The analysis of quantitative traits in wheat mapping populations

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

Abstract

This paper discusses the analysis of quantitative trait loci (QTLs) using molecular markers from a doubled haploid wheat mapping population arising from the Cranbrook Halberd cross. Two field trials are used to provide phenotypic information on the trait of interest, which is grain percentage protein. Methods for QTL analysis are reviewed together with methods for the analysis of field trials. The aim of the paper is to examine different approaches for QTL analysis, namely the conventional approach available in standard software, which ignores field variation, a 2-stage approach that provides adjusted phenotypic effects for a subsequent QTL analysis, and a joint marker and spatial analysis. The major effect, however, is the maturity class of the doubled haploid lines. Maturity and percent protein appear highly correlated genetically so QTL analysis shows marked changes if maturity is included as a covariate. More subtle changes occur due to field variation but this may not be the standard situation.

Keywords: best linear unbiased prediction, QTL analysis, REML, spatial analysis, field experiments.

Australian Journal of Agricultural Research 52(12) 1195 - 1206 (2001) doi:10.1071/AR01039