Skip to main content
SpringerLink
Log in

Correction of database SNP accession numbers misassigned to SNPs of the 8K IRSC apple SNP array

  • Short Communication
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Accurate SNP locus identifiers are essential for the correct matching and aggregation of multiple historical datasets. The National Center for Biotechnology Information (NCBI) issued unique “submitted SNP identification” numbers (ssIDs) for every published SNP submitted to its database. Discrepant ssID information was discovered for 78 SNPs for the 8K IRSC apple SNP array while attempting to collate multiple historical datasets, and a review of the archived SNP database from the NCBI led to their correction and a collation of SNP markers with no duplicate ssIDs. As the incorrect ssIDs were subsequently republished and uploaded to the Genome Database for Rosaceae, the aim of this short communication is to report the correct NCBI ssIDs for these 78 SNPs to correctly aggregate historical SNP data, prevent perpetuation of the misassigned ssIDs in further publications, and provide a citation for correcting the misassigned ssIDs in the Genome Database for Rosaceae (because the NCBI no longer supports storage of non-human SNP data).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  • Bianco L, Cestaro A, Sargent D, Banchi E, Derdak S, Guardo N (2014) Development and validation of a 20K single-nucleotide polymorphism (SNP) whole-genome genotyping array for apple (Malus × domestica Borkh). PLoS One 9:e110377

    Article  Google Scholar 

  • Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, van de Weg E, Gardiner SE, Bassil N, Peace C (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS ONE 7:e31745

    Article  Google Scholar 

  • Jung S, Lee T, Cheng C-H, Buble K, Zheng P, Yu J, Ficklin SP, Gasic K, Scott K, Frank M, Ru S, Hough H, Evans K, Olstead M, DeVetter LW, McFerson J, Coe M, Wegrzyn JL, Staton ME, Abbott AG, Main D (2019) 15 Years of GDR: new data and functionality in the Genome Database for Rosaceae. Nucleic Acids Res. 47:D1137–D1145

    Article  Google Scholar 

  • GDR (2020) https://www.rosaceae.org/search/snp_markers/. Accessed 24 July 2020

  • NCBI (2020a) https://www.ncbi.nlm.nih.gov/snp/docs/RefSNP_about/. Accessed 24 July 2020

  • NCBI (2020b) ftp://ftp.ncbi.nih.gov/snp/organisms/archive/apple_3750/ASN1_flat/. Accessed 23 June 2020

Download references

Acknowledgements

The authors would like to thank the original authors David Chagné and Luca Bianco for reviewing these changes and their support for publishing this communication.

Funding

This project was funded by USDA NIFA Specialty Crop Research Initiative projects “RosBREED 2: Combining disease resistance with horticultural quality in new rosaceous cultivars” (2014-51181-22378), “Genome Database for Rosaceae: Empowering specialty crop research through big-data driven discovery and application in breeding” (2014-51181-22376), USDA National Institute of Food and Agriculture National Research Support Project 10; NSF Plant Genome Research Program award #444573, NSF CIF21 Data infrastructure Building Blocks award #1443040; USDA Hatch project 1014919, Washington Tree Fruit Research Commission, Washington State University, and the University of Queensland.

Author information

Authors and Affiliations

  1. Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, 4072, Australia

    Daniel A. Edge-Garza, Miguel Villamil-Castro & Craig Hardner

  2. Department of Horticulture, Washington State University, Pullman, WA, 99164, USA

    Dorrie Main

Authors
  1. Daniel A. Edge-Garza
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Miguel Villamil-Castro
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dorrie Main
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Craig Hardner
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

DE-G identified and investigated the discrepant SNP identifiers, corrected them, and drafted the manuscript. MV-C assisted with collation of the historical data for comparison and interpretation. DM and CH supervised the study and edited the manuscript.

Corresponding author

Correspondence to Daniel A. Edge-Garza.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Data archiving statement

All relevant data are within the manuscript and errors presented will be corrected in the Genome Database for Rosaceae (www.rosaceae.org).

Additional information

Communicated by D. Chagné

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Edge-Garza, D.A., Villamil-Castro, M., Main, D. et al. Correction of database SNP accession numbers misassigned to SNPs of the 8K IRSC apple SNP array. Tree Genetics & Genomes 17, 17 (2021). https://doi.org/10.1007/s11295-021-01500-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-021-01500-3

Keywords

Search

Navigation