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Cross-species transferability and mapping of genomic and cDNA SSRs in pines

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Abstract

Two unigene datasets of Pinus taeda and Pinus pinaster were screened to detect di-, tri- and tetranucleotide repeated motifs using the SSRIT script. A total of 419 simple sequence repeats (SSRs) were identified, from which only 12.8% overlapped between the two sets. The position of the SSRs within their coding sequences were predicted using FrameD. Trinucleotides appeared to be the most abundant repeated motif (63 and 51% in P. taeda and P. pinaster, respectively) and tended to be found within translated regions (76% in both species), whereas dinucleotide repeats were preferentially found within the 5′- and 3′-untranslated regions (75 and 65%, respectively). Fifty-three primer pairs amplifying a single PCR fragment in the source species (mainly P. taeda), were tested for amplification in six other pine species. The amplification rate with other pine species was high and corresponded with the phylogenetic distance between species, varying from 64.6% in P. canariensis to 94.2% in P. radiata. Genomic SSRs were found to be less transferable; 58 of the 107 primer pairs (i.e., 54%) derived from P. radiata amplified a single fragment in P. pinaster. Nine cDNA-SSRs were located to their chromosomes in two P. pinaster linkage maps. The level of polymorphism of these cDNA-SSRs was compared to that of previously and newly developed genomic-SSRs. Overall, genomic SSRs tend to perform better in terms of heterozygosity and number of alleles. This study suggests that useful SSR markers can be developed from pine ESTs.

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References

  • Brown GR, Kadel EE III, Bassoni DL, Kiehne KL, Temesgen B, Van Buijtenen JP, Sewell MM, Marshall KA, Neale DB (2001) Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 159:799–809

    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 

  • Chagné D, Lalanne C, Madur D, Kumar S, Frigerio JM, Krier C, Decroocq S, Savoure A, Bou-Dagher KM, Bertocchi E, Brach J, Plomion C (2002) A high density genetic map of maritime pine based on AFLPs. Ann For Sci 59:627–636

    Article  Google Scholar 

  • Chagné D, Brown G, Lalanne C, Madur D, Pot D, Neale D, Plomion C (2003) Comparative genome and QTL mapping between maritime and loblolly pines. Mol Breed 12:185–195

    Article  CAS  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCough SR, Park WD, Ayer N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oriza sativa). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  • Christoffels A, van Gelder A, Greyling G, Miller R, Hide T, Hide W (2001) STACK: sequence tag alignment and consensus knowledgebase. Nucleic Acids Res 29:238–238

    Article  Google Scholar 

  • Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross-transferable to erianthus and sorghum. Plant Sci 160:1115–1123

    Article  CAS  PubMed  Google Scholar 

  • Costa P, Pot D, Dubos C, Frigerio J-M, Pionneau C, Bodénès C, Bertocchi E, Cervera MT, Remington DL, Plomion C (2000) A genetic map of maritime pine based on AFLP, RAPD and protein markers. Theor Appl Genet 100:39–48

    Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Dubos C, Plomion C (2003) Identification of water-deficit responsive genes in maritime pine (Pinus pinaster Ait.) roots. Plant Mol Biol 51:249–262

    Article  CAS  PubMed  Google Scholar 

  • Echt CS, Vendramin GG, Nelson CD, May-Marquardt P (1999) Microsatellite DNA as shared genetic markers among conifer species. Can J For Res 29:365–371

    Article  CAS  Google Scholar 

  • Elsik CG, Williams CG (2000) Retroelements contribute to the excess low-copy number DNA in pine. Mol Gen Genet 264:47–55

    Article  CAS  PubMed  Google Scholar 

  • Elsik CG, Williams CG (2001) Low-copy microsatellite recovery from a conifer genome. Theor Appl Genet 103:1189–1195

    Article  CAS  Google Scholar 

  • Elsik CG, Minihan VT, Hall SE, Scarpa AM, Williams CG (2000) Low-copy microsatellite markers for Pinus taeda L. Genome 43:550–555

    Article  CAS  PubMed  Google Scholar 

  • Eujayl I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    Article  CAS  PubMed  Google Scholar 

  • Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MAR (2003) Medicago trunculata EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422

    Article  PubMed  Google Scholar 

  • Frigerio JM, Dubos C, Chaumeil P, Salin F, Garcia V, Barré A, Plomion C (2004) Using transcriptome analysis to identify osmotic stress candidate genes in maritime pine (Pinus pinaster Ait.). In: Sustainable forestry, wood products and biotechnology, BIOFOR Proceedings (in press)

  • Gao L, Tang J, Li H, Jia J (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261

    Article  CAS  Google Scholar 

  • Gonzalez-Martinez SC, Robledo-Arnuncio JJ, Collada C, Diaz A, Williams CG, Alia R, Cervera MT (2004) Cross-amplification and sequence variation of microsatellite loci in Eurasian hard pines. Theor Appl Genet 109:103–111

