New DArT markers for oat provide enhanced map coverage and global germplasm characterization

Nicholas A. Tinker, Andrzej Kilian, Charlene P. Wight, Katarzyna Heller-Uszynska, Peter Wenzl, Howard W. Rines, Åsmund Bjørnstad, Catherine J. Howarth, Jean Luc Jannink, Joseph M. Anderson, Brian G. Rossnagel, Deon D. Stuthman, Mark E. Sorrells, Eric W. Jackson, Stine Tuvesson, Frederic L. Kolb, Olof Olsson, Luiz Federizzi, Marty L. Carson, Herbert W. OhmStephen J. Molnar, Graham J. Scoles, Peter E. Eckstein, J. Michael Bonman, Alf Ceplitis, Tim Langdon

Research output: Contribution to journalArticlepeer-review

123 Scopus citations


Background: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

Original languageEnglish (US)
Article number39
JournalBMC Genomics
StatePublished - Jan 21 2009

Bibliographical note

Funding Information:
We are grateful to the following institutions for generous funding that contributed to this work: The Quaker Oats Company [55], Quaker Tropicana Gatorade Canada [56], North American Millers Association [57], CropTai-lor [58], Biotechnology and Biological Sciences Research Council [59], and Anderson -USDA-ARS project 3602-21220-010-00D. At DArT Pty Ltd, a number of people contributed to technology development and data production, especially Eric Huttner, Jason Carling, Vanessa Caig, and Ling Xia. We recognize the excellent technical and professional assistance of many staff and collaborators including Dr. Phillip San Miguel, Allison Witt, and Viktoria Krasnyanskaya. Finally, we thank the following for providing additional germplasm and related information that contributed to this study: Carla Adtorre, Ron Barnett, Aaron Beattie, Howard Bockelman, Vern Burrows, Hermann Bürstmayr, Gongshe Hu, Axel Diederichsen, Stephen Harrison, David Hoffman (deceased), Heidi Kaeppler, Art McElroy, Michael McMullen, Jennifer Mitchell Fetch, Rickard Johnsson, Don Obert, Marcelo Pacheco, John Valentine, Weikai Yan, and Ju-Kyung Yu. We also recognize that there are many others who have contributed indirectly but generously to this work.


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