This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656
Aimers-Halliday J, Shelbourne CJA, Hong SO (1997) Issues in developing clonal forestry with P. radiata. In: Burdon RD, Moore JM (eds) “IUFRO’ 97 Genetics of Radiata Pine”, Proc IUFRO Conf 1–4 Dec and Workshop 5 Dec, Rotorua, New Zealand. FRI Bull 203:264–272
Alazard P (2001) Genetic gain in seeds from first generation seed orchards of maritime pine. Informations Forests, Afocel, France, No 628
Alía R, Gil L, Pardos JA (1995) Performance of 43 Pinus pinaster provenances on 5 locations in Central Spain. Silvae Genet 44:75–81
Alía R, Moro J, Denis JB (1997) Performance of Pinus pinaster Ait. provenances in Spain: interpretation of the genotype-environment interaction. Can J For Res 27:1548–1559
Allona I, Quinn M, Shoop I, Swope K, ST-Cyr S, Carlis J, Rield J, Retzel E, Campbell M, Sederoff R, Whetten RW (1998) Analysis of xylem formation in pine by cDNA sequencing. Proc Natl Acad Sci USA 95:9693–9698
Andrew RL, Peakall R, Wallis IR, Wood JT, Knight EJ, Foley WJ (2005) Marker-based quantitative genetics in the wild?: The heritability and genetic correlation of chemical defenses in Eucalyptus. Genetics 171:1989–1998
Apiolaza LA, Greaves BL (2001) Why are most breeders not using economic breeding objectives. In: IUFRO Symp “Developing the Eucalypt for the Future”, 10–14 Sept 2001 Valdivia, Chile
Arcade A, Faivre-Rampant P, Le Guerroue B, Paques LE, Prat D (1996) Quantitative traits and genetic markers: analysis of a factorial mating design in larch. In: Ahuja MR, Boerjan W, Neale D (eds) Somatic Cell Genetics and Molecular Genetics of Trees. Kluwer, Dordrecht, pp 211–216
Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218
Atwood RA, White TL, Huber DA (2002) Genetic parameters and gains for growth and wood properties in Florida source loblolly pine in the southeastern United States. Can J For Res 32:1025–1038
Auckland L, Bui T, Zhou Y, Shepherd M, Williams CG (2002) Conifer Microsatellite Handbook. Corporate Press, College Station, TX
Avila C, Muñz-Chapuli R, Plomion C, Frigerio J-M, Cánovas FM (2000) Two genes encoding distinct cytosolic glutamine synthetases are closely located in the pine genome. FEBS Lett 477:237–243
Bahrman N, Damerval C (1989) Linkage relationships of loci controlling protein amounts in maritime pine (Pinus pinaster Ait). Heredity 63:267–274
Ball RD (2001) Bayesian methods for quantitative trait loci mapping based on model selection: approximate analysis using the Bayesian Information Criterion. Genetics 159:1351–1364
Ball RD (2005) Experimental designs for reliable detection of linkage disequilibrium in unstructured random population association studies. Genetics 170:859–873
Barker CL, Donald T, Pauquet J, Ratnaparkhe MB, Bouquet A, Adam-Blondon AF, Thomas MR, Dry I (2005) Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library. Theor Appl Genet 111:370–377
Beaulieu J, Plourde A, Daoust G, Lamontagne L (1996) Genetic variation in juvenile growth of Pinus strobus in replicated Quebec provenance-progeny tests. For Genet 3:103–112
Beavis WD (1994) The power and deceit of QTL experiments: lessons from comparative QTL studies. In: Proc 49th Annu Corn and Sorghum Industry Res Conf, ASTA, Washington, DC, pp 250–266
Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3:13
Bell JC, Powell M, Devey ME, Moran GF (2004) DNA profiling, pedigree lineage analysis and monitoring in the Australian breeding program of radiata pine. Silvae Genet 53:130–134
Blada I (1994) Inter-specific hybridization of Swiss Stone Pine Pinus cembra L. Silvae Genet 43:14–20
Borzan Z, Papes D (1978) Karyotype analysis in Pinus: contribution to the standardization of the karyotype analysis and review of some applied techniques. Silvae Genet 27:144–150
Bowe LM, Coat G, de Pamphilis CW (2000) Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales’ closest relatives are conifers. Proc Natl Acad Sci USA 97:4092–4097
Bradshaw HD, Foster GS (1992) Marker-aided selection and propagation systems in trees: advantages of cloning for studying quantitative inheritance. Can J For Res 22:1044–1049
Bramlett DL, Burris LC (1995) Topworking young scions into reproductively-mature loblolly pine. In: Weir RJ, Hatcher AV (eds) Proc 23rd South For Tree Improv Conf, Asheville, NC, pp 234–241
Brendel O, Pot D, Plomion C, Rozenberg P, Guehl JM (2002) Genetic parameters and QTL analysis of ä13C and ring width in maritime pine. Plant Cell Environ 25:945–953
Brettschneider R (1998) RFLP analysis. In: Karp A, Isaac PG, Ingram DS (eds) Molecular Tools for Screening Biodiversity Plants and Animals. Chapman & Hall, London, pp 83–95
Brinker M, van Zyl L, Liu WB, Craig D, Sederoff RR, Clapham DH, von Arnold S (2004) Microarray analyses of gene expression during adventitious root development in Pinus contorta. Plant Physiol 135(3):1526–1539
Brown GR, Kadel III EE, 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
Brown GR, Bassoni DL, Gill GP, Fontana JR, Wheeler NC, Megraw RA, Davis MF, Sewell MM, Tuskan GA, Neale DB (2003) Identification of quantitative trait loci influencing wood property traits in loblolly pine. III. QTL verification and candidate gene mapping. Genetics 164:1537–1546
Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc Natl Acad Sci USA 101:15255–15260
Burban C, Petit RJ (2003) Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance. Mol Ecol 12:1487–1495
Burdon RD (1997) Genetic diversity for the future: conservation or creation and capture? In: Burdon RD, Moore JM (eds) “IUFRO’ 97 Genetics of Tadiata Pine”, Proc IUFRO Conf 1–4 Dec and workshop 5 Dec, Rotorua, New Zealand. FRI Bull 203:263–274
