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Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda

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Abstract.

A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.

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References

  • Brown GR, Kadel EE, Bassoni DL, Kiehne KL, Temesgen B, 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 

  • Campbell RB (1986) The interdependence of mating structure and inbreeding depression. Theor Pop Biol 30:232–244

    CAS  Google Scholar 

  • Cato SA, Gardner RC, Kent J, Richardson TE (2001) A rapid PCR-based method for genetically mapping ESTs. Theor Appl Genet 102:296–306

    Article  CAS  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 (in press)

  • Chang S, Puryear JD, Dias MADL, Funkhouser EA, Newton RJ, Cairney J (1996) Gene expression under water deficit in loblolly pine (Pinus taeda): isolation and characterization of cDNA clones. Physiol Plant 97:139–148

    Article  CAS  Google Scholar 

  • Chakravarti A, Lasher LK, Refer JE (1991) A maximum-likelihood method for estimating genome length using genetic linkage data. Genetics 128:175–182

    CAS  PubMed  Google Scholar 

  • Conkle MT (1981) Isozyme variation and linkage in six conifer species. Isozymes in North American Forest Trees and Forest Insects. Berkeley California, pp 11–17

  • Devey ME, Fiddler TA, Liu B-H, Knapp SJ, Neale DB (1994) An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor Appl Genet 88:273–278

    CAS  Google Scholar 

  • Devey ME, Bell JC, Smith DN, Neale DB, Moran GF (1996) A genetic linkage map for Pinus radiata based on RFLP, RAPD, and microsatellite markers. Theor Appl Genet 92:673–679

    CAS  Google Scholar 

  • Devey ME, Sewell MM, Uren TL, Neale DB (1999) Comparative mapping in loblolly and radiata pine using RFLP and microsatellite markers. Theor Appl Genet 99:656–662

    CAS  Google Scholar 

  • Doudrick RL, Heslop-Harrison JS, Nelson CD, Schmidt T, Nance WL, Schwarzacher T (1995) Karyotype of slash pine (Pinus elliottii var. elliottii) using patterns of fluorescence in situ hybridization and fluorochrome banding. J Hered 86:289–296

    Google Scholar 

  • Dvornyk V, Sirviö A, Mikkonen M, Savolainen O (2002) Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Mol Biol Evol 19:179–199

    CAS  PubMed  Google Scholar 

  • Echt CS, Vendramin GG, Nelson CD, Marquart 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 (2001) Families of clustered microsatellites in a conifer genome. Mol Genet Genomics 265:535–542

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Groover A, Devey M, Fiddler T, Lee J, Megraw R, Mitchell-Olds T, Sherman B, Vujcic S, Williams C, Neale D (1994) Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine. Genetics 138:1293–1300

    CAS  PubMed  Google Scholar 

  • Harry DE, Temesgen B, Neale DB (1998) Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones. Theor Appl Genet 97:327–336

    Article  CAS  Google Scholar 

  • Hizume F, Shibata F, Matsusaki Y, Garajova Z (2002) Chromosome identification and comparative karyotypic analysis of four Pinus species. Theor Appl Genet 105:491–497

    Article  Google Scholar 

  • Hurme P, Savolainen O (1999) Comparison of homology and linkage of RAPD markers between individual trees of Scots pine (Pinus sylvestris L.). Mol Ecol 8:15–22

    Article  CAS  Google Scholar 

  • Hurme P, Repo T, Pääkkönen T, Savolainen O (1997) Climatic adaptation of bud set and frost hardiness in Scots pine (Pinus sylvestris L.). Can J For Res 27:716–523

    Article  Google Scholar 

  • Hurme P, Sillanpää M, Repo T, Arjas E, Savolainen O (2000) Genetic basis of climatic adaptation in Scots pine by Bayesian QTL analysis. Genetics 156:1309–1322

    CAS  PubMed  Google Scholar 

  • Jermstad KD, Bassoni DL, Wheeler NC, Anekonda TS, Aitken SN, Adams WT, Neale DB (2001) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. II. Spring and fall cold-hardiness. Theor Appl Genet 102:1152–1158

    Article  CAS  Google Scholar 

  • Karhu A, Dieterich J-H, Savolainen O (2000) Long persistence times and rapid expansion of microsatellites in pines. Mol Biol Evol 17:259–265

    CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Kostia S, Varvio S-L, Vakkari P, Pulkkinen P (1995) Microsatellite sequences in a conifer, Pinus sylvestris. Genome 38:1244–1248

    CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Lagercrantz U (1998) Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150:1217–1228

    CAS  PubMed  Google Scholar 

  • Lander E, Green P, Abrahamson J, Barlow A, Daley M, Lincoln S, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    CAS  PubMed  Google Scholar 

  • Lerceteau E, Plomion C, Andresson B (2001) AFLP mapping and detection of quantitative trait loci (QTLs) for economically important traits in Pinus sylvestris: a preliminary study. Mol Breed 6:451–458

    Google Scholar 

  • Lu MZ, Szmidt AE, Wang X-R (1995) Inheritance of RAPD fragments in haploid and diploid tissue of Pinus sylvestris (L.). Heredity 74:582–589

    Google Scholar 

  • Meyers RM, Fischer SG, Maniatis T, Lerman LS (1985) Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. Nucleic Acids Res 13:3131–3145

