The analysis of quantitative trait loci in multi-environment trials using a multiplicative mixed model

A. P. Verbyla, P. J. Eckermann, R. Thompson and B. R. Cullis

Abstract

A new approach for multi-environment quantitative trait locus (QTL) analysis based on an appropriate genetic model is presented. To accommodate a multi-environment analysis, the size of a QTL effect is assumed to be a random effect. The approach results in a multiplicative mixed model for QTL × environment interaction of the factor analytic type. The full genetic model may also include a factor analytic model for the residual genotype × environment interaction, whereas the environmental model for the non-genetic variation involves local, global, and extraneous variation. The approach is used to determine QTLs for yield in the Arapiles × Franklin doubled haploid population of the National Barley Molecular Marker Program. Analysis leads to the determination of 8 QTLs. Many of these QTLs are associated with other traits.

Keywords: factor analytic models, genotype by environment interaction, mixed models, multiplicative mixed models, QTL analysis, regression interval analysis; residual variation.

Australian Journal of Agricultural Research 54(12) 1395 - 1408 (2003) doi:10.1071/AR02239