Burdon RD (2001) Genetic diversity and disease resistance: some considerations for research, breeding and deployment. Can J For Res 32:596–606
Burdon RD (2002) An introduction to pines. In: Pines of Silvi-cultural Importance. CABI, Wallingford, UK pp x–xxi
Burdon RD (2004) Breeding goals: Issues of goal-setting and applications. In: Walter C, Carson M (eds) Plantation Forest Biotechnology for the 21st Century, Research Signpost, Kerala, India, pp 101–118
Burdon RD, Bannister MH, Low CB (1992) Genetic Survey of Pinus radiata 4: variance structures and heritabilities in juvenile clones. NZ J For Sci 22:187–210
Burdon RD, Firth A, Low CB, Miller MA (1998) Multi-site provenance trials of Pinus radiata in New Zealand. In: Forest Genetic Resources 26:3–8, FAO, Rome
Burdon RD, Gea LD (2006) Pursuit of genetic gain and biotic risk management for Pinus radiata in New Zealand. In: Proc 13th Australasian Plant Breed Conf, Christchurch, New Zealand pp 75–85, http://www.apbc.org.nz
Burdon RD, Kumar S (2003) Stochastic modelling of the impact of four generations of pollen contamination in unpedigreed gene resources. Silvae Genet 52:1–7
Burdon RD, Kumar S (2004) Forwards versus backwards selection: trade-offs between expected genetic gain and risk avoidance. NZ J For Sci 34:3–21
Burdon RD, Low CB (1992) Genetic survey of Pinus radiata. 6: Wood properties: variation, heritabilites, and interrelationship with other traits. NZ J For Sci 22:228–245
Burdon RD, Miller JT (1992) Introduced forest trees of New Zealand: Recognition, role and seed source. 12. Radiata pine (Pinus radiata D. Don). NZ For Res Inst Bull 124/12 pp 59
Byun KO, Kim MZS, Shim SY, Hong SH, Sohn SI (1989) Review of pitch-loblolly hybrid pine (Pinus rigida and P. taeda) breeding researches in Korea and future strategy. Res Rep, For Genet Res Inst, Korea 25:204–211
Cahalan CM (1981) Provenance and clonal variation in growth, branching and phenology in Picea sitchensis and Pinus contorta. Silvae Genet 30:40–46
Cai Q, Zhang D, Liu ZL, Wang XR (2006) Chromosomal localization of 5S and 18S rDNA in five species of subgenus Strobus and their implications for genome evolution of Pinus. Ann Bot 97:715–722
Cánovas FM, Dumas-Gaudot E, Recorbet G, Jorrin J, Hans-Peter Mock HP, Rossignol M (2004) Plant proteome analysis. Proteomics 4:285–298
Cantón FR, García-Gutiérrez A, Gallardo F, de Vicente A, Cánovas FM (1993) Molecular characterization of a cDNA clone encoding glutamine synthetase from a gymnosperm: Pinus sylvestris. Plant Mol Biol 22:819–828
Cantón FR, Le Provost G, Garcia V, Barré A, Frigerio J-M, Paiva J, Fevereiro P, Avila C, Mouret J-F, de Daruvar A, Cánovas FM, Plomion C (2003) Transcriptome analysis of wood formation in maritime pine In: Espinel S, Barredo Y, Ritter E (eds) Sustainable Forestry, Wood Products and Biotechnology. DFA-AFA Press, Vitoria-Gasteiz, Spain, pp 333–347
Cato S, McMillan L, Donaldson L, Richardson T, Echt C, Gardner R (2006a) Wood formation from the base to the crown in Pinus Radiata: gradients of tracheid wall thickness, wood density, radial growth rate and gene expression. Plant Mol Biol 60:565–581
Cato SA, Pot D, Kumar S, Douglas J, Gardner RC, Wilcox PL (2006b) Balancing selection in a dehydrin gene associated with increased wood density and decreased radial growth in Pinus radiata (Abstr). In: Plant & Animal Genome XIV Conf, San Diego
Cato SA, Richardson TE (1996) Inter-and intra-specific polymorphism at chloroplast SSR loci and the inheritance of plastids in Pinus radiata D. Don. Theor Appl Genet 93:587–592
Cervera MT, Plomion C, Malpica CA (2000a) Molecular markers and genome mapping in woody plants. In: Jain SM, Minocha SC (eds) Molecular Biology of Woody Plants. Kluwer, Dordrecht, pp 375–394
Cervera MT, Remington D, Frigerio JM, Storme V, Ivens B, Boerjan W, Plomion C (2000b) Improved AFLP analysis of tree species. Can J For Res 30:1608–1616
Chagné D, Brown G, Lalanne C, Madur D, Pot D, Neale DB, Plomion C (2003) Comparative genome and QTL mapping between maritime and loblolly pines. Mol Breed 12:185–195
Chagné D, Chaumeil P, Ramboer A, Collada C, Guevara A, Cervera M-T, Vendramin GG, Garcia V, Frigerio JM, Echt C, Richardson T, Plomion C (2004) Cross species transferability and mapping of genomic and cDNA SSRs in pines. Theor Appl Genet 109:1204–12
Chagné D, Lalanne C, Madur D, Kumar S, Frigerio JM, Krier C, Decroocq S, Savouré A, Bou-Dagher-Kharrat M, Bertocchi E, Brach J, Plomion C (2002) A high density geneticmap of Maritime pine based on AFLPs. Ann For Sci 59:627–636
Chambers PGS, Borralho NMG (1999) A simple model to examine the impact of changes in wood traits on the cost of thermomechanical pulping and high-brightness newsprint production with radiata pine. Can J For Res 29:1615–1626
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 Planta 97:139–148
Chaumeil P (2006) Plasticité moléculaire de deux écotypes de pin maritime soumis à unstress osmotique. Thèse de Doctorat. Université Henri Poincaré, Nancy I, Nancy
Ciavatta VT, Morillon R, Pullman GS, Chrispeels MJ, Cairney J (2001) An aquaglyceroporin is abundantly expressed early in the development of the suspensor and theembryo proper of loblolly pine. Plant Physiol 127:1556–1567
Claros MG, Cantón FR, Cánovas FM (2004) Construction of a pine BAC genomic library and bioinformatics platform for automated high-throughput sequence analysis (Abstr). 2nd Annual Meeting of the Spanish Forest Functional Genomics Network. Pontevedra, Spain, 29 Nov 2004. http://www.difo.uah.es/forestgenomics/pontevedra_04/Gonzalo%20CLAROS.pdf
Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S (2001) High-throughput screening for induced point mutations. Plant Physiol 126:480–484
Conkle MT (1981) Isozyme variation and linkage in six conifer species. In: Proc Isozymes of North American Forest Trees and Insects, USD Forest Service, General Technical Report PSW-48, pp 11–17
Costa P (1999) Réponse moléculaire, physiologique et génétique du pin maritime à une contrainte hydrique. PhD thesis. Univ of Nancy
Costa P, Plomion C (1999) Genetic analysis of needle protein in Maritime pine. 2. Quantitative variation of protein accumulation. Silvae Genet 48:146–150
Costa P, Pot D, Dubos C, Frigerio JM, Pionneau C, Bodenes 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
Costa, P, Bahrman, N, Frigerio, J-M, Kremer A, Plomion C (1998) Water-deficit-responsive proteins in maritime pine. Plant Mol Biol 38:587–596
Cornelius J (1994) Heritabilities and additive genetic coefficients of variation in forest trees. Can J For Res 24:372–379
Danjon F (1995) Observed selection effects on height growth, diameter and stem form in maritime pine. Silvae Genet 44(1):10–19
Darvasi A, Soller M (1994) Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 138:1365–1373
Darvasi A, Weinreb A, Minke V, Weller JI, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134:943–951
Devey ME, Fiddler TA, Liu BH, 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
Devey ME, Fino-Mix A, Kinloch BB Jr, Neale DB (1995) Random amplified polymorphic DNA markers tightly linked to a gene for resistance to white pine blister rust in sugar pine. Proc Natl Acad Sci USA 92:2066–2070
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 6:673–679
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
Devey ME, Bell JC, Uren TL, Moran GF (2003) A set of microsatellite markers for fingerprinting and breeding applications in Pinus radiata. Genome 45:984–989
Devey ME, Carson SD, Nolan MF, Matheson AC, Te Riini C, Hohepa J (2004a) QTL associations for density and diameter in Pinus radiata and the potential for marker-aided selection. Theor Appl Genet 108:516–524
Devey ME, Groom KA, Nolan MF, Bell JC, Dudzinski MJ, Old KM, Matheson AC, Moran GF (2004b) Detection and verification of quantitative trait loci for resistance to Dothistroma needle blight in Pinus radiata. Theor Appl Genet 108:1056–1063
Dhakal LP, White TL, Hodge GR (1996) Realized genetic gains from slash pine (Pinus elliottii) tree improvement. Silvae Genet 45:190–197
Dilbirligi M, Erayman M, Sandhu D, Sidhu D, Gill KS (2004) Identification of wheat chromosomal regions containing expressed resistance genes. Genetics 166:461–481
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
Drewry A (1982) G-banded chromosomes in Pinus resinosa. J Hered 73:305–306
Du Toit B, Smith C, Carlson C, Esprey L, Allen R, Little K (1998) Eucalypt and pine plantations in South Africa. In: Nambiar EKS, Cossalter C, Triarks A (eds) Workshop Proceedings. CIFOR, 16–20 Feb 1998, South Africa, pp 23–30
Dubos C, Plomion C (2003) Identification of water-deficit responsive genes in maritime pine (Pinus pinaster Ait.) roots. Plant Mol Biol 51(2):249–262
Dubos C, Provost G, Pot D, Salin F, Lalane C, Madur D, Frigerio JM, Plomion C (2003) Identification and characterization of water-stress-responsive genes in hydroponically grown maritime pine (Pinus pinaster) seedlings. Tree Physiol 23:169–179
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 19:179–188
Echt CS, DeVerno LL, Anzidei M, Vendramin GG (1998) Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait. Mol Ecol 7:307–317
Echt CS, Burns R (1999) PCR primer pair sequences and SSRs for various P. taeda ESTs. Available on the dendrome Web site at http://dendrome.ucdavis.edu/Gen_res.htm, accessed 20 March 2006
Echt CS, Nelson CD (1997) Linkage mapping and genome length in eastern white pine (Pinus strobus L.). Theor Appl Genet 94:1031–1037
Echt CS, Saha S, Deemer D, Nelson CD (2006) Evaluation of pine EST-SSR markers. In: Plant & Animal Genome XIV Conf, San Diego, W-117 (http://www.intlpag.org/14/abstracts/PAG14_W117.html, accessed 20 March 2006)
Edwards MD, Page NJ (1994) Evaluation of marker-assisted selection through computer simulation. Theor Appl Genet 88:376–382
Edwards MD, Stuber CW, Wendel JF (1987) Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113–125
Egertsdotter U, van Zyl LM, Mackay J, Peter G, Kirst M, Clark C, Whetten R, Sederoff R (2004) Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes. Plant Biol 6:654–663
Elsik CG, Williams CG (2000) Retroelements contribute to the excess low-copy-number DNA in pine. Mol Gen Genet 264:47–55
Elsik CG, Williams CG (2001) Low copy microsatellite recovery form a conifergenome. Theor Appl Genet 103:1189–1195
Emebiri LC, Devey ME, Matheson AC, Slee MU (1997) Linkage of RAPD markers to NESTUR, a stem growth index in radiata pine seedlings. Theor Appl Genet 95:119–124
Emebiri LC, Devey ME, Matheson AC, Slee MU (1998) Agerelated changes in the expression of QTLs for growth in radiata pine seedlings. Theor Appl Genet 97:1053–1061
Epperson BK, Allard RW (1989) Spatial autocorrelation analysis of the distribution of genotypes within population of lodgepole pine. Genetics 121:369–377
Falkenhagen E (1991) Provenanace variation in Pinus radiate at six sites in South Africa. Silvae Genet 40:41–50
Farjon A (1984) Pines. Drawings and description of the genus Pinus. Brill, Leiden
Farjon A (2001) World checklist and bibliography of conifers, 2nd edn. The Royal Botanic Gardens, Kew, UK
