Skip to main content
SpringerLink
Log in

Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

A ‘core set’ of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley genome. PIC values for the selected SSR and SNP markers ranged between 0.32–0.72 (average 0.58) and 0.28–0.50 (average 0.42), respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations (r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs) and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing haplotypes in a better way for the corresponding SNP marker.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Bundock PC, Henry RJ (2004) Single nucleotide polymorphism, haplotype diversity and recombination in the Isa gene of barley. Theor Appl Genet 109:543–551

    Article  PubMed  CAS  Google Scholar 

  • Bundock PC, Christopher JT, Eggler P, Ablett G, Henry RJ, Holton TA (2003) Single nucleotide polymorphisms in cytochrome P450 genes from barley. Theor Appl Genet 106:676–682

    PubMed  CAS  Google Scholar 

  • Chiapparino E, Lee D, Donini P (2004) Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS-PCR. Genome 47:414–420

    PubMed  CAS  Google Scholar 

  • Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, halpotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:19

    Article  PubMed  Google Scholar 

  • Coryell VH, Jessen H, Schupp JM, Webb D, Keim P 1999 Allele-specific hybridization markers for soybean. Theor Appl Genet 98:690–696

    Article  CAS  Google Scholar 

  • Costa JM, Corey A, Hayes PM, Jobet C, Kleinhofs A, Kopisch-Obusch A, Kramer SF, Kudrna D, Li M, Riera-Lizarazu O, Sato K, Szucs P, Toojinda T, Vales MI, Wolfe RI (2001) Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population. Theor Appl Genet 103:415–424

    Article  CAS  Google Scholar 

  • Fernandez ME, Figueiras AM, Benito C (2002) The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. Theor Appl Genet 104:845–851

    Article  PubMed  CAS  Google Scholar 

  • Eujayl I, Sorrells M, Baum M, Wolters P, Powell W (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs. Euphytica 119:39–43

    Article  CAS  Google Scholar 

  • Graner A, Jahoor A, Schondelmaier H, Siedler K, Pillen K, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256

    Article  Google Scholar 

  • Gupta PK, 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

    Article  CAS  Google Scholar 

  • Kanazin V, Talbert H, See D, DeCamp P, Nevo E, Blake T (2002) Discovery and assay of single nucleotide polymorphsims in barley (Hordeum vulgare). Plant Mol Biol 48:529–537

    Article  PubMed  CAS  Google Scholar 

  • Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ (1993) A molecular isozyme and morphological map of barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712

    Article  CAS  Google Scholar 

  • Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A (2001a) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145–151

    Article  PubMed  CAS  Google Scholar 

  • Kota R, Wolf M, Michalek W, Graner A (2001b) Application of DHPLC for mapping of single nucleotide polymorphisms (SNPs) in barley (Hordeum vulgare L.). Genome 44:523–528

    Article  PubMed  CAS  Google Scholar 

  • Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A (2003) Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genom 270:224–233

    Google Scholar 

  • Kota R, Varshney RK, Prasad M, Zhang H, Stein N, Graner A (2007) EST-derived single nucleotide polymorphism (SNP) markers for assembling genetic and physical maps of the barley genome. Funct Integr Genom. doi:10.1007/s10142-007-0060-9

    Google Scholar 

  • Leigh F, Lea V, Law J, Wolters P, Powell W, Donini O (2003) Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat. Euphytica 133:359–366

    Article  CAS  Google Scholar 

  • Lörz H, Wenzel G (2004) Molecular marker systems in plant breeding and crop improvement. Springer Verlag, Germany, pp 476

    Google Scholar 

  • Macaulay M, Ramsay L, Powell W, Waugh R (2001) A representative, highly informative ‘genotyping set’ of barley SSRs. Theor Appl Genet 102:801–809

    Article  CAS  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Matus IA, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45:1095–1106

    Article  PubMed  CAS  Google Scholar 

  • Miyashita NT, Kawabe A, Innan H (1999) DNA variation in the wild plant Arabidopsis thaliana revealed by amplified fragment length polymorphism analysis. Genetics 152:1723–1731

    PubMed  CAS  Google Scholar 

  • Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155

    Article  PubMed  CAS  Google Scholar 

  • Nyrén P (2006) The history of pyrosequencing. Methods Mol Biol 373:1–14

    Google Scholar 

  • Pettersson M, Bylund M, Alderborn A (2003) Molecular haplotype determination using allele-specific PCR and pyrosequencing. Genomics 82:390–396

