SSR and SNP diversity in a barley germplasm collection

Varshney, R K and Salem, K F M and Baum, M and Roder, M S and Graner, A and Borner, A (2008) SSR and SNP diversity in a barley germplasm collection. Plant Genetic Resources, 6 (2). pp. 167-174. ISSN 1479-2621

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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.

Item Type: Article
Subjects: Others > Agriculture-Farming, Production, Technology, Economics
Depositing User: Library ICRISAT
Date Deposited: 20 Oct 2011 10:55
Last Modified: 20 Oct 2011 10:55
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Funders: Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung-GTZ project
Acknowledgement: We thank Jan Valkoun (ICARDA) for providing seed of the barley accessions. This research was financially supported in part by the GTZ project 2002.7860.6-001.00 and Contract 1060503, provided by BMZ (Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung), Germany.
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