Farjon A, Styles BT (1997) Pinus (Pinaceae). Monograph 75, Flora Neotropica. New York Botanical Gardens, New York
Farnir F, Grisart B, Coppieters W, Riquet J, Berzi P, Cambisano N, Karim L, Mni M, Moisio S, Simon P, Wagenaar D, Vilkki J, Georges M (2002) Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14. Genetics 161:275–287
Fernando RL, Grossman M (1989) Marker-assisted selection using best linear unbiased prediction. Genet Sel Evol 21:246–477
Fisher PJ, Gardner RC, Richardson TE (1996) Single locus microsatellites isolated using 5’ anchored PCR. Nucleic Acids Res 24:4369–4371
Fisher PJ, Gardner RC, Richardson TE (1998) Characteristics of single and multi-copy microsatellities from Pinus radiata. Theor Appl Genet 96:969–979
Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374
Folkertsma RT, Spassova MI, Prins M, Stevens MR, Hille J, Goldbach RW (1999) Construction of a bacterial artificial chromosome (BAC) library of Lycopersicon esculentum cv. Stevens and its application to physically map the Sw-5 locus. Mol Breed 5:197–207
Friesen N, Brandes A, Heslop-Harrison JS (2001) Diversity, origin, and distribution of retrotransposons (gypsy andcopia) in conifers. Mol Biol Evol 18:1176–1188
Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467
García-Gil MR, Mikkonen M, Savolainen O (2003) Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol Ecol 12:1195–1206
García-Gutiérrez A, Cantón FR, Gallardo F, Sánchez-Jiménez F, Cánovas FM (1995) Expression of ferredoxin-dependent glutamate synthase in dark-grown pine seedlings. Plant Mol Biol 27:115–128
Gaussen H (1960) Les Gymnospermes actuelles et fossils. Fascicule VI. Généralités, genre Pinus; Faculté des Sciences, Toulouse
Geada López G, Kamiya K, Harada K (2002) Phylogenetic relationships of Diploxylon pines (subgenus Pinus) based on plastid sequence data. Int J Plant Sci 163:737–747
Geldermann H (1975) Investigations on inheritance of quantitative characters in animals by gene markers. I. Methods. Theor Appl Genet 46:319–330
Georges M, Nielsen D, Mackinnon M, Mishra A, Okimoto R, Pasquino AT, Sargeant LS, Sorensen A, Steele MR, Zhao X, Womack JE, Hoeschele I (1995) Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics 139:907–920
Gerber S, Rodolphe F (1994) An estimation of the genome length of maritime pine (Pinus pinaster Ait). Theor Appl Genet 88:289–292
Gerber S, Rodolphe F, Bahrman N, Baradat P (1993) Seed-protein variation in maritime pine (Pinus pinaster Ait.) revealed by two-dimensional electrophoresis: genetic determinism and construction of a linkage map. Theor Appl Genet 85:521–528
Gernandt DS, Geada Lopez G, Ortiz Garcia S, Liston A (2005) Phylogeny and classification of Pinus. Taxon 54:29–42
Gernandt DS, Liston A, Pinero D (2003) Phylogenetics of Pinus subsections Cembroides and Nelsoniae inferred from cpDNA sequences. Syst Bot 28:657–673
Gion JM, Lalanne C, Le Provost G, Ferry-Dumazet H, Paiva J, Chaumeil P, Frigerio JM, Brach J, Barré A, de Daruvar A, Claverol S, Bonneu M, Sommerer N, Negroni L, Plomion C, Gion J-M, Lalanne C, et al. (2005) The proteome of maritime pine wood forming tissue. Proteomics 5:3731–3751
Gómez MA, González-Martínez SC, Collada C, Climent J, Gil L (2003) Complex population genetic structure in the endemic Canary Island pine revealed using chloroplast microsatellite markers. Theor Appl Genet 107:1123–1131
González-Martínez SC, Gerber S, Cervera MT, Martínez-Zapater J, Gil L, Alía R (2002) Seed gene flow and fine-scale structure in a Mediterranean pine (Pinus pinaster Ait.) using nuclear microsatellite markers. Theor Appl Genet 104:1290–1297
González-Martínez SC, Robledo-Arnuncio JJ, Collada C, Díaz A, Williams CG, Alía R, Cervera MT (2004) Crossamplification and sequence variation of microsatellite loci in Eurasian hard pines. Theor Appl Genet 109:103–11
González-Martínez SC, Ersoz E, Brown GR, Wheeler NC, Neale DB (2006a) DNA sequence variation and selection of tag SNPs at candidate genes for drought-stress response in Pinus taeda. Genetics 172:1915–1926
González-Martínez SC, Krutovsky KV, Neale DB (2006b) Forest-tree population genomics and adaptive evolution. New Phytol 170:227–238
Govindaraju D, Lewis P, Cullis C (1992) Phylogenetic analysis of pines using ribosomal DNA restriction fragment length polymorphisms. Plant Syst Evol 179:141–153
Grace SL, Hamrick JL, Platt WJ (2004) Estimation of seed dispersal in an old-growth population of Longleaf Pine (Pinus palustris) using maternity exclusion analysis. Castanea 69:207–215
Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross mapping strategy and RAPD markers. Genetics 137:1121–1137
Greaves BL (1999) The value of tree improvement: A case study in radiata pine grown for structural sawn timber and linerboard. In: Nepveu G (ed) Connection between silviculture and wood quality through modelling approaches and simulation software. Proc IUFRO Workshop, 5–12 Dec 1999, France, pp 448–459
Groover AT, Devey ME, Lee JM, Megraw R, Mitchell-Olds T, Sherman B, Vujcic S, Williams C, Neale DB (1994) Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine. Genetics 138:1293–1300
Groover AT, Williams CG, Devey ME, Lee JM, Neale DB (1995) Sex-related differences in meiotic recombination frequency in Pinus taeda. J Hered 86:157–158
Grotkopp E, Rejmanek M, Sanderson MJ, Rost TL (2004) Evolution of genome size in pines (Pinus) and its life-history correlates: supertree analyses. Evolution 58:1705–0729
Guevara MA, Chagné D, Almeida MH, Byrne M, Collada C, Favre JM, Harvengt L, Jeandroz S, Orazio C, Plomion C, Ramboer A, Rocheta M, Sebastiani F, Soto A, Vendramin GG, Cervera MT (2005a) Isolation and characterization of nuclear microsatellite loci in P. pinaster. Mol Ecol Notes 5:57–59
