Multifactorial methods integrating haplotype and epistasis effects for genomic estimation and prediction of quantitative traits

Yang Da, Zuoxiang Liang, Dzianis Prakapenka

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


The rapid growth in genomic selection data provides unprecedented opportunities to discover and utilize complex genetic effects for improving phenotypes, but the methodology is lacking. Epistasis effects are interaction effects, and haplotype effects may contain local high-order epistasis effects. Multifactorial methods with SNP, haplotype, and epistasis effects up to the third-order are developed to investigate the contributions of global low-order and local high-order epistasis effects to the phenotypic variance and the accuracy of genomic prediction of quantitative traits. These methods include genomic best linear unbiased prediction (GBLUP) with associated reliability for individuals with and without phenotypic observations, including a computationally efficient GBLUP method for large validation populations, and genomic restricted maximum estimation (GREML) of the variance and associated heritability using a combination of EM-REML and AI-REML iterative algorithms. These methods were developed for two models, Model-I with 10 effect types and Model-II with 13 effect types, including intra- and inter-chromosome pairwise epistasis effects that replace the pairwise epistasis effects of Model-I. GREML heritability estimate and GBLUP effect estimate for each effect of an effect type are derived, except for third-order epistasis effects. The multifactorial models evaluate each effect type based on the phenotypic values adjusted for the remaining effect types and can use more effect types than separate models of SNP, haplotype, and epistasis effects, providing a methodology capability to evaluate the contributions of complex genetic effects to the phenotypic variance and prediction accuracy and to discover and utilize complex genetic effects for improving the phenotypes of quantitative traits.

Original languageEnglish (US)
Article number922369
JournalFrontiers in Genetics
StatePublished - Oct 14 2022

Bibliographical note

Funding Information:
This research was supported by the National Institutes of Health’s National Human Genome Research Institute, grant R01HG012425, as part of the NSF/NIH Enabling Discovery through Genomics (EDGE) Program; grant 2020-67015-31133 from the USDA National Institute of Food and Agriculture; and project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The use of the Ceres and Atlas computers in this research was supported by USDA-ARS projects 8042-31000-002-00-D and 8042-31000-001-00-D.

Publisher Copyright:
Copyright © 2022 Da, Liang and Prakapenka.


  • SNP
  • epistasis
  • haplotype
  • multifactorial model

PubMed: MeSH publication types

  • Journal Article


Dive into the research topics of 'Multifactorial methods integrating haplotype and epistasis effects for genomic estimation and prediction of quantitative traits'. Together they form a unique fingerprint.

Cite this