IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v6y2015i1d10.1038_ncomms7914.html
   My bibliography  Save this article

High-resolution genetic mapping of maize pan-genome sequence anchors

Author

Listed:
  • Fei Lu

    (Institute for Genomic Diversity, Cornell University)

  • Maria C. Romay

    (Institute for Genomic Diversity, Cornell University)

  • Jeffrey C. Glaubitz

    (Institute for Genomic Diversity, Cornell University)

  • Peter J. Bradbury

    (United States Department of Agriculture/Agricultural Research Service)

  • Robert J. Elshire

    (Institute for Genomic Diversity, Cornell University)

  • Tianyu Wang

    (Institute of Crop Science, Chinese Academy of Agricultural Sciences)

  • Yu Li

    (Institute of Crop Science, Chinese Academy of Agricultural Sciences)

  • Yongxiang Li

    (Institute of Crop Science, Chinese Academy of Agricultural Sciences)

  • Kassa Semagn

    (International Maize and Wheat Improvement Center (CIMMYT))

  • Xuecai Zhang

    (International Maize and Wheat Improvement Center (CIMMYT))

  • Alvaro G. Hernandez

    (Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign)

  • Mark A. Mikel

    (Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign
    University of Illinois at Urbana-Champaign)

  • Ilya Soifer

    (NRGENE)

  • Omer Barad

    (NRGENE)

  • Edward S. Buckler

    (Institute for Genomic Diversity, Cornell University
    United States Department of Agriculture/Agricultural Research Service)

Abstract

In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a ‘pan-genome’, which is essential to fully understand the genetic control of phenotypes. However, the pan-genome’s complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops.

Suggested Citation

  • Fei Lu & Maria C. Romay & Jeffrey C. Glaubitz & Peter J. Bradbury & Robert J. Elshire & Tianyu Wang & Yu Li & Yongxiang Li & Kassa Semagn & Xuecai Zhang & Alvaro G. Hernandez & Mark A. Mikel & Ilya So, 2015. "High-resolution genetic mapping of maize pan-genome sequence anchors," Nature Communications, Nature, vol. 6(1), pages 1-8, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7914
    DOI: 10.1038/ncomms7914
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms7914
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms7914?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Sylvain Aubry, 2023. "Genebanking plant genetic resources in the postgenomic era," Agriculture and Human Values, Springer;The Agriculture, Food, & Human Values Society (AFHVS), vol. 40(3), pages 961-971, September.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7914. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.