Genome-Wide Association Studies for Autopolyploids - Potato

Genome-wide association studies (GWAS) are widely used in diploid species to discover causal loci in diversity and breeding populations. The most common statistical method for GWAS is the Q+K mixed model, in which Q and K refer to the structure and kinship matrices, respectively, that are used to control for the effects of population structure. The objectives of this research were to (1) adapt the Q+K methodology for use with bi-allelic, co-dominant markers in autotetraploids, (2) test these models in a diversity panel of 200 potato lines, and (3) make the software available as a user-friendly R package. Unlike earlier approaches to association mapping in autotetraploids, we studied a number of models for gene action, including additive, simplex dominance, and duplex dominance, while employing a faster algorithm that can accommodate larger datasets. Consistent with previous studies, highly significant QTL for tuber shape and eye depth colocalized on chromosome 10 when using an additive model. Under the assumption of complete dominance, the chromosome 10 QTL were not significant, illustrating the influence of the gene model on the results. For most traits, only marginally significant QTL were detected, most likely due to insufficient statistical power. For simulated traits with a heritability of 0.3, the median power was only 0.03. Potential causes for the low power were investigated by varying the population size and marker density in simulated, random-mating autotetraploid populations. The results of the simulation suggest that the size of the diversity panel was the primary limiting factor for statistical power.