Research article
New DArT markers for oat provide enhanced map coverage and global germplasm characterization
-
* Corresponding author: Nicholas A Tinker nick.tinker@agr.gc.ca
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
BMC Genomics 2009, 10:39 doi:10.1186/1471-2164-10-39
Published: 21 January 2009Additional files
Additional File 1:
List of varieties. Inventory of 182 oat varieties and accessions used in DArT marker development and diversity analysis.
Format: XLS Size: 139KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 2:
List of markers. Complete listing of DArT markers and associated clones showing marker clusters (bins) based on scores, map positions, and clone similarity based on sequence assembly.
Format: XLS Size: 381KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 3:
DNA Sequences. FASTA formatted DNA sequence data containing 2670 vector-trimmed sequences corresponding to 2573 unique DArT clones, and 490 consensus sequences from an assembly of the above.
Format: TXT Size: 1.6MB Download file
Additional File 4:
BLAST identity. Potential clone identity based on BLAST for non-redundant set of 1774 DArT clone sequences (consensus and singletons).
Format: XLS Size: 460KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 5:
Marker mapping data. Molecular marker data set (in Mapmaker [35] format) including all DArT scores as well as framework marker scores (from [9]) for a set of 80 RIL progenies from the 'Kanota' × 'Ogle' mapping population.
Format: TXT Size: 118KB Download file
Additional File 6:
Map comparison. Expanded version of 'Kanota' × 'Ogle' 2008 DArT map showing increased density of DArT markers with annotated comparisons to the previous map [9].
Format: PDF Size: 1.2MB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional File 7:
Framework Molecular Map of KxO. Framework version of a molecular marker map in Kanota × Ogle with integrated DArT markers. This is a high-resolution version of the cartoon map presented in Figure 4.
Format: PDF Size: 30KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional File 8:
Detailed map placements. HTML version of the new 'Kanota' × 'Ogle' DArT framework map, listing approximate placement for additional markers, including more recently published markers.
Format: PDF Size: 395KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional File 9:
Marker diversity data. Non-redundant DArT marker data set for the germplasm diversity study, containing a full set of data from 1295 non-redundant markers and 182 oat varieties, and a nearly orthogonal set with 1295 markers and 134 varieties.
Format: XLS Size: 3.2MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 10:
Cluster analysis of orthogonal varieties. This is a high-resolution multi-page version of Figure 6.
Format: PDF Size: 99KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional File 11:
Cluster analysis of all varieties. UPGMA cluster analysis of germplasm diversity based on 182 oat varieties, including those that were not orthogonal across all three discovery arrays.
Format: PDF Size: 23KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional File 12:
Pedigree clusters. UPGMA cluster analysis of pedigree distances (D) among 182 oat varieties not orthogonal across all three discovery arrays.
Format: PDF Size: 43KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional File 13:
Potentially duplicated markers. List of 156 DArT markers for which there is some evidence that the marker may map to more than one locus. Three types of evidence are explained in the table legend.
Format: XLS Size: 30KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 14:
Clusters with and without potentially duplicated markers. Analysis of orthogonal diversity data by "Fanny" routine in statistical package 'R'. Fanny finds fuzzy clusters at a given cluster number, 'K'. These analyses were performed with K = 40 on the complete data set (134 × 1295), and, for comparison, on the same data set with potentially duplicated markers removed (see Additional file 13).
Format: XLS Size: 31KB Download file
This file can be viewed with: Microsoft Excel Viewer