Affymetrix Axiom® Strawberry Genotyping Array Delivers Automated Analysis for High-Resolution Genome Scanning of Octoploid Strawberry

04 Nov 2013
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Affymetrix, Inc. announces the launch of Axiom Strawberry Genotyping Array (also called International Strawberry 90K SNP array or IStraw90), the only solution that successfully enables high-resolution genotyping and fully automated data analysis of the octoploid strawberry genome. This 90,000 SNP array will enable complex trait research and set the stage for multi-trait, marker-assisted breeding of the cultivated garden strawberry (Fragaria × ananassa).

The cultivated garden strawberry is an allo-octoploid with a chromosome number of 2n=8x=56. While there are other genotyping technologies available to scan genomes of agricultural species at high resolution, most have been designed for diploids. With Affymetrix' advanced bioinformatics and innovative design strategy, Axiom Genotyping Solution provides genome-wide genotyping and accurately calls the genotypes of both diploid and polyploid species. This technology has already been successfully applied to complex genomes such as maize, rose, wheat, trout, and salmon.

Axiom Strawberry Genotyping Array was designed through a public-private partnership between Affymetrix and the International RosBREED SNP Consortium (IRSC), an arm of the "RosBREED" project dedicated to the genetic improvement of rosaceous crops. The RosBREED team including Genotyping Team Leader Nahla Bassil (USDA-ARS, Corvallis), Demonstration Breeder Tom Davis (University of New Hampshire geneticist), and Pedigree-Based Analysis Team Leader Eric van de Weg (Wageningen University & Research Center) partnered with the Affymetrix array design and bioinformatics teams to devise SNP selection and data analysis strategies. RosBREED announced the availability of the array through its September 2013 newsletter. Preliminary results from the array were presented at the 2013 annual conference of the American Society for Horticultural Science.

"IStraw90 gives us the capability to create high-resolution genetic maps of the strawberry genome and work towards enabling marker-assisted breeding for strawberry breeders worldwide," stated Nahla Bassil. "The International RosBREED SNP consortium has been working towards enabling discovery and validation of valuable trait loci. IStraw90 will facilitate many of RosBREED's goals and expedite marker-assisted breeding in strawberry."

"The successful design and analysis of the data from the allo-octoploid strawberry genome was possible only because of the expertise, commitment, and collaborative efforts of the Axiom myDesign custom array, bioinformatics, and product support teams within Affymetrix," stated Eric van de Weg. "It is awesome to have the tools to construct such high marker-density maps generated in such a short time. We expect this array to be a valuable resource for genome-wide analysis and marker-assisted breeding in many American, European and other breeding programs."

"Genotyping the octoploid strawberry genome demonstrates the power and precision of the Axiom Genotyping platform to type genetic variants within complex genomes," said Andy Last, Executive Vice President of the Genetic Analysis Business Unit at Affymetrix. "The array design process and updates to the automated analysis software used with Axiom Strawberry Genotyping Array are significant milestones for our platform because they enable the worldwide plant and animal genotyping community to leverage the Axiom myDesign customization process and analysis software to genotype even more species of interest."

Axiom Strawberry Genotyping Array will complement the catalog of Axiom Agrigenomics Genotyping Arrays that are available for multiple species, including bovine, chicken, and buffalo. These products have been used for genome-wide association studies, quantitative trait locus mapping, genome mapping, and breeding activities that make use of marker-assisted selection and genomic selection. As scientists make progress in decoding genomes of various plants, animals, and fish using next-generation sequencing platforms, they can advance their research and commercial objectives by translating those discoveries to routine applications on the Axiom Genotyping platform.

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Sarah Thomas
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