Estimation of Interaction Effects among Nucleotide Sequence Variants in Animal Genomes

Abstract

Estimating genetic interaction effects in animal genomics would be one of the most challenging studies because the phenotypic variation for economically important traits might be largely explained by interaction effects among multiple nucleotide sequence variants under various environmental exposures. Genetic improvement of economic animals would be expected by understanding multi-locus genetic interaction effects associated with economic traits. Most analyses in animal breeding and genetics, however, have excluded the possibility of genetic interaction effects in their analytical models. This review discusses a historical estimation of the genetic interaction and difficulties in analyzing the interaction effects. Furthermore, two recently developed methods for assessing genetic interactions are introduced to animal genomics. One is the restricted partition method, as a nonparametric grouping-based approach, that iteratively utilizes grouping of genotypes with the smallest difference into a new group, and the other is the Bayesian method that draws inferences about the genetic interaction effects based on their marginal posterior distributions and attains the marginalization of the joint posterior distribution through Gibbs sampling as a Markov chain Monte Carlo. Further developing appropriate and efficient methods for assessing genetic interactions would be urgent to achieve accurate understanding of genetic architecture for complex traits of economic animals.

The quantitative genetic basis of clinal divergence in phenotypic plasticity

“…The extent to which adaptive evolution occurs predominately via additive or nonadditive effects has direct implications for speciation models and the evolution of reproductive isolation (Dobzhansky ; Mayr ; Carson and Templeton ; Orr ), the evolution of sex and recombination (Maynard Smith ; Barton ), the maintenance of genetic variation (Gimelfarb ; Hermisson et al. ), animal and plant breeding (Lee and Kim ; Fethi et al. ), and conservation genetics (Fenster et al.…”