A representative, highly informative 'genotyping set' of barley SSRs

M. Macaulay, L. Ramsay, W. Powell, R. Waugh (Lead / Corresponding author)

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107 Citations (Scopus)


We have developed a 'genotyping set' of 48 SSR-based genetic markers for application in genetical studies of barley. The SSRs are a subset of a collection of approximately 600 SSRs available to the barley research community. They have been specifically chosen according to the following criteria: (1) they are single locus; (2) their product quality is good under standard assay conditions; (3) they are distributed across the barley genome; and (4) they exhibit reasonably high polymorphic information content (PIC) values in the cultivated barley gene-pool. To maximise genotyping throughput, one of each SSR primer pair was 5′ end-labelled with either fam, hex or tet fluorochromes to allow automated data capture after running the samples on a DNA sequencer. SSR product sizes were assembled from a reference set of 24 barley genotypes which allowed the construction of 'graphical genotypes' of each of the individual lines. The graphical genotypes provide a convenient tool for interrogating genetic similarity in the individuals surveyed. The product sizes were compared to those obtained from end-labelling one of the primers with 33P and separating the products by denaturing PAGE followed by autoradiography. Although inconsistencies in size were common, they could generally be easily resolved. A reference manual for use of the 'genotyping set' has been produced and is available as a PDF download file at http://www.scri.sari.ac.uk/ssr/pdf. These well-characterised barley SSRs, for the first time, provide a common set of robust PCR-based tools which can be used to integrate and compare information collected from fundamental and/or applied genetic studies on barley in different laboratories across the world.

Original languageEnglish
Pages (from-to)801-809
Number of pages9
JournalTheoretical and Applied Genetics
Issue number6-7
Publication statusPublished - 26 Jun 2001


  • Automation
  • Barley
  • Genotyping
  • Mapping
  • SSRs

ASJC Scopus subject areas

  • Biotechnology
  • General Medicine
  • Agronomy and Crop Science
  • Genetics


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