    Article  PubMed  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Purugganan MD, Suddith JI (1999) Molecular population genetics of floral homeotic loci: departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana. Genetics 151:839–848

    PubMed  CAS  Google Scholar 

  • Rafalski A (2002) Application of single nucleotide polymorphsims in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  PubMed  CAS  Google Scholar 

  • Rohlf FJ (1998) NTSYS-pc numerical taxonomy and multivariate analysis system. Version 2.02. Exeter Publications Setauket, New York

    Google Scholar 

  • Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722

    Article  CAS  Google Scholar 

  • Russell J, Booth A, Fuller J, Harrower B, Hedley P, Machray G, Powell W (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley. Genome 47:389–398

    Article  PubMed  CAS  Google Scholar 

  • Schneider K, Weisshaar B, Borchardt DC, Salamini F (2001) SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Mol Breed 8:63–74

    Article  CAS  Google Scholar 

  • Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I, Graner A (2007) A 1000 loci transcript map of the barley genome- new anchoring points for integrative grass genomics. Theor Appl Genet 114:823–839

    Article  PubMed  CAS  Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA. Nucleic Acids Res 17:6463

    Article  PubMed  CAS  Google Scholar 

  • Tenaillon MI, Sawkins MC, Long AD, Gaut B, Doebley JF, Brandon S (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.). Proc Natl Acad Sci (USA) 98:9161–9166

    Article  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Thiel T, Kota R, Grosse I, Stein N, Graner A (2004) SNP2CAPS: a SNP and InDel analysis tool for CAPS marker development. Nucleic Acids Res 32(1):e5

    Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W – improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Prasad M, Graner A (2004) Molecular marker maps of barley: a resource for intra- and interspecific genomics. In: Lörz H, Wenzel G (eds) Molecular markers in improvement of agriculture and forestry. Springer Verlag, Germany, pp 229–243

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers: features and applications. Trends Biotechnol 23:48–55

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Grosse I, Hahnel U, Thiel T, Rudd S, Zhang H, Prasad M, Stein N, Langridge P, Graner A (2006) Genetic mapping and physical mapping (BAC-identification) of EST-derived microsatellite markers in barley (Hordeum vulgare L.). Theor Appl Genet 113:239–250

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Beier U, Khlestkina EK, Kota R, Korzun V, Graner A, Börner A (2007a) Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies. Theor Appl Genet 114:1105–1116

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007b) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173:638–649

    Article  CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Fritjers A, Pot J, Peleman J, Kupier M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  • Wang RL, Stec A, Hey J, Lukens L, Doebley J (1999) The limits of selection in maize. Nature 398:236–239

    Article  PubMed  CAS  Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

    Article  PubMed  CAS  Google Scholar 

  • Wolfe RI, Franckowiak JD (1991) Multiple dominant and recessive genetic marker stocks in spring barley. Barley Genet Newsl 20:117–121

    Google Scholar 

  • Woodhead M, Russell J, Squirrell J, Hollingsworth PM, Mackenzie K, Gibby M, Powell W (2005) Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions. Mol Ecol 14:1681–1695

    Article  PubMed  CAS  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, van Tassell C, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We are thankful to U. Beier for her excellent technical assistance and to Nils Stein for useful discussions. This work was financially supported by a GTZ project (no. 2002.7860.6-001.00 and Contract no. 1060503) sponsored by BMZ (Bundesministerium für Wirtschaftliche Zusammenarbeit und Entwicklung), Germany.

Author information

Author notes

  1. R. K. Varshney

    Present address: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Greater Hyderabad, AP, India

Authors and Affiliations

  1. Leibniz Institute of Plant Genetics & Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany

    R. K. Varshney, T. Thiel, T. Sretenovic-Rajicic & A. Graner

  2. International Centre for Agricultural Research in Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria

    M. Baum, J. Valkoun, P. Guo, S. Grando & S. Ceccarelli

Authors
  1. R. K. Varshney
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. T. Thiel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. T. Sretenovic-Rajicic
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. M. Baum
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. Valkoun
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. P. Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. S. Grando
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. S. Ceccarelli
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. A. Graner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. K. Varshney.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Varshney, R.K., Thiel, T., Sretenovic-Rajicic, T. et al. Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley. Mol Breeding 22, 1–13 (2008). https://doi.org/10.1007/s11032-007-9151-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-007-9151-5

Keywords

Search

Navigation