SNP Genotyping of Aquaculture Species Using Affymetrix® Axiom® Genotyping Solution and Affymetrix® Genotyping Console™ Software

Array-based technologies offer the flexibility and affordability to consolidate multiple genotyping applications under a single platform. Innovations in assay and bioinformatics analysis pipelines allow for genotyping of all relevant markers of interest, even for complex genomes. Axiom® Genotyping Solution, the latest evolution of microarray technology from Affymetrix, offers a simplified genotyping workflow from DNA to data. Axiom has been optimized for validating sequencing discoveries, genome-wide analysis, and routine screening with the highest accuracy, reproducibility and affordability.

Aquaculture species including fish and amphibians are particularly difficult to genotype because of their polyploid genomes that are the result of recent whole genome duplication events. Sequencing-based genotyping techniques are cost effective but can be ineffective in genotyping aquaculture species due to missing data, false SNPs from low coverage or sequencing errors, complex genome assemblies and complicated analysis pipelines. In contrast, the Axiom® GT1 algorithm uses Bayesian statistics to accurately assign genotypes to cluster data from polyploid genomes. The easy-to-use automated analysis pipeline offers the capability to genotype thousands of samples across hundreds of thousands of markers quickly, easily and accurately. The Axiom® Genotyping Solution has been used for genotyping multiple aquaculture species including salmon, trout, catfish, and carp.

Application of microarray technology in aquaculture continues to evolve with the Axiom® 384HT format. This recent innovation in processing 384 samples simultaneously, including analysis, at extremely economical price points has enabled the technology to go from research to mainstream commercial agrigenomics.