A New Approach for Copy Number Estimation in Polyploids

In polyploids, the copy number (or marker dosage) of a dominant marker is the number of copies of a dominant allele carried by a parent. It is estimated using a hypothesis testing procedure. This procedure, however, suffers from issues associated with multiple testing and assumes all chromosomes pair uniformly. In this paper, a new Bayesian approach is presented for estimating the copy number of a dominant marker in polyploids. By using a probability model that explicitly accounts for preferentially paired chromosomes, the Bayesian approach more closely reflects reality. Its superiority over the hypothesis testing procedure is evidenced through the analysis of simulated and sugarcane data. The Bayesian methodology described in this paper is implemented in a C program, bdose, which is freely available (see Supplementary Materials).