DOI: 10.25338/b8gw62
title: Data from: A medium-density genotyping platform for cultivated strawberry using DArTag technology

description: 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 and 5K production panels for genotyping of large strawberry
 populations. We show that the 3K and 5K DArTag panels are able to target
 and amplify homologous alleles within subgenomic sequences with low
 amplification bias between reference and alter- nate alleles, supporting
 accurate genotype calling while producing marker geno- types that can be
 treated as functionally diploid for quantitative genetic analy- sis. The
 3K and 5K target SNPs show high levels of polymorphism in diverse F. ×
 ananassa germplasm and UC Davis cultivars, with mean pairwise diversity
 (π) estimates of 0.40 and 0.32, and mean heterozygous genotype frequencies
 of 0.35 and 0.33, respectively.
description: # 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 MIP
 panel and WGS-validated OTVs with coverage from 5K MIP amplicon sequences.
 Supplemental File 5. Variant site database (VCF format) containing target
 SNPs in the 3K MIP panel and WGS-validated OTVs with coverage from 3K MIP
 amplicon sequences. ## Sharing/access Information Links to other publicly
 accessible locations of the data: -currently none-