Open Access Highly Accessed Research article

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

Nicholas A Tinker1*, Andrzej Kilian2, Charlene P Wight1, Katarzyna Heller-Uszynska2, Peter Wenzl2, Howard W Rines3, Åsmund Bjørnstad4, Catherine J Howarth5, Jean-Luc Jannink6, Joseph M Anderson7, Brian G Rossnagel8, Deon D Stuthman9, Mark E Sorrells10, Eric W Jackson11, Stine Tuvesson12, Frederic L Kolb13, Olof Olsson14, Luiz Carlos Federizzi15, Marty L Carson16, Herbert W Ohm17, Stephen J Molnar1, Graham J Scoles8, Peter E Eckstein8, J Michael Bonman11, Alf Ceplitis12 and Tim Langdon5

Author Affiliations

1 Agriculture and Agri-Food Canada, ECORC, K.W. Neatby Bldg., 960 Carling Ave., C.E. Farm, Ottawa, ON K1A 0C6, Canada

2 Diversity Arrays Technology P/L, 1 Wilf Crane Cr., Yarralumla, Canberra, ACT 2600, Australia

3 USDA-ARS & University of Minnesota, Dept. of Agronomy and Plant Genetics, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA

4 Norwegian University of Life Sciences, Department of Plant and Environmental Sciences, N-1432 Ås, Norway

5 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK

6 USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University Dept. of Plant Breeding and Genetics, 407 Bradfield Hall, Ithaca, NY 14853, USA

7 USDA-ARS, Purdue University, Agronomy Department, 915 W. State St., West Lafayette, IN 47907-2054, USA

8 Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada

9 University of Minnesota, Dept. Of Agronomy and Plant Genetics, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA

10 Cornell University, Dept. of Plant Breeding and Biometry, 252 Emerson Hall, Ithaca, NY 14853-1902, USA

11 USDA-ARS, 1691 South 2700 West, Aberdeen, ID 83210, USA

12 Svalöf Weibull AB, Cereal Breeding Department, S-268 81 Svalöv, Sweden

13 University of Illinois, Department of Crop Sciences, 1102 S. Goodwin Avenue, Urbana, IL 61801, USA

14 Department of Plant and Environmental Sciences, Carl Skottsbergs gata 22B, Box 461, Gothenburg University, SE40530 Göteborg, Sweden

15 Universidade Federal do Rio Grande do Sul, Departamento de Plantas de Lavoura, Caixa Postal 776, 91.501-970 – Porto Alegre – RS, Brazil

16 USDA-ARS, Cereal Disease Lab, & University of Minnesota, 1551 Lindig Ave., St. Paul, MN 55108, USA

17 Department of Agronomy, 915 W. State St., Purdue University, West Lafayette, IN 47907-2054, USA

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BMC Genomics 2009, 10:39  doi:10.1186/1471-2164-10-39

Published: 21 January 2009

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.