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United States Department of Agriculture

Agricultural Research Service

Research Project: SMALL GRAINS GENETICS AND GERMPLASM ENHANCEMENT

Location: Small Grains and Potato Germplasm Research

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

Authors
item Tinker, Nicholas -
item Kilian, Andrzej -
item Wright, Charlene -
item Heller-Uszynska, Katarzyna -
item Wenzl, Peter -
item Rines, Howard
item Bjornstad, Asmund -
item Howarth, Catherine -
item Jannink, Jean-Luc
item Anderson, Joseph
item Rossnagle, Brian -
item Stuthman, Deon -
item Sorrells, Mark -
item Jackson, Eric
item Tuvesson, Stine -
item Kolb, Frederic -
item Olsson, Olof -
item Federizzi, Luiz -
item Carson, Martin
item Ohm, Herbert -
item Molnar, Stephen -
item Scoles, Graham -
item Eckstein, Peter -
item Bonman, John
item Ceplitis, Alf -
item Langdon, Tim -

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 21, 2009
Publication Date: January 21, 2009
Repository URL: http://riley.nal.usda.gov/nal_web/digi/submission.html
Citation: Tinker, N.A., Kilian, A., Wright, C.P., Heller-Uszynska, K., Wenzl, P., Rines, H.W., Bjornstad, A., Howarth, C., Jannink, J., Anderson, J.M., Rossnagle, B.G., Stuthman, D.D., Sorrells, M.E., Jackson, E.W., Tuvesson, S., Kolb, F.L., Olsson, O., Federizzi, L.C., Carson, M.L., Ohm, H.W., Molnar, S.J., Scoles, G.J., Eckstein, P.E., Bonman, J.M., Ceplitis, A., Langdon, T. 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Medical Genetics. 10:39.

Interpretive Summary: Development of new oat varieties with improved agronomics, disease resistance, and beneficial traits for human health is a long-term proposition. Current variety development takes at least eight years. Recent advancements in molecular marker applications in plant breeding have shown that they can reduce variety developmental time by 50 percent. The major problem with this in oat is the lack of molecular tools. Researchers at the USDA ARS in Aberdeen, ID recently collaborated with a consortium of international scientist to develop more than 2,000 genetic markers. These markers are now being used world-wide to improve oat, making it more productive and beneficial for human consumption.

Technical Abstract: 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.

Last Modified: 4/24/2014