Guevara MA, Soto A, Collada C, Plomion C, Savolainen O, Neale DB, González-Martínez SC, Cerevera MT (2005b) Genomics applied to the study of adaptation in pine species. Invest Agrar Syst Recur For 14:292–306
Gugerli F, Senn J, Anzidei M, Madaghiele A, Buchler U, Sperisen C, Vendramin GG (2001) Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships of Swiss stone pine (Pinus cembra), Siberian stone pine (P. sibirica) and Siberian dwarf pine (P. pumila). Mol Ecol 10:1489–1497
Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Mol Biol 57:461–485
Gwaze DP, Harding KJ, Purnell RC, Bridgwater FE (2002) Optimum selection age for wood density in loblolly Pine. Can J For Res 32:1393–1399
Gwaze DP, Zhou Y, Reyes-Valdés MH, Al-Rababah MA, Williams CG (2003) Haplotypic QTL mapping in an outbred pedigree. Genet Res 81:43–50
Hamrick JL, Godt JW (1990) Allozyme diversity in plant species. In: Brown A, Clegg MT, Kahler AL, Weir BS (eds) Plant Population Genetics, Breeding and Genetic Resources. Sinauer, Sunderland, MA, pp 43–63
Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Phil Trans R Soc Lond B Biol Sci 351:1291–1298
Hannrup B, Ekberg I (1998) Age-age correlations for tracheid length and wood density in Pinus sylvestris. Can J For Res 28:1373–1379
Hannrup B, Ekberg I, Persson A (2000) Genetic correlations among wood, growth capacity and stem traits in Pinus sylvestris. Can J For Res 15:161–170
Harkins DM, Johnson GN, Skaggs PA, Mix AD, Dupper GE, Devey ME, Kinloch Jr BB, Neale DB (1998) Saturation mapping of a major gene for resistance to white pine blister rust in sugar pine. Theor Appl Genet 97:1355–1360
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
Hartmann HT, Kester DE, Davies FT Jr (1990) Plant Propagation Principles and Practices, 5th edn. Prentice Hall, Englewood Cliffs, NJ
Hayashi E, Kondo T, Terada K, Kuramoto N, Goto Y, Okamura M, Kawasaki H (2001) Linkage map of Japanese black pine based on AFLP and RAPD markers including markers linked to resistance against the pine needle gall midge. Theor Appl Genet 102:871–875
Hayashi E, Kondo T, Terada K, Kuramoto N, Kawasaki S (2004) Identification of AFLP markers linked to a resistance gene against pine needle gall midge in Japanese balck pine. Theor Appl Genet 108:1177–1181
Heath LS, Ramakrishnan N, Sederoff RR, Whetten RW, Chevone BI, Struble CA, Jouenne VY, Chen D, van Zyl LM, Grene R (2002) Studying the functional genomics of stress responses in loblolly pine with the “Expresso microarray experiment management system”. Comp Funct Genom 3:226–243
Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95–108
Hizume M, Arai M, Tanaka A (1990) Chromosome banding in the genus Pinus. III. Fluorescent banding pattern of P. luchuensis and its relationships among the Japanese diploxylon pines. Bot Mag Tokyo 103:103–111
Hizume M, Ohgiku A, Tanaka A (1989) Chromosome banding in the genus Pinus. II. Interspecific variation of fluorescent banding patterns in P. densiflora and P. thunbergii. Bot Mag Tokyo 102:25–36
Hizume M, Shibata F, Matsusaki Y, Garajova Z (2002) Chromosome identification and comparative karyotypic analyses of four Pinus species. Theor Appl Genet 105:491–497
Hodge GR, Dvorak WS (1999) Genetic parameters and provenance variation of Pinus tecunumanii in 78 international trials. For Genet 6:157–180
Hodge GR, Volker PW, Potts BM, Owen JV (1996) A comparison of genetic information from open-pollinated and control-pollinated progeny tests in two Eucalypt species. Theor Appl Genet 92:53–63
Hospital F, Goldringer I, Openshaw S (2000) Efficient marker-based recurrent selection for multiple quantitative trait loci. Genet Res 75:357–368
Hospital F, Moreau L, Lacoudre F, Charcosset A, Gallais A (1997) More on the efficiency of marker-assisted selection. Theor Appl Genet 95:1181–1189
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
Hyun SK (1976) Inter-specific hybridization in pines with the special reference to Pinus rigida and P. taeda. Silvae Genet 25:188–191
Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European Aspen (Populus tremula L., Salicaceae). Genetics 169:945–953
Isik F, Li B, Frampton J, Goldfarb B (2004) Efficiency of seedlings and rooted cuttings for testing and selection in Pinus taeda. For Sci 50:44–53
Islam-Faridi MN, Chang Y-L, Zhang HB, Kinlaw C, Doudrick RL, Neale DB, Echt CS, Price HJ, Stelly DM (1998) Construction of a pine BAC library. In: Plant & Animal Genome VI Conf, San Diego
Islam-Faridi MN, Mujeeb-Kazi A (1995) Visualization of Secale cereale DNA in wheat germplasm by FISH. Theor Appl Genet 90:595–600
Islam-Faridi MN, Nelson CD, Kubisiak TL (2007) Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L.). Genome (in press)
Islam-Faridi MN, Nelson CD, Kubisiak TL, Gullirmo MV, Mc-Namara VH, Price HJ, Stelly DM (2003) Loblolly pine karyotype using FISH and DAPI positive banding. In: Proc 27th Southern For Tree Improv Conf, 25–27 June 2003, Stillwater, OK, pp 184–188
Ivkovic M, Kumar S, Wu H (2006) Adding value to the end-products of radiatapine: A review of breeding for structural timber production. In: Proc 13th Australasian Plant Breed Conf, 18–22 April 2006, Christchurch, NZ, pp 273–278
Jackson RB, Schlesinger WH (2004) Curbing the U.S. carbon deficit. Proc Natl Acad Sci USA 101:15827–15829
Jacobs MD, Gardner RC, Murray BG (2000) Cytological characterization of heterochromatin and rDNA in Pinus radiate and P. taeda. Plant Syst Evo1 223:71–79
Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205–211
