Current panel name: AStrawberry DArTag UC Davis K (4.0)
Version description: (4.0)
Availability: Yes
Public Strawberry DArTag Panel
Description: USC developed mid-density panels of molecular inversion probes (MIPs) to be deployed with the “DArTag” marker platform to provide a low-cost, high-throughput genotyping solution for strawberry genomic prediction. In total, 7742 target single nucleotide polymorphism (SNP) regions were used to generate MIP assays that were tested with a screening panel of 376 octoploid Fragaria accessions. We evaluated the performance of DArTag assays based on genotype 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 alternate alleles, supporting accurate genotype calling while producing marker genotypes that can be treated as functionally diploid for quantitative genetic analysis. The 3K and 5K target SNPs show high levels of polymorphism i 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.
Results and Data Sharing: DArT offers multiple data output formats. Users are encouraged to work with DArT to ensure the data type they desire is provided. Users are also strongly encouraged to request the Missing Allele Discovery Counts (MADC) file from DArT when placing orders. This file contains the read counts of each 81-bp michrohaplotype detected in each sample and at each locus. Breeding Insight requests that the MADC file and sample metadata also be sent to bi-genotyping@cornell.edu to be added to the public microhaplotype database for fixed allele naming and public data sharing. Proprietary sample metadata can be privatized in the database for IP protection.
Citation and attribution: Strawberry panel with 5K markers developed with technical and financial support from the team at University California Davis (Steven Knapp, Mitchell Joseph Feldmann and Michael Hardigan) and described in the paper by Hardigan et al 2023. Please refer to this paper when reporting the results based on using this panel. Hardigan, M. A., Feldmann, M. J., Carling, J., Zhu, A., Kilian, A., Famula, R. A., Cole, G. S., & Knapp, S. J. (2023). A medium-density genotyping platform for cultivated strawberry using DArTag technology. The Plant Genome, 16, e20399.https://doi.org/10.1002/tpg2.20399
