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 and Edward S. Buckler ()
Additional contact information
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
Ilya Soifer: NRGENE
Omer Barad: NRGENE
Edward S. Buckler: Institute for Genomic Diversity, Cornell University

Nature Communications, 2015, vol. 6, issue 1, 1-8

Abstract: 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.

Date: 2015
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DOI: 10.1038/ncomms7914

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