    PubMed  Google Scholar 

  • Mikola J (1982) Bud-set phenology as an indicator of climatic adaptation of Scots pine in Finland. Silva Fennica 16:178–184

    Google Scholar 

  • Myburg AA, Remington DL, O'Malley DM, Sederoff RR, Whetten RW (2001) High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer. BioTechniques 30:348–357

    CAS  PubMed  Google Scholar 

  • Niebling CR, Johnson K, Gerhold HD (1987) Electrophoretic analysis of genetic linkage in Scots pine (Pinus sylvestris L). Biochem Genet 25:803–814

    CAS  PubMed  Google Scholar 

  • Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA 86:2766–2770

    PubMed  Google Scholar 

  • Perry DJ, Bousquet J (1998) Sequence-tagged-site markers of arbitrary genes: development, characterization and analysis of linkage in black spruce. Genetics 149:1089–1098

    CAS  PubMed  Google Scholar 

  • Perry DJ, Furnier GR (1996) Pinus banksiana has at least seven expressed alcohol dehydrogenase genes in two linked groups. Proc Natl Acad Sci USA 93:13,020–13,023

    CAS  PubMed  Google Scholar 

  • Plomion C, O'Malley DM, Durel CE (1995) Genomic analysis in maritime pine (Pinus pinaster). Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual. Theor Appl Genet 90:1028–1034

    CAS  Google Scholar 

  • Plomion C, Hurme P, Frigerio J-M, Ridolphi M, Pot D, Pionneau C, Avila C, Gallardo F, David H, Neuttelings G, Campbell M, Canova FM, Savolainen O, Kremer A (1999) Developing SSCP markers for comparative mapping and QTL characterization in pines. Mol Breed 5:21–31

    CAS  Google Scholar 

  • Prager EM, Fowler DP, Wilson AC (1976) Rates of evolution of conifers. Evolution 30:637–649

    Google Scholar 

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

  • Remington DL, Whetten RW, Liu BH, O'Malley DM (1999) Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor Appl Genet 98:1279–1292

    Article  CAS  Google Scholar 

  • Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175

    Article  CAS  PubMed  Google Scholar 

  • Rudin D, Ekberg I (1978) Linkage studies in Pinus sylvestris L. using macrogametophyte allozymes. Silvae Genet 27:1–12

    CAS  Google Scholar 

  • Sax K, Sax HJ (1933) Chromosome number and morphology in the conifers. J Arnold Arbor 14:356–375

    Google Scholar 

  • Sewell M, Sherman BK, Neale DB (1999) A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics 151:321–330

    CAS  PubMed  Google Scholar 

  • Soranzo N, Provan J, Powell W (1998) Characterization of microsatellite loci in Pinus sylvestris L. Mol Ecol 7:1260–1261

    CAS  PubMed  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

    CAS  Google Scholar 

  • Szmidt AE, Muona O (1989) Linkage relationships of allozyme loci in Pinus sylvestris. Hereditas 111:91–97

    CAS  Google Scholar 

  • Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM (2001) Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theor Appl Genet 102:664–675

    CAS  Google Scholar 

  • Voorrips RE (2001) MapChart v. 2.0: windows software for the graphical representation of linkage maps and QTLs. Plant Research International, Wageningen, The Netherlands

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

    CAS  PubMed  Google Scholar 

  • Wakamiya I, Newton RJ, Johnston JS, Price HJ (1993) Genome size and environmental factors in the genus Pinus. Am J Bot 80:1235–1241

    Google Scholar 

  • Yazdani R, Muona O, Rudin D, Szmidt AE (1985) Genetic structure of a Pinus sylvestris L. seed tree stand and a naturally regenerated understory. For Sci 31:430–436

    Google Scholar 

  • Yazdani R, Yeh FC, Rimsha J (1995) Genomic mapping of Pinus sylvestris (L.) using random amplified polymorphic DNA markers. For Genet 2:109–116

    Google Scholar 

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Acknowledgements.

This work was supported by a grant from the Finnish Technology Development Center (TEKES) and from the Environment and Natural Resources Research Council to OS. D.B.N. and G.R.B. are supported by USDA/NRI Plant Genome grants 95-37300 and 00-35300-9316. M.M. was supported by Academy of Finland grant no. 45692. We thank R.R. Sederoff for facilities and support during AFLP analyses at the NCSU, Raleigh, USA.

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Authors and Affiliations

  1. Department of Biology, University of Oulu, FIN-90014 University of Oulu, Finland

    P. Komulainen, M. Mikkonen, A. Karhu, M. R. García-Gil & O. Savolainen

  2. Institute of Forest Genetics, Pacific Southwest Research Station, U.S. Department of Agriculture Forest Service, Davis, CA 95616 and Department of Environmental Horticulture, University of California, Davis, California 95616, USA

    G. R. Brown & D. B. Neale

  3. Forest Biotechnology Group, Department of Forestry, North Carolina State University, Raleigh, NC 27695-8008, USA

    D. O'Malley & B. Lee

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  1. P. Komulainen
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  4. A. Karhu
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Correspondence to O. Savolainen.

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Communicated by C. Möllers

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Komulainen, P., Brown, G.R., Mikkonen, M. et al. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda . Theor Appl Genet 107, 667–678 (2003). https://doi.org/10.1007/s00122-003-1312-2

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