A medium-density genotyping platform for cultivated strawberry using DArTag technology

Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high-density ge- netic marker platforms designed for strawberry. We developed mid-density pan- els of molecular inversion probes (MIPs) to be deployed with the ‘DArTag’ marker platform to provide a low-cost, high-throughput genotyping solution for straw- berry genomic prediction. In total, 7,742 target SNP regions were used to gener- ate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on geno- type segregation, amplicon coverage, and their ability to produce subgenome- specific amplicon alignments to the FaRR1 assembly and subsequent alignment- based variant calls with strong concordance to DArT’s alignment-free, count- based genotype reports. We used a combination of marker performance metrics and physical distribution in the FaRR1 assembly to select 3K an..., , , # Title of Dataset: A medium-density genotyping platform for cultivated strawberry using DArTag technology

Supplemental data files associated with the study 'A medium-density genotyping platform for cultivated strawberry using DArTag technology'. Supplemental figures and tables can be obtained directly from The Plant Genome published manuscript page.

## Description of the Data and file structure

\*Includes supplemental data files associated with the study 'A medium-density genotyping platform for cultivated strawberry using DArTag technology'.

Supplemental File 1. Target SNPs, alleles, and corresponding FaRR1 design regions submitted for MIP assay design in round-1 (panel 1) and round-2 (panel 2).

Supplemental File 2. DArTag report generated for MIP assays constructed after round-1 submission.

Supplemental File 3. DArTag report generated for MIP assays constructed after round-2 submission.

Supplemental File 4. Variant site database (VCF format) containing target SNPs in the 5K M...