Evaluation of a genome-wide approach to multiple marker association considering different marker densities

Genome-wide approaches to analyze single nucleotide polymorphism (SNP) data have proliferated due to the increased availability and affordability of markers, but in practice a small number of markers may be selected from sets that do not approach dense genome-wide coverage. This study focused on a genome-wide approach to identify markers useful to a breeding program using a Bayesian method to estimate effects for markers distributed across the genome at varied densities. A simulated dataset containing 4665 individual phenotypes for a quantitative trait and genotypes for 6000 SNPs spaced in 0.1 cM increments across six chromosomes was analyzed using a Bayesian approach in which effects for all single markers are simultaneously estimated. The dataset was also analyzed with marker densities reduced to 0.5, 1.0, 2.0 and 5.0 cM. Type I errors were not a major concern but replications of each analysis were performed to determine acceptance of estimated marker effects.

The Bayesian analysis of the original dataset was able to estimate genetic values for markers in a small number of regions while shrinking other marker effects to zero. Analysis of the reduced density datasets also showed clear signals in a small number of regions where some effects appeared to be distributed across multiple markers. Replicates of the analyses provided evidence for regions with moderate and large effects.

A Bayesian multiple marker approach appears to be suitable for predicting genetic values, even with reduced density datasets where large numbers of markers are not yet available for many species. These predicted genetic values can be implemented in marker assisted selection programs.