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Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

Arnis Druka1, Ilze Druka12, Arthur G Centeno3, Hongqiang Li3, Zhaohui Sun3, William TB Thomas1, Nicola Bonar1, Brian J Steffenson4, Steven E Ullrich5, Andris Kleinhofs5, Roger P Wise67, Timothy J Close8, Elena Potokina9, Zewei Luo9, Carola Wagner10, Günther F Schweizer11, David F Marshall1, Michael J Kearsey9, Robert W Williams3* and Robbie Waugh1*

Author Affiliations

1 Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK

2 School of Computing and Creative Technologies, University of Abertay, Dundee, DD1 1HG, UK

3 Department of Anatomy and Neurobiology, University of Tennessee, Memphis TN 38163, USA

4 Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA

5 Department of Crop and Soil Sciences, Washington State University, Pullman WA99164, USA

6 Corn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames IA 50011, USA

7 Department of Plant Pathology, Iowa State University, Ames IA 50011, USA

8 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

9 School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK

10 Department of Plant Breeding, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany

11 Institute for Crop Production and Plant Breeding, Dep. Genome Analysis, Bavarian State Research Center for Agriculture, Am Gereuth 6, 85354 Freising-Weihenstephan, Germany

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BMC Genetics 2008, 9:73  doi:10.1186/1471-2156-9-73

Published: 18 November 2008

Additional files

Additional file 1:

Table S1. Inference of mRNA abundance regulation by cis-elements or trans-factors. This is a tab delimited table, the first row contains column headings. 'Cosegregating marker' – DNA marker ID that co-segregates with the gene underlying the 'Probe set'. 'Probe Set' – Affymetrix' Barley1 GeneChip probe set ID. 'DNA marker chromosome' and 'DNA marker position' – 'Cosegregating marker' locus parameters. 'mRNA abundance QTL chromosome', 'mRNA abundance QTL position' and 'LRS' – mRNA abundance QTL parameters of the gene underlying 'Probe set'. LRS – Likelihood Ratio Statistic. 'cis/trans' – c – cis, t – trans, inference on cis- or trans regulation of the gene underlying 'Probe set'.

Format: TXT Size: 16KB Download file

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Additional file 2:

Table S2. The Barley1 GeneChip probe sets that report significant mRNA abundance QTL and have rice homologs for the underlying genes. This is a tab delimited table, the first row represents column headings. 'ProbeSet' – Affymetrix' Barley1 GeneChip probe set IDs. 'LRS' – LRS (Likelihood Ratio Statistic) of the mRNA abundance QTL reported by the 'ProbeSet'. 'LRS_range' – subdivision of the LRS into 'low' and 'high' groups. 'Locus' and 'barley chromosome/marker' – location parameters of the mRNA abundance QTL. 'Rice Chr' and 'Rice 5" – location parameters of the rice homologs.

Format: TXT Size: 543KB Download file

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Additional file 3:

Table S3. Principal Components scores of the key traits that segregate in the SM population. This is a tab delimited file, first row represents column headings. F1–F4 represent factors of individual traits.

Format: TXT Size: 25KB Download file

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