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Open Access Highly Accessed Research article

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Peter Wenzl12, Haobing Li3, Jason Carling12, Meixue Zhou4, Harsh Raman5, Edie Paul6, Phillippa Hearnden7, Christina Maier8, Ling Xia12, Vanessa Caig12, Jaroslava Ovesná9, Mehmet Cakir10, David Poulsen11, Junping Wang5, Rosy Raman5, Kevin P Smith12, Gary J Muehlbauer12, Ken J Chalmers7, Andris Kleinhofs8, Eric Huttner12 and Andrzej Kilian12*

Author Affiliations

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

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BMC Genomics 2006, 7:206  doi:10.1186/1471-2164-7-206

Published: 12 August 2006

Abstract

Background

Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers.

Results

The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits.

Conclusion

Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.