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

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 Soifer, Omer Barad, Edward S. Buckler

Research output: Contribution to journalArticlepeer-review

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 â € pan-genomeâ €™, which is essential to fully understand the genetic control of phenotypes. However, the pan-genomeâ €™ 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

Original languageEnglish (US)
Article number6914
JournalNature communications
Volume6
DOIs
StatePublished - Apr 16 2015

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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