Targeted genotyping-by-sequencing of potato and software for imputation

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTM technology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTM SNP array to maximize genome coverage and polymorphism rates. When sample depth was summarized by marker, the power law μ~σ0.8 was consistently observed between the mean (μ) and standard deviation (σ). The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root-mean-squared-error) less than 0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Our hypothesis that linkage analysis would be highly accurate for imputing tetraploid marker data was confirmed: the RMSE was 0.15 compared to 0.95 by the Random Forest method in a half-diallel population. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics. ### Competing Interest Statement A. Kilian is an employee of Diversity Arrays Technology, the company that provides the DArTag genotyping service.