Skip to main content
SpringerLink
Log in

Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Traditionally, simple sequence repeat (SSR) markers have been developed from libraries of genomic DNA. However, the large, repetitive nature of conifer genomes makes development of robust, single-copy SSR markers from genomic DNA difficult. Expressed sequence tags (ESTs), or sequences of messenger RNA, offer the opportunity to exploit single, low-copy, conserved sequence motifs for SSR development. From a 20,275-unigene spruce EST set, we identified 44 candidate EST-SSR markers. Of these, 25 amplified and were polymorphic in white, Sitka, and black spruce; 20 amplified in all 23 spruce species tested; the remaining five amplified in all except one species. In addition, 101 previously described spruce SSRs (mostly developed from genomic DNA), were tested. Of these, 17 amplified across white, Sitka, and black spruce. The 25 EST-SSRs had approximately 9% less heterozygosity than the 17 genomic-derived SSRs (mean H=0.65 vs 0.72), but appeared to have less null alleles, as evidenced by much lower apparent inbreeding (mean F=0.046 vs 0.126). These robust SSRs are of particular use in comparative studies, and as the EST-SSRs are within the expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.

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
Fig. 4

Similar content being viewed by others

References

  • Arnold C, Rossetto M, McNally J, Henry RJ (2002) The application of SSRs characterized for grape (Vitis vinifera) to conservation studies in Vitaceae. Am J Bot 89:22–28

    CAS  Google Scholar 

  • Bérubé Y, Ritland CE, Ritland K (2003) Isolation, characterization, and cross-species utility of microsatellites in yellow cedar (Chamaecyparis nootkatensis). Genome 46:353–361

    Article  PubMed  Google Scholar 

  • Besnard G, Achere V, Faivre Rampant P, Favre JM, Jeandroz S (2003) A set of cross-species amplifying microsatellite markers developed from DNA sequence databanks in Picea (Pinaceae). Mol Ecol Notes 3:380–383

    Article  CAS  Google Scholar 

  • Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455–457

    Article  CAS  PubMed  Google Scholar 

  • Bruford MW, Wayne RK (1993) Microsatellites and their application to population genetic studies. Curr Opin Genet Dev 3:939–943

    CAS  PubMed  Google Scholar 

  • Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854

    CAS  PubMed  Google Scholar 

  • Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Morissette J, Weissenbach J (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380:152–154

    Article  CAS  PubMed  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 23:13–15

    Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using PHRED II. Error probabilities. Genome Res 8:186–194

    CAS  PubMed  Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using PHRED. I. Accuracy assessment. Genome Res 8:175–185

    CAS  PubMed  Google Scholar 

  • Felsenstein J (1995) PHYLIP (Phylogeny Inference Package), ver 3.57c, University of Washington

  • Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW (1995) An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463–471

    CAS  PubMed  Google Scholar 

  • Hodgetts RB, Aleksiuk MA, Brown A, Clarke C, Macdonald E, Nadeem S, Khasa D (2001) Development of microsatellite markers for white spruce (Picea glauca) and related species. Theor Appl Genet 102:1252–1258

    Article  CAS  Google Scholar 

  • Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877

    Article  CAS  PubMed  Google Scholar 

  • Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390

    Article  CAS  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  CAS  PubMed  Google Scholar 

  • Neff BD (2004) Mean d2 and divergence time: transformations and standardizations. J Hered 95:165–171

    Article  CAS  PubMed  Google Scholar 

  • Oetting WS, Lee HK, Flanders DJ, Wiesner GL, Sellers TA, King RA (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30:450–458

    Article  CAS  PubMed  Google Scholar 

  • Paglia G, Morgante M (1998) PCR-based multiplex DNA fingerprinting techniques for the analysis of conifer genomes. Mol Breed 4:173–177

    Article  CAS  Google Scholar 

  • Pfeiffer A, Olivieri AM, Morgante M (1997) Identification and characterization of microsatellites in Norway spruce (Picea abies K.). Genome 40:411–419

    CAS  PubMed  Google Scholar 

  • Queller DC, Strassmann JE, Hughes CR (1993) Microsatellites and kinship. Trends Ecol Evol 8:285–288

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Rajora OP, Rahman MH, Dayanandan S, Mosseler A (2000) Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca) and their usefulness in other spruce species. Mol Gen Genet 264:871–882

    Google Scholar 

  • Ritland C, Ritland K (2000) DNA fragment markers in plants. In: Baker AJ (ed) Molecular methods in ecology. Blackwell, Oxford, pp 208–234

  • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386

  • Saha S, Karaca M, Jenkins JN, Zipf AE, Reddy OUK, Kantety RV (2003) Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130:355–364

    Article  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Schlötterer C (2001) Genealogical inference of closely related species based on microsatellites. Genet Res 78:209–212

    PubMed  Google Scholar 

  • Scotti I, Magni F, Fink R, Powell W, Binelli G, Hedley PE (2000) Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences. Genome 43:41–46

    Article  CAS  PubMed  Google Scholar 

  • Scotti I, Magni F, Paglia G, Morgante M (2002a) Trinucleotide microsatellites in Norway spruce (Picea abies): their features and the development of molecular markers. Theor Appl Genet 106:40–50

    CAS  PubMed  Google Scholar 

  • Scotti I, Paglia G, Magni F, Morgante M (2002b) Efficient development of dinucleotide microsatellite markers in Norway spruce (Picea abies Karst.) through dot-blot selection. Theor Appl Genet 104:1035–1041

    Article  CAS  PubMed  Google Scholar 

  • Sigurgeirsson A, Szmidt AE (1993) Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea. Nord J Bot 13:233–246

    CAS  Google Scholar 

  • Soares MB, Bonaldo MF, Jelene, P, Su L, Lawton L, Efstratiadis A (1994) Construction and characterization of a normalized cDNA library. Proc Natl Acad Sci USA 91:9228–9232

    CAS  PubMed  Google Scholar 

  • Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339–1348

    Article  CAS  PubMed  Google Scholar 

  • Ven WTG van de, McNicol RJ (1996) Microsatellites as DNA markers in Sitka spruce. Theor Appl Genet 93:613–617

    Article  Google Scholar 

  • Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication Proc Natl Acad Sci USA 99:9650–9655

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Genome Canada and the Province of British Columbia, through the Genome BC Forestry Genome Project, funded this research. We acknowledge the support of the Vancouver Genome Sciences Centre for EST sequencing and database development. We thank Dr. Sally Aitken (University of British Columbia) for the white spruce collections, Washington Gapare (University of British Columbia) for the Sitka spruce collections, and Dr. Om Rajora (Dalhousie University) for the black spruce collections. Dr. Barry Jaquish of the B.C. Ministry of Forests Kalamalka research station provided the spruce species collection.

Author information

Authors and Affiliations

  1. Department of Forest Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Dainis Rungis, Yanik Bérubé, Jun Zhang, Steven Ralph, Carol E. Ritland, Jörg Bohlmann & Kermit Ritland

  2. Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Brian E. Ellis, Carl Douglas & Jörg Bohlmann

  3. Biotechnology Laboratory, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Brian E. Ellis & Jörg Bohlmann

Authors
  1. Dainis Rungis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yanik Bérubé
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Steven Ralph
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Carol E. Ritland
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Brian E. Ellis
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Carl Douglas
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jörg Bohlmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Kermit Ritland
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kermit Ritland.

Additional information

Communicated by O. Savolainen

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rungis, D., Bérubé, Y., Zhang, J. et al. Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor Appl Genet 109, 1283–1294 (2004). https://doi.org/10.1007/s00122-004-1742-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-004-1742-5

Keywords

Search

Navigation