High-throughput automated genotyping of plants requires a technology that is robust in the face of complex plant genomes, and cost-effective for processing large numbers of samples.
Plant genomes may be polyploid, comprised of high copy number sequences, and/or sub-population structural diversity. The Axiom® Genotyping Solution has three components that address these complexities. One, it uses the Axiom GT1 algorithm which dynamically adapts to cluster variation produced by plant genomes. Two, novel genotyping algorithms are used for markers in regions of high genomic complexity. Three, markers are sorted into relevant genomic classes, and the potentially most accurate and polymorphic markers are sorted into the PolyHighResolution class. The analysis workflow, algorithms and results are presented for allo-octoploid, cultivated strawberry samples that were genotyped with the IStraw90TM Axiom® Genotyping Array (in a 96-array layout) designed by the RosBREED project. Genotypes for SNPs in the PolyHighResolution class have greater than 99.8% reproducibility, and low Mendelian inheritance error rates.
Cost effective genotyping is enabled by the Axiom® 384-array layout, where 384 samples are simultaneously processed in a 384 microplate for analyzing up to 35,000 polyploid or 50,0000 diploid SNPs per sample. Markers that have been identified as highly performing, such as those in the PolyHighResolution class as identified by the Axiom® Genotyping Analysis on Axiom 96-array layout can be transferred to Axiom 384-array layout with 100% fidelity. The multi-species capability of the Axiom 384-array layout enables the design of a single array for markers from all rosaceous species that can be used in marker-assisted breeding.
