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 ..., , , # Data from \"Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR\"

[https://doi.org/10.5061/dryad.8pk0p2nw4](https://doi.org/10.5061/dryad.8pk0p2nw4)

File S1. Potato DArTag V1 data for 703 samples in Variant Call Format (VCF). The V1 panel had 2503 markers.

File S2. Metadata for the samples in File S1 (CSV). First column (id) matches the sample ID in File S1. The second column (year) is the submission year: 2020, 2021, or 2022.

File S3. Potato DArTag V2 data for 375 samples in Variant Call Format (VCF). The V2 panel had 3915 markers.

File S4. DArTag Missing Allele Discovery Counts for the samples in File S3 (CSV). The first three columns are \"AlleleID\", \"CloneID\", and \"AlleleSequence\". CloneID is the marker name; AlleleID is the haplotype name, and AlleleSequence is the 81 bp haplotype. The first row contains the plate id, and the second row contains the sample id.

File S5. Potato V4 SNP array data for 298 samples and 15,187 markers, in Variant Call Form...