Current panel name: Potato_DArTag_4K (2.0)
Panel name for soft release: Potato_DArTag_EiB_4K_Diploid (1.0)
Version description: (1.0) original 4K design, described as the “V2” design in Endelman et al. 2024
(2.0) updated 4K design with additional essential markers; most recent version available
Availability: Yes
Description:
Potato_DArTag_4K version 2 is a mid-density DArTag panel for 3,921 marker loci, developed for potato breeding and genetics. The panel was developed by external collaborators at the University of Wisconsin-Madison, the International Potato Center, the University of Minnesota, and the University of Georgia-Athens, in collaboration with DArT, for public use. DArTag assays use custom-designed oligos to amplify targeted SNPs and their flanking sequences prior to Next Generation Sequencing (NGS). The sequenced amplicons are demultiplexed and targeted SNPs/haplotypes are analyzed using DArT P/L’s proprietary pipeline.
The genome-wide marker loci were selected from the potato Infinium SNP array platforms, primarily the 22K V3 and 31K V4 arrays, to maintain compatibility with existing potato marker data while maximizing genome coverage and polymorphism rates. In addition to genome-wide markers, the panel includes essential markers for breeding-relevant traits, including resistance to potato virus Y, golden cyst nematode, and potato wart, as well as multi-allelic markers for maturity and tuber shape.
The current version, Potato_DArTag_4K (2.0), builds on the previous Potato_DArTag_EiB_4K_Diploid (1.0) panel. The two versions use largely overlapping marker sets, with version 2.0 retaining the core genome-wide marker framework and adding several additional essential markers for breeding-relevant traits. The panel is suitable for genotyping diploid and tetraploid potato germplasm for breeding decisions, marker-assisted selection, linkage mapping, genomic prediction, and evaluation of trait-associated loci. Usage of the panel outside of Solanum tuberosum, or outside the germplasm represented during panel development, has not been fully tested and could result in higher missing data and fewer informative markers. Access to the panel can be found on DArT’s website (https://www.diversityarrays.com/services/targeted-genotying/).
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 microhaplotype detected in each sample and at each locus. Breeding Insight requests that the MADC file and sample metadata also be sent to bi-genotyping@ufl.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:
The potato DArTag panel was developed by external collaborators, and is described in Endelman et al. 2024. Potato DArTag panels were developed as part of the CGIAR Excellence in Breeding (EiB) Platform’s mid-density genotyping program. The original 2.5K design was supported by the EiB Platform and the Crops to End Hunger Initiative; the 4K design, which carries forward a substantial number of those genome-wide markers, was supported by USDA NIFA Award 2019-51181-30021, with additional support from PepsiCo for genomic resources used in marker validation. Please cite this publication when reporting results based on this panel:
Endelman, J. B., Kante, M., Lindqvist-Kreuze, H., Kilian, A., Shannon, L. M., Caraza-Harter, M. V., Vaillancourt, B., Mailloux, K., Hamilton, J. P., & Buell, C. R. (2024). Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR. The Plant Genome, 17, e20484. https://doi.org/10.1002/tpg2.20484
