Research article

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

Peter Wenzl^1,2 , Haobing Li³ , Jason Carling^1,2 , Meixue Zhou⁴ , Harsh Raman⁵ , Edie Paul⁶ , Phillippa Hearnden⁷ , Christina Maier⁸ , Ling Xia^1,2 , Vanessa Caig^1,2 , Jaroslava Ovesná⁹ , Mehmet Cakir¹⁰ , David Poulsen¹¹ , Junping Wang⁵ , Rosy Raman⁵ , Kevin P Smith¹² , Gary J Muehlbauer¹² , Ken J Chalmers⁷ , Andris Kleinhofs⁸ , Eric Huttner^1,2 and Andrzej Kilian^1,2

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

author email corresponding author email

BMC Genomics 2006, 7:206doi: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.