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genom 270:315–323

    Article  CAS  Google Scholar 

  • Kamm A, Doudrick RL, Heslop-Harrison JS, Schmidt T (1996) The genomic and physical organization of Ty1- copia-like sequences as component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proc Natl Acad Sci USA 93:2708–2713

    Article  CAS  PubMed  Google Scholar 

  • Kantety RV, LaRota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum wheat. Plant Mol Biol 48:501–510

    Article  CAS  PubMed  Google Scholar 

  • Kinlaw CG, Neale DB (1997) Complex gene families in pine genomes. Trends Plant Sci 2:356–359

    Article  Google Scholar 

  • Kirst M, Johnston AF, Baucom C, Ulrich E, Hubbard K, Staggs R, Paule C, Retzel E, Whetten R, Sederoff R (2003) Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana. Proc Natl Acad Sci USA 100:7383–7388

    Article  PubMed  Google Scholar 

  • Komulainen P, Brown GR, Mikkonen M, Karhu A, Garcia-Gil MR, O’Malley D, Lee B, Neale DB, Savolainen O (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 107:667–678

    Article  CAS  PubMed  Google Scholar 

  • Kossack DS, Kinlaw CS (1999) IFG, a gypsy-like retrotransposon in Pinus (Pinaceae), has an extensive history in pines. Plant Mol Biol 39:417–426

    Article  CAS  PubMed  Google Scholar 

  • Kriebel HB (1985) DNA sequences components in the Pinus strobus nuclear genome. Can J For Res 15:1–4

    CAS  Google Scholar 

  • Kutil BL, Williams CG (2001) Triplet-repeat microsatellites shared among hard and soft pines. J Hered 92:327–332

    Article  CAS  PubMed  Google Scholar 

  • Leitch IJ, Hanson L, Winfield M, Parker J, Bennett MD (2001) Nuclear DNA C-values complete familial representation in gymnosperms. Ann Bot 88:843–849

    Article  CAS  Google Scholar 

  • Mariette S, Chagné D, Decroocq S, Vendramin GG, Lalanne C, Madur D, Plomion C (2001) Microsatellite markers for Pinus pinaster Ait. Ann For Sci 58:203–206

    Article  Google Scholar 

  • Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80

    CAS  PubMed  Google Scholar 

  • Mirov NT (1967) The genus Pinus. Ronald, New York

    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 

  • Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275–1287

    CAS  PubMed  Google Scholar 

  • Price RA, Liston A, Strauss SH (1998) Phylogeny and systematics of Pinus. In: Richardson DM (ed) Ecology and biogeography of Pinus. Cambridge University Press, Cambridge, pp 49–68

    Google Scholar 

  • Ritter E, Aragones A, Markussen T, Achere V, Espinel S, Fladung M, Wrobel S, Faivre-Rampant P, Jeandroz S, Favre J-M (2002) Construction and exploitation of a multifunctional and saturated genetic map for coniferous species. Ann For Sci 59:637–643

    Article  Google Scholar 

  • Salzberg SL, Delcher AL, Kasif F, White O (1998) Microbial gene identification using Markov interpolated models. Nucleic Acids Res 26:544–548

    Article  CAS  PubMed  Google Scholar 

  • Schiex T, Gouzy J, Moisan A, de Oliveira Y (2003) FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res 31:3738–3741

    Article  CAS  PubMed  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN v.2000, Genetics and Biometry Laboratory, University of Geneva, Switzerland

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  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 GP, 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 GP, 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 

  • Shepherd M, Cross M, Maguire TL, Dieters MJ, Williams CG, Henry RJ (2002) Transpecific microsatellites for hard pines. Theor Appl Genet 104:819–827

    Article  CAS  PubMed  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCough SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genet Res 11:1441–1452

    Article  CAS  Google Scholar 

  • Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genet Res 10:967–981

    Article  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) Joinmap 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen. Website: http://www.joinmap.nl

  • Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol 7:537–546

    CAS  PubMed  Google Scholar 

  • Zhou Y, Bui T, Auckland LD, Williams CG (2002) Undermethylated DNA as a source of microsatellite from a conifer genome. Genome 45:91–99

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

D.C. was funded by the French Ministry of Research. This research was supported by grants from France (Ministère de l’Agriculture et de la Pêche-DERF No. 61.45.80.15/02) and the European Union (TREESNIPS project: QLK3-CT-2002-01973). The maritime pine ESTs were produced with the support of the Aquitaine Région (n°2002 0307002A) and INRA (Lignome) as well as the European Union (GEMINI: QLK5-CT-1999-00942). The work at New Zealand Forest Research was funded by New Zealand’s Foundation for Research, Science and Technology (CO4X005).

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Correspondence to C. Plomion.

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Communicated by D.B. Neale

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Chagné, D., Chaumeil, P., Ramboer, A. et al. Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet 109, 1204–1214 (2004). https://doi.org/10.1007/s00122-004-1683-z

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