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Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome

  • R. K. Varshney
  • I. Grosse
  • U. Hähnel
  • R. Siefken
  • M. Prasad
  • N. Stein
  • P. Langridge
  • L. Altschmied
  • A. Graner
Original Paper

Abstract

A set of 111,090 barley expressed sequence tags (ESTs) was searched for the presence of microsatellite motifs [simple sequence repeat (SSRs)] and yielded 2,823 non-redundant SSR-containing ESTs (SSR–ESTs). From this, a set of 754 primer pairs was designed of which 525 primer pairs yielded an amplicon and as a result, 185 EST-derived microsatellite loci (EST–SSRs) were placed onto a genetic map of barley. The markers show a uniform distribution along all seven linkage groups ranging from 21 (7H) to 35 (3H) markers. Polymorphism information content values ranged from of 0.24 to 0.78 (average 0.48). To further investigate the physical distribution of the EST–SSRs in the barley genome, a bacterial artificial chromosomes (BAC) library was screened. Out of 129 markers tested, BAC addresses were obtained for 127 EST–SSR markers. Twenty-seven BACs, forming eight contigs, were hit by two or three EST–SSRs each. This unexpectedly high incidence of EST–SSRs physically linked at the sub-megabase level provides additional evidence of an uneven distribution of genes and the segmentation of the barley genome in gene-rich and gene-poor regions.

Keywords

Bacterial Artificial Chromosome Bacterial Artificial Chromosome Clone Polymorphism Information Content Bacterial Artificial Chromosome Library Barley Genome 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

We are grateful to Timothy J. Close (University of California, Riverside, USA) for his valuable suggestions on the physical mapping data. We thank Uwe Scholz and Christian Künne (IPK) for performing cluster analysis of SSR-ESTs of IPK and non-IPK ESTs, and Paul Krapivsky (Boston University, Boston, USA), Stefan Posch (Martin Luther University Halle-Wittenberg, Halle, Germany) and Roland Schnee (IPK) for helpful discussions. We also thank Christine Künzel, Anita Czech, Brigitte Schmidt and Ingelore Dommers for technical assistance. The present work was funded by grants from the Grain Research and Development Corporation, Australia (GRDC, UA476), the Federal Ministry of Education and Research (BMBF, GABI-PLANT 312271A,B,C) and BMBF Bioinformatics Centre, Gatersleben/Halle 0312706A).

Supplementary material

122_2006_289_MOESM1_ESM.doc (298 kb)
Supplementary material

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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • R. K. Varshney
    • 1
    • 3
  • I. Grosse
    • 1
  • U. Hähnel
    • 1
  • R. Siefken
    • 1
    • 4
  • M. Prasad
    • 1
    • 5
  • N. Stein
    • 1
  • P. Langridge
    • 2
  • L. Altschmied
    • 1
  • A. Graner
    • 1
  1. 1.Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  2. 2.Australian Centre for Plant Functional GenomicsUniversity of AdelaideGlen OsmondAustralia
  3. 3.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  4. 4.TECAN Deutschland GmbHCrailsheimGermany
  5. 5.National Centre for Plant Genome Research (NCPGR)New DelhiIndia

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