Jewell DC, Islam-Faridi MN (1994) Details of a technique for somatic chromosome preparation and C-banding of maize. In: Freeling M, Walbot V (eds) The Maize Hand Book. Springer, Berlin Heidelberg New York, pp 484–493
Jiang C, Zeng ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140:1111–1127
Jiang JM, Liu ZX, Lu BS, Jiang JM, Liu ZX, Lu BS (1999) Provenance genetic variation analysis of loblolly pine and determination of suitable provenances (areas). For Res Beijing 12:485–492
Johnson GR, Wheeler NC, Strauss SH (2000) Financial feasibility of marker-aided selection in Douglas-fir. Can J For Res 30:1942–1952
Kamm A, Doudrick RL, Heslop-Harrison JS, Schmidt T (1996) The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proc Natl Acad Sci USA 93:2708–2713
Kao C-H, Zeng J, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203–1216
Karhu A, Hurme P, Karjalainen M, Karvonen P, Kärkäinen K, Neal DB, Savolainen O (1996) Do molecular markers reflect patterns of differentiation in adaptive traits of conifers? Theor Appl Genet 93:215–221
Kärkäinen K, Savolainen O (1993) The degree of early inbreeding depression determines the selfing rate at the seed stage: model and results from Pinus sylvestris (Scots pine). Heredity 71:160–166
Kaya Z, Neale DB (1995) Utility of random amplified polymorphic DNA (RAPD)markers for linkage mapping in Turkish red pine (Pinus brutia Ten). Silvae Genet 44:110–116
Kaya Z, Sewell MM, Neale DB (1999) Identification of quantitative trait loci influencing annual height-and diameter-increment growth in loblolly pine (Pinus taeda L.). Theor Appl Genet 98:586–592
Kayihan GC, Huber DA, Morse AM, White TL, Davis JM (2005) Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theor Appl Genet 110:948–958
Kent J, Richardson TE (1997) Fluorescently labelled, multiplexed chloroplast microsatellites for high-throughput paternity analysis in Pinus radiata. NZ J For Sci 27:305–312
Khoshoo TN (1961) Chromosome numbers in gymnosperms. Silvae Genet 10:1–9
Kinlaw CS, Neale DB (1997) Complex gene families in pine genomes. Trends Plant Sci 2:356–359
Kinloch BB, Parks GK, Flower CW (1970) White pine blister rust: Simply inherited resistance in sugar pine. Science 167:193–195
Kirst M, Johnson 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
Kirst M, Myburg AA, De Leon JP, Kirst ME, Scott J, Sederoff R (2004) Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of Eucalyptus. Plant Physiol 135:2368–2378
Kirst M, Cordeiro CM, Rezende GDSP, Grattapaglia D (2005) Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. J Hered 96:161–166
Knott S, Neale DN, Sewell MM, Haley C (1997) Multiple marker mapping of quantitative trait loci in an outbred pedigree of loblolly pine. Theor Appl Genet 94:810–820
Komulainen P, Brown GR, Mikkonen M, Karhu A, Garcia-Gil MR, O’Malley DM, Lee B, Neale DB, Savolainen O (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 107:667–678
Kondo T, Terada K, Hayashi E, Kuramoto N, Okamura M, Kawasaki H (2000) RAPD markers linked to a gene for resistance to pine needle gall midge in Japanese black pine (Pinus thunbergii). Theor Appl Genet 100:391–395
Korol AB, Ronin YI, Kirzhner VM (1995) Interval mapping of quantitative trait loci employing correlated traits complexes. Genetics 140:1137–1147
Korol AB, Ronin YI, Nevo E, Hayes PM (1998) Multi-interval mapping of correlated trait complexes. Heredity 80:273–284
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
Kremer A (1992) Predictions of age-age correlations of total height based on serial correlations between height increments in Maritime pine (Pinus pinaster Ait.). Theor Appl Genet 85:152–158
Kriebel HB (1985) DNA sequence components of the Pinus strobus nuclear genome. Can J For Res 15:1–4
Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139–144
Krupkin AB, Liston A, Strauss SH (1996) Phylogenetic analysis of the hard pines (Pinus subgenus Pinus, Pinaceae) from chloroplast DNA restriction site analysis. Am J Bot 83:489–498
Krutovsky KV, Neale DB (2005) Nucleotide diversity and linkage disequilibrium in cold hardiness and wood quality related candidate genes in Douglas-fir. Genetics 171:2029–2041
Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB (2004) Comparative mapping in the Pinaceae. Genetics 168:447–461
Kuang H, Richardson TE, Carson SD, Bongarten B (1999b) Genetic analysis of inbreeding depression in plus tree 850.55 of Pinus radiata D. Don. II. Genetics of viability genes. Theor Appl Genet 99:140–146
Kuang H, Richardson TE, Carson SD, Wilcox PL, Bongarten B (1999a) Genetic analysis of inbreeding depress sion in plus tree 850.055 of Pinus radiata D. Don. 1. Genetic map with distorted markers. Theor Appl Genet 98:697–703
Kubisiak TL, Nelson CD, Nance WL, Stine M (1995) RAPD linkage mapping in a longleaf pine × slash pine F1 family. Theor Appl Genet 90:1119–1127
Kubisiak TL, Nelson CD, Nance WL, Stine M (1996) Comparison of RAPD linkage maps constructed for a single longleaf pine from both haploid and diploid mapping populations. For Genet 3:230–211
Kubisiak TL, Nelson CD, Nowak J, Friend AL (2000) Genetic linkage mapping of genomic regions conferring tolerance to high aluminum in slash pine. J Sust For 10:69–78
Kubisiak TL, Nelson, CD, Stine M (1997) RAPD mapping of genomic regions influencing early height growth in longleaf pine × slash pine F1 hybrids. In: Proc 24th Southern For Tree Improv Conf, Orlando, FL, 9–12 June 1997, pp 198–206
Kumar S (2004) Genetic parameter estimates for wood stiffness, strength, internal checking and resin bleeding for radiate pine. Can J For Res 34:2601–2610
