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The Plant Genome Abstract - Original Research

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


This article in TPG

  1. Vol. 9 No. 2
    unlockOPEN ACCESS
    Received: Oct 21, 2015
    Accepted: Jan 23, 2016
    Published: May 13, 2016May 13, 2016

    * Corresponding author(s): jschluet@uncc.edu
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  1. Ashley S. Chaffina,
  2. Yung-Fen Huangbc,
  3. Scott Smithd,
  4. Wubishet A. Bekeleb,
  5. Ebrahiem Babikere,
  6. Belaghihalli N. Gnaneshfg,
  7. Bradley J. Foresmanh,
  8. Steven G. Blanchardai,
  9. Jeremy J. Jayai,
  10. Robert W. Reidai,
  11. Charlene P. Wightb,
  12. Shiaoman Chaoj,
  13. Rebekah Oliverk,
  14. Emir Islamovicel,
  15. Frederic L. Kolbh,
  16. Curt McCartneyg,
  17. Jennifer W. Mitchell Fetchm,
  18. Aaron D. Beattien,
  19. Åsmund Bjørnstado,
  20. J. Michael Bonmane,
  21. Tim Langdonp,
  22. Catherine J. Howarthp,
  23. Cory R. Brouwerai,
  24. Eric N. Jellenq,
  25. Kathy Esvelt Klose,
  26. Jesse A. Polandr,
  27. Tzung-Fu Hsiehd,
  28. Ryan Browns,
  29. Eric Jacksont,
  30. Jessica A. Schlueter *a and
  31. Nicholas A. Tinker *b
  1. a Dep. Bioinformatics and Genomics, Univ. North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223
    b Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, CE Farm, KW Neatby Bldg, Ottawa, ON K1A 0C6, Canada
    c Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
    d Dep. Plant and Microbial Biology, North Carolina State Univ., 600 Laureate Way, Raleigh, NC 27695 and Plants for Human Health Institute, North Carolina State Univ., Kannapolis, NC 28081
    e Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 S 2700 W, Aberdeen, ID 83210
    f Dep. Plant Sci., Univ. Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
    g Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
    h Dep. Crop Sciences, 1102 South Goodwin Ave, Univ. Illinois, Urbana, IL 61801
    i Bioinformatics Services Division, Univ. North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081
    j Cereal Crops Research, USDA-ARS, 1605 Albrecht Blvd N, Fargo, ND 58102
    k Dep. Plant Sciences, PO Box 6050, North Dakota State University, Fargo, ND 58108
    l BASF Plant Science LP, 26 Davis Dr, Research Triangle Park, NC 27709
    m Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB R7A 5Y3, Canada
    n Dep. Plant Sciences, 51 Campus Drive, Univ. Saskatchewan, Saskatoon, SK S7N 5A8, Canada
    o Dep. Plant and Environmental Sciences, PO Box 5003, Norwegian Univ. Life Sciences, N-1432 Ås, Norway
    p Inst. Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EE, UK
    q Dep. Plant and Wildlife Sciences, 5009 LSB, Brigham Young Univ., Provo, UT 84602
    r Wheat Genetics Resource Center, Dep. Plant Pathology and Dep. Agronomy, 4024 Throckmorton Plant Sciences Center, Kansas State Univ., Manhattan, KS 66506
    s United States Patent and Trademark Office, 400 Dulany Street, Alexandria, VA 22314
    t General Mills Crop Sciences, 1990 Kimball Ave, Manhattan, KS 66506
Core Ideas:
  • We constructed a hexaploid oat consensus map from 12 populations representing 19 parents.
  • The map represents the most common physical chromosome arrangements in oat.
  • Deviations from the consensus map may indicate physical rearrangements.
  • Large chromosomal translocations vary among different varieties.
  • There is regional synteny with rice but considerable subgenome rearrangement.


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.

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