SNP Genotyping of Autotetraploid Species Using Affymetrix Axiom® Genotyping Solution and Fittetra Software

Background: Large-scale, high-throughput SNP genotyping of humans has become very common due to the development of high-density DNA oligonucleotide arrays. Plant and animal genomes have additional challenges beyond those found in the human genome, including the complex structure of polyploid genomes and high levels of nucleotide and structural diversity. Automated genotype calling software for autotetraploid species has only recently become available. These calls are determined by categorizing the two allele signals at a bi-allelic SNP into five possible genotypes (aaaa, aaab, aabb, abbb, bbbb). Affymetrix Axiom^® Genotyping Solution produces allelic data that can be processed by automated genotype calling software for tetraploid species.

Results: We describe the data analysis workflow for genotyping, assigning call values, and visualizing results with genotype cluster plots for autotetraploid species. Our examples of the workflow begin with processing allelic intensity data using high-density Affymetrix Axiom^® microarray data on two autotetraploid species. Summarized allelic intensity data was then generated using Axiom Genotyping Solution and Axiom^® Best Practices Workflow. The R package fitTetra (Voorrips, et al., BMC Bioinformatics 12:172, 2011), which was developed specifically to produce automated genotype calls for tetraploid species, was used with Axiom Genotyping Solution output to produce the calls for both data sets. Genotype calls were validated with visual inspections of genotype cluster plots from the Affymetrix-developed R package SNPolisher^TM, which contains functions for visualizing autotetraploid intensity clusters. This workflow covers the entire genotyping process for autotetraploid species.