Kumar S, Garrick DJ (2001) Genetic response to within-family selection using molecular markers in some radiata pine breeding schemes. Can J For Res 31:779–785
Kumar S, Richardson TE (2005) Inferring heritability and relatedness using molecular markers in radiata pine. Mol Breed 15:55–64
Kumar S, Spelman R, Garrick D, Richardson TE, Wilcox PL (2000) Multiple marker mapping of quantitative trait loci on chromosome three in an outbred pedigree of radiate pine. Theor Appl Genet 100:926–933
Kumar S, Echt C, Wilcox PL, Richardson TE (2004) Testing for linkage disequilibrium in the New Zealand radiata pine breeding population. Theor Appl Genet 108:292–298
Kumar S, Gerber S, Richardson TE (2006) Pedigree reconstruction using SSR markers in a radiata pine breeding programme. In: Proc 13th Australasian Plant Breed Conf, 17–21 April, Christchurch, New Zealand pp 578–583, http://www.apbc.org.nz
Kutil BL, Williams CG (2001) Triplet-repeat microsatellites shared among hard and soft pines. J Hered 92:327–32
Lambeth C (2000) Realized genetic gains for first generation improved loblolly pine in 45 tests in coastal North Carolina. J Appl For 24:140–144
Lambeth C, Lee BC, O’Malley D, Wheeler N (2001) Polymix breeding with parental analysis of progeny: an alternative to full-sib breeding and testing. Theor Appl Genet 103:930–943
Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS (2005) The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.). Genome 48:1120–1126
Lamprecht H (1990) Silviculture in the Tropics: tropical forest ecosystems and their tree species-possibilities and methods for their long-term utilization. GTZ, Eschborn, Germany
Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
Laurie CC, Chasalow SD, LeDeaux JR, McCarroll R, Bush D, Hauge B, Lai C, Clark D, Rocheford TR, Dudley JW (2004) The genetic architecture of response to long-term artificial selection for oil concentration in themaize kernel. Genetics 168:2141–2155
Le Dantec L, Chagné D, Pot D, Cantin O, Garnier-Géré P, Bedon F, Frigerio JM, Chaumeil P, Léger P, García V, Laigret F, de Daruvar A, Plomion C (2004) Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol Biol 54:461–470
Le Provost G, Paiva J, Pot D, Brach J, Plomion C (2003) Seasonal variation in transcript accumulation in wood forming tissues of maritime pine (Pinus pinaster Ait.) with emphasis on a cell wall Glycine Rich Protein. Planta 217:820–830
Ledig FT (1998) Genetic variation in Pinus. In: Richardson DM (ed) Ecology and Biogeography of Pinus. Cambridge University Press, Cambridge, UK, pp 251–280
Ledig FT, Conkle MT (1983) Gene diversity and genetic structure in a narrow endemic Torrey pine (Pinus torreyana Parry ex Carr). Evolution 37:79–85
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
Lerceteau EC, Plomion C, Andersson B (2000) AFLP mapping and detection of quantitative trait loci (QTLs) for economically important traits in Pinus sylvestris: a preliminary study. Mol Breed 6:451–458
Li C, Yeh FC (2001) Construction of a framework map in Pinus contorta subsp. latifolia using random amplified polymorphic DNA markers. Genome 44:147–153
Liston A, Robinson WA, Pinero D, Alvarez-Buylla ER (1999) Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Mol Phylogenet Evol 11:95–109
Liu ZL, Zhang D, Hong DY, Wang XR (2003) Chromosomal localization of 5S and 18S-5.8S-25S ribosomal DNA sites in five Asian pines using fluorescence in situ hybridization. Theor Appl Genet 106:198–204
Lopez-Upton J, White TL, Huber DA (2000) Species differences in early growth and rust incidence of loblolly and slash pine. For Ecol Mng 132:211–222
Lorenz WW, Dean JFD (2002) SAGE profiling and demonstration of differential gene expression along the axial developmental gradient of lignifying xylem in loblolly pine (Pinus taeda). Tree Physiol 22:301–310
Lorenz WW, Sun F, Liang C, Kolychev D, Wang H, Zhao X, Cordonnier-Pratt MM, Pratt LH, Dean JFD (2005) Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiol 26:1–16
Lorenz WW, Sun F, Liang C, Kolychev D, Wang H, Zhao X, Cordonnier-Pratt MM, Pratt LH, Dean JF (2006) Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiol 26:1–16
Lowe WJ, Byram TD, Bridgwater FE (1999) Selecting loblolly pine parents for seed orchards to minimise the costs of producing pulp. For Sci 45:213–216
Lubaretz O, Fuchs J, Ahne R, Meister A, Schubert I (1996) Karyotyping of three Pinaceae species via fluorescent in situ hybridization and computer-aided chromosome analysis. Theor Appl Genet 92:411–416
Luikart G, England P, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4:981–994
Lund MS, Sorensen P, Guldbrantsen B, Sorensen DA (2003) Multitrait fine mapping of quantitative trait loci using combined linkage disequilibrium and linkage analysis. Genetics 163:405–410
Ma XF, Szmidt A, Wang WR (2006) Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci. Mol Biol Evol 23:807–816
MacPherson P, Filion WG (1981) Karyotype analysis and the distribution of constitutive heterochromatin in five species of Pinus. J Hered 72:193–198
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
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
Markussen T, Fladung M, Achere V, Favre JM, Faivre-Rampant P, Aragones A, Da Silva Perez, Havengt L, Ritter E (2003) Identification of QTLs controlling growth, chemical and physical wood property traits inPinus pinaster (Ait.). Silvae Genet 52:8–15
Marquardt PE, Epperson BK (2004) Spatial and population genetic structure of microsatellites in white pine. Mol Ecol 13:3305–3315
