showed an advantage over genomic covariances among single crosses when one or both parents of the single cross were untested. Overall, our results suggest that genomic prediction of single crosses in the early stages of a hybrid breeding pipeline holds great potential to redesign hybrid breeding and increase its efficiency.

Original languageEnglish (US)
Pages (from-to)3443-3453
Number of pages11
JournalG3: Genes, Genomes, Genetics
Issue number11
StatePublished - 2016

Bibliographical note

Funding Information:
We are indebted to Rita H. Mumm for her vision in the design of the unique germplasm used in this study. We thank the editor and four anonymous reviewers of the earlier versions of this manuscript for their helpful input and suggestions. This research was supported by United States Department of Agriculture National Institute of Food and Agriculture grant ILLU-802-614. D.C.K. was supported by an Indian Council of Agricultural Research International Fellowship, and S.M.P. was supported by an Illinois Corn Marketing Board Fellowship in Plant Breeding.

Publisher Copyright:
© 2016 Kadam et al.


  • GenPred
  • Generalcombining ability
  • Genomic prediction
  • Genomic selection
  • Genotyping by sequencing
  • Hybrid breeding
  • Shared data resources
  • Specific combining ability


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