Allo-Polyploid Genotyping Algorithm on Affymetrix® Axiom® Arrays

A variety of plant species offer unique challenges to accurate genotyping due to complexity associated with polyploid genomes with a high density of segmental duplications. In allo-polyploid species, SNPs segregating in one sub-genome tend to exhibit particular clustering behaviors due to the allele-dosage contribution of the alternate sub-genomes. As a result, such allo-polyploid SNPs demonstrate three major genotype clustering patterns; the diploid-like pattern where sub-genomes’ effects counteract each other (denoted as AB/(AA)n/(BB)n) and the two compressed, shifted diploid patterns (denoted as AB/(AA)n or AB/(BB)n).  AxiomGT1 is an automated clustering algorithm used by the Axiom^® Genotyping Console^™Software, and features adaptive, dynamic clustering.  However, such allo-polyploid patterns pose difficulties with sample genotyping performance. Therefore, there is a need for continuing improvement of statistical methods for accurate genotyping of allo-polyploid species.

We have developed a statistical approach called “FitAllo” that is compatible with the Affymetrix^® Axiom^® Genotyping Solution.  FitAllo is derived from “fitTetra” (Voorrips et al.;BMC Bioinformatics 2011, 12:172) and employs the Baum-Welch algorithm to ascertain specific SNP patterns [AB/(AA(n)/(BB)n or AB/(AA)n or AB/(BB)n] in order to derive the center locations of each genotype cluster. These cluster locations can then be used as SNP-specific priors for the AxiomGT1 algorithm. We applied FitAllo to bread wheat varietals (allo-hexaploid) genotype data from Axiom^® custom genotyping arrays and demonstrated substantially improved genotyping accuracy in allo-polyploids. We anticipate FitAllo to be widely applicable in plant genotyping in conjunction with the Axiom^® Genotyping Solution.