Estimation of copy number in polyploid plants: the good, the bad, and the ugly

Genetic studies in polyploid plants rely heavily on the collection of data from dominant marker loci. A dominant marker locus is a locus for which only the presence or absence of an observable (dominant) allele is recorded. Before these marker loci can be used for genetic exploration, the number of copies of a dominant allele carried by a parent (copy number) must be determined for each marker locus. Copy number in polyploids is estimated using a hypothesis testing procedure. The performance of this estimation procedure has never been evaluated. In this paper, I quantify whether the highly sought after single-copy markers can be accurately identified, if the performance of the estimation procedure improves with increasing sample size, and whether the estimation procedure is capable of accurately estimating the copy number of high copy markers. I found that the probability of incorrectly estimating copy number is quite low and that more data can actually reduce the accuracy of the estimation procedure when the testing assumptions are violated. Fortunately, when a significant result is obtained, it is almost always correct. The challenge often is in obtaining a significant result.