A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Authors Organisations
  • Ashley S. Chaffin(Author)
    University of North Carolina at Charlotte
  • Yung-Fen Huang(Author)
    Agriculture and Agri-Food Canada
    National Taiwan University
  • Scott Smith(Author)
    North Carolina State University
  • Wubishet A. Bekele(Author)
    Agriculture and Agri-Food Canada
  • Ebrahiem Babiker(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Belaghihalli N. Gnanesh(Author)
    University of Manitoba
    Agriculture and Agri-Food Canada
  • Bradley J. Foresman(Author)
    University of Illinois at Urbana-Champaign
  • Steven G. Blanchard(Author)
    University of North Carolina at Charlotte
  • Jeremy J. Jay(Author)
    University of North Carolina at Charlotte
  • Robert W. Reid(Author)
    University of North Carolina at Charlotte
  • Charlene P. Wight(Author)
    Agriculture and Agri-Food Canada
  • Shiaoman Chao(Author)
    USDA-ARS Cereal Crops Research Unit
  • Rebekah E. Oliver(Author)
    North Dakota State University
  • Emir Islamovic(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
    BASF Plant Science
  • Frederic L. Kolb(Author)
    University of Illinois at Urbana-Champaign
  • Curt Mccartney(Author)
    Agriculture and Agri-Food Canada
  • Jennifer W. Mitchell Fetch(Author)
    Agriculture and Agri-Food Canada
  • Aaron D. Beattie(Author)
    University of Saskatchewan
  • Åsmund Bjørnstad(Author)
    Norwegian University of Life Sciences
  • J. Michael Bonman(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Tim Langdon(Author)
  • Catherine Howarth(Author)
  • Cory R. Brouwer(Author)
    University of North Carolina at Charlotte
  • Eric N. Jellen(Author)
    Brigham Young University
  • Kathy Esvelt Klos(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Jesse A. Poland(Author)
    Kansas State University
  • Tzung-fu Hsieh(Author)
    North Carolina State University
  • Ryan Brown(Author)
    United States Patent and Trademark Office
  • Eric W. Jackson(Author)
    General Mills Crop Sciences
  • Jessica A. Schlueter(Author)
    University of North Carolina at Charlotte
  • Nicholas A. Tinker(Author)
    Agriculture and Agri-Food Canada
Type Article
Original languageEnglish
Article number0102
Number of pages21
JournalThe Plant Genome
Issue number2
Publication statusPublished - 01 Jul 2016
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Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.


  • Avena/genetics, Chromosome Mapping, Chromosomes, Plant/genetics, Genetic Linkage, Genome, Plant/genetics, Genotype, North America, Polymorphism, Single Nucleotide, Polyploidy, Synteny