Matheson AC, Lindgren D (1985) Gain from the clonal and the clonal seed orchard options compared for tree breeding programs. Theor Appl Genet 71:242–249
Matziris DI (1995) Provenance variation of Pinus radiata grown in Greece. Silvae Genet 44:88–96
McKeand S, Mullin T, Byram T, White TL (2003) Deployment of genetically improved loblolly and slash pines in the South USA. J For 101:32–37
Mergen F (1958) Natural polyploidy in slash pine. For Sci 4:283–295
Miksche JP, Hotta Y (19931973) DNA base composition and repetitious DNA in several conifers. Chromosoma 41:29–36
Millar CI (1998) Early evolution of pines. In: Richardson DM (ed) Ecology and Biogeography of Pinus. Cambridge University Press, Cambridge, UK, pp 69–91
Mitton JB (1992) The dynamic mating system of conifers. New For 6:187–216
Moore G, Devos KM, Wang Z, Gale MD (1995) Grasses, line up and form a circle. Curr Biol 5(7):737–739
Moran GF, Bell JC, Hilliker AJ (1983) Greater meiotic recombination in male vs. female gametes in Pinus radiata. J Hered 74:62
Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol 14:214–219
Morgante M, Vendramin GG, Rossi P, Olivieri AM (1993) Selection against in breds in early life-cycle phases in Pinus leucodermis. Heredity 70:622–627
Morin PA, Luikart G, Wayne RK, and the SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–2169
Morse AM, Nelson CD, Covert SF, Holliday AG, Smith KE, Davis JM (2004) Pine genes regulated by the necrotrophic pathogen Fusarium circinatum. Theor Appl Genet 109:922–932
Morse AM, Nelson CD, Covert SF, Smith KE, Davis JM (2004) Pine genes regulated by the necrotrophic pathogen, Fusarium circinatum. Theoretical and Applied Genetics 109:922–932
Morton NE (1991) Parameters of the human genome. Proc Natl Acad Sci USA 88:7474–7476
Mosig MO, Lipkin E, Khutoreskaya G, Tchourzyna E, Soller M, Friedmann A (2001) A whole genome scan for quantitative trait loci affecting milk protein percentage in Israeli-Holstein cattle, by means of selective milk DNA pooling in a Daughter design, using an adjusted false discovery rate criterion. Genetics 157:1683–1698
Moura VPG, Dvorak WS, Hodge GR (1998) Provenance and family variation of Pinus oocarpa grown in the Brazilian cerrado. For Ecol Manage 109:315–322
Müller-Starck G (1998) Isozymes. In: Karp A, Isaac PG, Ingram DS (eds) Molecular Tools for Screening Biodiversity: Plants and Animals. Chapman and Hall, London, UK, pp 75–81
Muona O, Harju A (1989) Effective population sizes, genetic variability and mating system in natural stands and seed orchards of Pinus sylvestris. Silvae Genet 38:221–228
Muona O, Yazdani R, Rudin R (1987) Genetic change between life stages in Pinus sylvestris: allozymes variation in seeds and planted seedlings. Silvae Genet 35:39–42
Murray B (1998) Nuclear DNA amounts in gymnosperms. Ann Bot 82(Suppl A):3–15
Myburg H, Morse AM, Amerson HV, Kubisiak TL, Huber DA, Osborne JA, Garcia SA, Nelson CD, Davis JM, Covert SF, van Zyl LM (2006) Differential gene expression in loblolly pine (Pinus taeda L.) challenged with the fusiform rust fungus, Cronartium quercuum f. sp. fusiforme. Physiological and Molecular Plant Pathology 69:79–101
Myers RM, Maniatis T, Lerman LS (1987) Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 155:501–527
Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9:325–330
Neale DB, Sederoff RR (1989) Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. Theor Appl Genet 77:212–216
Neale DB, Williams CG (1991) Restriction fragment length polymorphism mapping in conifers and applications to forest genetics and tree improvement. Can J For Res 21:545–554
Nelson CD, Echt CS (2003) New models for marker-assisted selection in tree breeding. In: McKinley C (ed) Proc 27th South For Tree Improv Conf, Stillwater, OK, p 114
Nelson CD, Echt CS (2004) Marker-directed population improvement. In: Li B, McKeand S (eds) Proc IUFRO Joint Conf of Div 2, For Genet Tree Breed in the Age of Genomics: Progress and Future, Charleston, SC, p 255
Nelson CD, Kubisiak TL, Johnson G, Burdine C, Bridgwater FE (2003) Microsatellite analysis of loblolly pine. In: Plant & Animal Genome XI Conf, San Diego, p 560 (http://www.intl-pag.org/11/abstracts/P5i_P560_XI.html, accessed 20 March 2006)
Nelson CD, Kubisiak, TL, Stine M, Nance WL (1994) A genetic linkage map of longleaf pine (Pinus palustris Mill.) basedon random amplified polymorphic DNAs. J Hered 85:433–439
Nelson CD, Nance WL, Doudrick RL (1993) A partial genetic linkage map of slash pine (Pinus elliottii Engelm. var. elliottii) based on random amplified polymorphic DNAs. Theor Appl Genet 8:145–151
Nelson JC (1997) QGENE: software for marker-based genomic analysis and breeding. Mol Breed 3:239–245
Nikles DG (2000) Experience with some Pinus hybrids in Queensland, Australia. In: Dungey HS, Dieters MJ, Nikles DG (Compl) Hybrid Breeding and Genetics of Forest Trees. Proc of QFRI/CRC-SPF Symp, 9–14 April 2000, Noosa, Queensland, Australia. Dept of Pri Indus, Brisbane, pp 14–26
No E, Zhou Y, Loopstra CA (2000) Sequences upstream and downstream of two xylem-specific pine genes influence their expression. Plant Sci 160:77–86
NSF (2005) NSF, USDA and DOE Award $32 Million to Sequence Corn Genome. Press Release 05-197. National Science Foundation. 11-15-2005. http://www.nsf.gov/news/news_summ.jsp?cntn_id=104608
O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins J Biol Chem 250:4007–4021
O’Malley D, Grattaplagia D. Chaparro JX, Wilcox PL, Amerson HV, Liu B-H, Whetton R, McKeand S, Kuhlman EG, McCord S, Crane B, Sederoff RR (1996) Molecular markers, forest genetics and tree breeding. In: Gustafson JP, Flavell RB (eds) