Research article
A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits
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* Corresponding author: Andrzej Kilian a.kilian@diversityarrays.com
1 Triticarte P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
2 DArT P/L, PO Box 7141 Yarralumla, Canberra, ACT 2600, Australia
3 School of Agricultural Science, University of Tasmania, PO Box 252-54, Hobart TAS 7001, Australia
4 Tasmanian Institute of Agricultural Research, PO Box 46, Kings Meadows TAS 7249, Australia
5 NSW Agricultural Genomics Centre and NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, PMB, Wagga Wagga NSW 2650, Australia
6 GeneFlow Inc., 14582 Olde Kent Rd., Centreville VA 20120, USA
7 School of Agriculture, Food and Wine, Plant Genomics Centre, The University of Adelaide, PMB1, Glen Osmond SA 5064, Australia
8 Dept. Crop and Soil Sciences and School of Molecular Biosciences, Washington State University, Pullman WA 99164-6420, USA
9 Research Institute of Crop Production, Drnovská 507, 161 06 Prague 6, Czech Republic
10 Molecular Plant Breeding CRC, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
11 Department of Primary Industries & Fisheries, Plant Science, MS 508 Warwick, QLD 4370, Australia
12 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
BMC Genomics 2006, 7:206 doi:10.1186/1471-2164-7-206
Published: 12 August 2006Additional files
Additional file 1:
Component maps. PDF file with graphical representations of individual maps. The maps were built separately for seven populations with sufficient numbers of markers and lines (Table 3).
Format: PDF Size: 175KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 2:
Locus positions in component maps. Excel spreadsheet with the locus positions of the component maps.
Format: XLS Size: 477KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 3:
Relationship between DArT marker quality values and marker call rates. PDF file with a plot of marker call rate vs. the quality value of DArT markers.
Format: PDF Size: 111KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
Features of loci of the consensus map. Excel spreadsheet containing a list of all consensus map loci and their features. Data include locus alias names (including those used by Wenzl et al. [16]]), the chromosome and position of each locus, the number of loci to which each marker was mapped, the number of populations in which each locus was mapped, and the across-populations average and standard deviation of the DArT locus quality parameter.
Format: XLS Size: 871KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 5:
Segregation data and graphical genotypes. Excel file with ten spreadsheets, each containing the segregation data of a single population arranged according to the locus order of the consensus map. The genotype data are painted in colors to visualize the graphical genotypes underlying the maps.
Format: XLS Size: 7.7MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 6:
Consensus map. PDF file with a detailed graphical representation of the consensus map including locus names.
Format: PDF Size: 108KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 7:
Statistics of consensus map by chromosome. PDF file with a table containing chromosome-specific values for the number of loci, the number of bins, inter-bin distances and map lengths in cM.
Format: PDF Size: 44KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 8:
Multi-locus markers. PDF file with a table containing the numbers of DArT and non-DArT markers that map to two or more loci.
Format: PDF Size: 26KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 9:
Influence of dataset composition on locus-ordering precision. PDF file with two graphs showing the dependencies of (i) the correlation coefficients between two alternative sets of locus positions and (ii) the degree of SARF increase relative to individually optimized component maps, on the percentage of non-DArT loci in individual datasets.
Format: PDF Size: 49KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 10:
Number of 'bPb' DArT markers linked to trait-influencing loci on different chromosomes. PDF file with a table containing the within-chromosome averages of the number of 'bPb' DArT markers in the vicinity of loci influencing agricultural traits.
Format: PDF Size: 30KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 11:
List of marker-trait associations. Excel spreadsheet containing a list of loci influencing agricultural traits, including information on closely linked SSR, RFLP, STS and DArT markers.
Format: XLS Size: 63KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 12:
Distribution of loci affecting agricultural traits. PDF file with a graphical representation of the consensus map in which only loci affecting agricultural traits and closely linked markers are highlighted.
Format: PDF Size: 94KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 13:
Perl script for integrating new loci. Text file with perl code for integrating new loci into a fixed framework map. Execution of this file requires perl 5.8 to be installed first. Instructions for preparing the input files are displayed upon executing the program. An improved version of this script may be available from Peter Wenzl peter@DiversityArrays.com or Andrzej Kilian andrzej@DiversityArrays.com at DArT P/L [58].
Format: PL Size: 87KB Download file
Additional file 14:
Perl script for merging datasets and binning loci. Text file with perl code for (i) merging segregation data of multiple populations and (ii) binning loci based on their segregation signatures concatenated across all populations. Execution of this file requires perl 5.8 to be installed first. Instructions for preparing the input files are displayed when executing the program. An improved version of this script may be available from Peter Wenzl peter@DiversityArrays.com or Andrzej Kilian andrzej@DiversityArrays.com at DArT P/L [58].
Format: PL Size: 117KB Download file
Additional file 15:
Perl script for computing map distances. Text file with perl code for computing map distances for a given locus order from the segregation data of multiple populations based on the multipoint algorithm of Lalouel [40]. Execution of this file requires installation of perl 5.8 and the Math::Matrix perl module. Instructions for preparing the input files are displayed when executing the program. An improved version of this script may be available from Peter Wenzl peter@DiversityArrays.com or Andrzej Kilian andrzej@DiversityArrays.com at DArT P/L [58].
Format: PL Size: 113KB Download file