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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #323339
Title: A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement

Author
item CHAFFIN, ASHLEY - University Of North Carolina
item HUANG, YUNG-FEN - National Taiwan University
item SMITH, SCOTT - North Carolina State University
item BEKELE, WUBISHET - Agriculture And Agri-Food Canada
item Babiker, Ebrahiem
item GNANESH, BELAGHIHALLI - University Of Manitoba
item FORESMAN, BRADLEY - University Of Illinois
item BLANCHARD, STEVEN - University Of North Carolina
item JAY, JEREMY - University Of North Carolina
item REID, ROBERT - University Of North Carolina
item WIGHT, CHARLENE - Agriculture And Agri-Food Canada
item Chao, Shiaoman
item OLIVER, REBECCA - North Dakota State University
item ISLAMOVIC, EMIR - Basf Plant Science Llc
item KOLB, FREDERIC - University Of Illinois
item MCCARTNEY, CURT - Agriculture And Agri-Food Canada
item MITCHELL FETCH, JENNIFER - Agriculture And Agri-Food Canada
item BEATTIE, AARON - University Of Saskatchewan
item BJORNSTAD, ASMUND - Norwegian University Of Life Sciences
item Bonman, John
item LANGDON, TIM - Aberystwyth University
item HOWARTH, CAHTERINE - Aberystwyth University
item BROUWER, CORY - University Of North Carolina
item JELLEN, ERIC - Brigham Young University
item Esvelt Klos, Kathy
item POLAND, JESSE - Kansas State University
item HSIEH, TZUNG-FU - North Carolina State University
item BROWN, RYAN - United States Patent And Trademark Office
item JACKSON, ERIC - General Mills, Inc
item SCHLUETER, JESSICA - University Of North Carolina
item TINKER, NICHOLAS - Agriculture And Agri-Food Canada

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/23/2016
Publication Date: 5/13/2016
Citation: Chaffin, A.S., Huang, Y., Smith, S., Bekele, W.A., Babiker, E.M., Gnanesh, B.N., Foresman, B.J., Blanchard, S.G., Jay, J.J., Reid, R.W., Wight, C.P., Chao, S., Oliver, R., Islamovic, E., Kolb, F.L., McCartney, C., Mitchell Fetch, J.W., Beattie, A.D., Bjornstad, A., Bonman, J.M., Langdon, T., Howarth, C.J., Brouwer, C.R., Jellen, E.N., Esvelt Klos, K.L., Poland, J., Hsieh, T., Brown, R., Jackson, E., Schlueter, J.A., Tinker, N.A. 2016. A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement. The Plant Genome. 9(2). doi: 10.3835/plantgenome2015.10.0102.

Interpretive Summary: The use of advanced genomic technologies is critical to meeting the needs of oat producers for high-yielding, high-quality oat varieties. A new high-density genetic linkage map representative of most commonly grown oat varieties has been produced. The largest number of molecular genetic markers to-date (9,678) has been ordered into 21 groups. This corresponds to the 21 chromosomes of hexaploid oat, some of which have been identified with high confidence. This map will allow researchers to compare results across studies, and to develop molecular genetic tools for oat improvement.

Technical Abstract: Hexaploid oat (Avena sativa, 2n = 6x = 42) is a member of the Poaceae family with a very large genome (~13 Gb) containing 21 chromosome pairs: seven from each of two similar ancestral diploids (A and D) and seven from a more diverged ancestral diploid (C). Physical rearrangements among ancestral oat chromosomes and potential heterogeneity among parental genomes of bi-parental populations have hindered the development of linkage maps that are comparable across studies. 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 SNP array and a genotyping-by-sequencing strategy were collected from progeny of 12 bi-parental recombinant inbred line populations involving 20 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 reveal that the hexaploid oat genome has been highly reconstructed relative to its ancestral diploid genomes, possibly as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, likely accounting for the failure of some linkage groups to match the consensus.