University collaborates with Affymetrix on genotyping arrays for sustainable wheat production

The University of Bristol has developed the Axiom Wheat Genotyping Array (Axiom Wheat Array), consisting of 817,000 markers analysed data from experiments as part of an effort to understand wheat genetics and breeding with a goal of ensuring guaranteed sustainable production, as part of the Biotechnology and Biological Sciences Research Council (BBSRC)-funded Wheat Improvement Strategic Program (WISP).

The aim of WISP is to produce new and novel wheat germplasm via three complementary 'pillars' (landraces, synthetics, and ancestral gene introgression), each of which will broaden the pool of genetic variation in elite wheat cultivars by a different route.

The design of Axiom Wheat Array is unique because it includes functional and positional annotation information for a variety of wheat species. The SNPs (DNA sequence variations) on Axiom Wheat Array include markers from hexaploid landraces and those from the synthetic and ancestral lines exhibiting different ploidy levels. Results from the array will be presented at the 2014 Plant and Animal Genome conference (PAG XXII), in San Diego, California.

"The results from Axiom Wheat Array are fantastic and have helped WISP achieve one of the main goals, which is to track the different segments of the 'wheat relative' line and incorporate them into hexaploid bread wheat through the breeding process. The follow-on focused arrays will offer wheat breeders the capability to understand polymorphisms between their current breeding lines," says professor Keith Edwards, project leader and professor of Cereal Functional Genomics at the School of Biological Sciences and a member of the University's Cabot Institute.

"We were thrilled to be able to complete the design and analysis in less than three months and in time to present the results at the Plant and Animal Genome meeting. This was made possible mainly because of the expertise, commitment, and collaborative efforts of the bioinformatics and product support teams at Affymetrix," he adds.

A subset of the 817,000 markers found on Axiom Wheat Array will be transferred with 100 per cent fidelity onto Axiom 384HT-format arrays to create multiple focused wheat array designs.

Each of these Axiom wheat array designs will contain approximately 35,000 markers and each design is expected to serve a different purpose in wheat breeding. The 384HT format enables ultra high-throughput processing of 384 samples simultaneously and will be used to screen thousands of samples in a highly cost-effective manner. Affymetrix will make these new Axiom arrays publicly available before the spring wheat season.

With Affymetrix' advanced bioinformatics and innovative design strategies, Axiom genotyping array designs routinely support genome-wide genotyping and accurately call the genotypes of both diploid and polyploid species.

The Axiom Wheat Genotyping arrays in the 384HT format will complement the catalog of Axiom Genotyping Arrays for Agrigenomics that are available for multiple species including salmon, maize, strawberry, rose, 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 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 platform.