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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, Gatersleben D-06466, Germany
Khaled F. M. Salem
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben D-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, Gatersleben D-06466, Germany
Andreas Graner
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben D-06466, Germany
Andreas Börner
Affiliation:
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben D-06466, Germany
*
*Corresponding author. E-mail: [email protected]
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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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References

Anderson, JA, Churchill, GA, Autrique, JE, Tanksley, SD and Sorrells, ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36: 181–186.CrossRefGoogle ScholarPubMed
Gupta, PK and Varshney, RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163–185.CrossRefGoogle Scholar
Kanazin, V, Talbert, H, See, D, DeCamp, P, Nevo, E and Blake, T (2002) Discovery and assay of single nucleotide polymorphsims in barley (Hordeum vulgare). Plant Molecular Biology 48: 529–537.CrossRefGoogle Scholar
Kota, R, Varshney, RK, Thiel, T, Dehmer, KJ and Graner, A (2001a) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135: 145–151.CrossRefGoogle ScholarPubMed
Kota, R, Wolf, M, Michalek, W and Graner, A (2001b) Application of DHPLC for mapping of single nucleotide polymorphisms (SNPs) in barley (Hordeum vulgare L.). Genome 44: 523–528.CrossRefGoogle ScholarPubMed
Kota, R, Varshney, RK, Prasad, M, Zhang, H, Stein, N and Graner, A (2007) EST-derived single nucleotide polymorphism (SNP) markers for assembling genetic and physical maps of the barley genome. Functional and Integrative Genomics, doi: 10.1007/s10142-007-0060-9.CrossRefGoogle Scholar
Li, JZ, Sjakste, TG, Röder, MS and Ganal, MW (2003) Development and genetic mapping of 127 new microsatellite markers in barley. Theoretical and Applied Genetics 107: 1021–1027.CrossRefGoogle ScholarPubMed
Liedloff, A (1999) Mantel non Parametric Test Calculator, Version 2.0. School of Natural Resource Sciences, Queensland University of Technology, Queensland, Australia.Google Scholar
Liu, ZW, Biyashev, RM and Saghai Maroof, MA (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theoretical and Applied Genetics 93: 869–876.CrossRefGoogle ScholarPubMed
Malysheva-Otto, LV, Ganal, MW and Röder, MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genetics 7: 6.CrossRefGoogle Scholar
Mantel, N (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27: 209–220.Google Scholar
Orabi, J, Backes, G, Wolday, A, Yahyaoui, A and Jahoor, A (2007) The Horn of Africa as a centre of barley diversification and a potential domestication site. Theoretical and Applied Genetics 114: 1117–1127.CrossRefGoogle Scholar
Pandey, M, Wagner, C, Friedt, W and Ordon, F (2006) Genetic relatedness and population differentiation of Himalayan hulless barley (Hordeum vulgare L.) landraces inferred with SSRs. Theoretical and Applied Genetics 113: 715–729.CrossRefGoogle ScholarPubMed
Pozzi, C, Rossini, L, Vecchietti, A and Salamini, F (2004) Genes and genome changes during domestication of cereals. In: Gupta, PK and Varshney, RK (eds) Cereal Genomics. Dordrecht: Kluwer Academic Publishers, pp. 165–198.Google Scholar
Ramsay, L, Macaulay, M, Ivanissevich, DS, MacLean, K, Cardle, L, Fuller, J, Edwards, KJ, Tuvesson, S, Morgante, M, Massari, A, Maestri, E, Marmiroli, N, Sjakste, T, Ganal, M, Powell, W and Waugh, R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156: 1997–2005.CrossRefGoogle ScholarPubMed
Röder, MS, Korzun, V, Wendehake, K, Plaschke, J, Tixier, MH, Leroy, P and Ganal, MW (1998) A microsatellite map of wheat. Genetics 149: 2007–2023.CrossRefGoogle ScholarPubMed
Rohlf, FJ (1998) NTSYS-pc numerical taxonomy and multivariate analysis system. Version 2.02. Exeter Publications Setauket, New York.Google Scholar
Rostoks, N, Ramsay, L, MacKenzie, K, Cardle, L, Bhat, PR, Roose, ML, Svensson, JT, Stein, N, Varshney, RK, Marshall, DF, Graner, A, Close, TJ and Waugh, R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proceedings of the National Academy of Sciences USA 103: 18656–18661.CrossRefGoogle ScholarPubMed
Russell, JR, Fuller, JD, Macaulay, M, Hatz, BG, Jahoor, A, Powell, W and Waugh, R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied Genetics 95: 714–722.CrossRefGoogle Scholar
Russell, J, Booth, A, Fuller, J, Harrower, B, Hedley, P, Machray, G and Powell, W (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome 47: 389–398.CrossRefGoogle ScholarPubMed
Struss, P and Plieske, J (1998) The use of microsatellite markers for detection of genetic diversity in barley populations. Theoretical and Applied Genetics 97: 308–315.CrossRefGoogle Scholar
Thiel, T, Michalek, W, Varshney, RK and Graner, A (2003) Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106: 411–422.CrossRefGoogle ScholarPubMed
Varshney, RK, Graner, A and Sorrells, ME (2005) Genic microsatellite markers: features and applications. Trends in Biotechnology 23: 48–55.CrossRefGoogle ScholarPubMed
Varshney, RK, Grosse, I, Hahnel, U, Thiel, T, Rudd, S, Zhang, H, Prasad, M, Stein, N, Langridge, P and Graner, A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theoretical and Applied Genetics 113: 239–250.CrossRefGoogle ScholarPubMed
Varshney, RK, Beier, U, Khlestkina, EK, Kota, R, Korzun, V, Graner, A and Börner, A (2007a) Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies. Theoretical and Applied Genetics 114: 1105–1116.CrossRefGoogle Scholar
Varshney, RK, Marcel, TC, Ramsay, L, Russell, J, Röder, M, Stein, N, Waugh, R, Langridge, P, Niks, RE and Graner, A (2007b) A high density barley microsatellite map with 775 SSR loci. Theoretical and Applied Genetics 114: 1091–1103.CrossRefGoogle ScholarPubMed
Varshney, RK, Thiel, T, Sretenovic-Rajicic, T, Baum, M, Valkoun, J, Guo, P, Grando, S, Ceccarelli, S and Graner, A (2007c) Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley. Molecular Breeding, doi: 10.1007/s11032-007-9151-5.CrossRefGoogle Scholar