Estimating additive and non-additive genetic variances and predicting genetic merits using genome-wide dense single nucleotide polymorphism markers

PLoS One. 2012;7(9):e45293. doi: 10.1371/journal.pone.0045293. Epub 2012 Sep 13.


Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP) markers. In addition, this study for the first time proposed a method to construct dominance relationship matrix using SNP markers and demonstrated it in detail. The proposed model was implemented to investigate the amounts of additive genetic, dominance and epistatic variations, and assessed the accuracy and unbiasedness of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects (MAD), and 4) a full model including all three genetic components (MAED). Estimates of narrow-sense heritability were 0.397, 0.373, 0.379 and 0.357 for models MA, MAE, MAD and MAED, respectively. Estimated dominance variance and additive by additive epistatic variance accounted for 5.6% and 9.5% of the total phenotypic variance, respectively. Based on model MAED, the estimate of broad-sense heritability was 0.506. Reliabilities of genomic predicted breeding values for the animals without performance records were 28.5%, 28.8%, 29.2% and 29.5% for models MA, MAE, MAD and MAED, respectively. In addition, models including non-additive genetic effects improved unbiasedness of genomic predictions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding
  • Epistasis, Genetic
  • Female
  • Genetic Markers*
  • Genetic Variation
  • Genome*
  • Genome-Wide Association Study
  • Genotype
  • Inheritance Patterns*
  • Linear Models
  • Male
  • Models, Genetic*
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • Swine / genetics*
  • Weight Gain


  • Genetic Markers

Grant support

The work was performed in the project (grant no. 3405-11-0279) funded by the Danish Ministry of Food, Agriculture and Fisheries, Pig Research Centre and Aarhus University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.