Data from: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR

“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. 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. Using the software polyBreedR, an R package for the
manipulation and analysis of polyploid marker data, the RMSE for
imputation by linkage analysis was 0.15 in a small half-diallel population
(N=85), which was significantly lower than the RMSE of 0.42 with the
Random Forest method. 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.