Smith et al. [ 21] provides a comprehensive review of mixed model approaches to the analysis of METs, which considers the phenotypic response as partitioned into cultivar effects, environmental effects, cultivar by environment interaction effects, and within-environment effects.
In our EAM, all the main-effect quantitative trait loci (QTLs), environmental effects, QTL-by-environment interactions and QTL-by-QTL interactions were included in a full model and estimated by empirical Bayes approach.
To test for genetic effects, environment effects, and genotype-by-environment-interaction effects on the smolts, one-half of the progeny from each cross group was reared in a traditional hatchery environment.
Observed phenotypes depend on many factors, including environmental effects, genotype-by-environment (GxE) interactions, and epistatic interactions (Lewontin 2000; Chandler et al. 2013).
QTL identified in individual environment were expected to contain mixed effects of additive effect (A) and additive-by-environment interaction effect (AE), while QTLs obtained across environments were with A and AE, respectively.
QTL mapping based on the data estimated in individual photoperiod environments led to the identification of the QTL with mixed effects of additive effect (A) and additive-by-environment interaction effect (AE) for flowering time in the RILs in maize.
Firstly, QTL analyses for flowering time and photoperiod sensitivity in maize were conducted in individual photoperiod environments separately, and then, the total genetic effect was partitioned into additive effect (A) and additive-by-environment interaction effect (AE) by using a mixed-model-based composite interval mapping (MCIM) method.
Grain yield data were analyzed using the additive main effects and multiplicative interaction (AMMI) and the genotype main effect plus genotype-by-environment interaction (GGE) biplot methods.
Crossover was the main effect of genotype-by-environment interaction indicating that the selection of high-yielding and stable peach genotype would be a laborious task for breeders.
