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SSR and SNP diversity in a barley germplasm collection

Published online by Cambridge University Press:  14 May 2008

Rajeev K. Varshney ,
Khaled F. M. Salem ,
Michael Baum ,
Marion S. Roder ,
Andreas Graner  and
Andreas Börner
Rajeev K. Varshney*
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, GaterslebenD-06466, Germany
Khaled F. M. Salem
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, GaterslebenD-06466, Germany
Michael Baum
Affiliation:
International Centre for Agricultural Research in Dryland Areas (ICARDA), PO Box 5466, Aleppo, Syria
Marion S. Roder
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, GaterslebenD-06466, Germany
Andreas Graner
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, GaterslebenD-06466, Germany
Andreas Börner
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, GaterslebenD-06466, Germany
*
*Corresponding author. E-mail: r.k.varshney@cgiar.org
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Abstract

Sets of microsatellites extracted from both a genomic library (gSSRs) and from expressed sequence tag sequence (eSSRs), and single nucleotide polymorphisms (SNPs) were applied to assess the levels of genetic diversity in a sample of 70 barley accessions, originating from 28 countries in Asia, Africa, the Middle East and Europe. The eSSR assays detected a mean of 9.5 alleles per locus, and the gSSRs only 5.7 alleles per locus, but the polymorphism information content values for the two assay types were indistinguishable. Strong and statistically significant correlations were observed between the eSSR and gSSR (r = 0.86, P < 0.05), the eSSR and SNP (r = 0.74, P < 0.05) and the gSSR and SNP genotypes (r = 0.67, P < 0.05). Accessions originating from the Middle East and Asia had the highest levels of genetic diversity. Pairwise genetic similarity ranged from 0.16 to 0.87 (mean 0.43), indicating that the sample was genetically diverse. When clustered on the basis of genotype, Asian and African accessions tended to be grouped together, but those originating from the Middle East were not concentrated in any particular cluster.

Keywords

barleyeSSRgSSRmolecular markersSNP
Type
Research Article
Information
Plant Genetic Resources , Volume 6 , Issue 2 , August 2008 , pp. 167 - 174
Copyright
Copyright © NIAB 2008

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