RWGAIM: an efficient high-dimensional random whole genome average (QTL) interval mapping approach

Mapping of quantitative trait loci (QTLs) underlying variation in quantitative traits continues to be a powerful tool in genetic study of plants and other organisms. Whole genome average interval mapping (WGAIM), a mixed model QTL mapping approach using all intervals or markers simultaneously, has been demonstrated to outperform composite interval mapping, a common approach for QTL analysis. However, the advent of high-throughput high-dimensional marker platforms provides a challenge. To overcome this, a dimension reduction technique is proposed for WGAIM for efficient analysis of a large number of markers. This approach results in reduced computing time as it is dependent on the number of genetic lines (or individuals) rather than the number of intervals (or markers). The approach allows for the full set of potential QTL effects to be recovered. A proposed random effects version of WGAIM aims to reduce bias in the estimated size of QTL effects. Lastly, the two-stage outlier procedure used in WGAIM is replaced by a single stage approach to reduce possible bias in the selection of putative QTL in both WGAIM and the random effects version. Simulation is used to demonstrate the efficiency of the dimension reduction approach as well as demonstrate that while the approaches are very similar, the random WGAIM performs better than the original and modified fixed WGAIM by reducing bias and in terms of mean square error of prediction of estimated QTL effects. Finally, an analysis of a doubled haploid population is used to illustrate the three approaches.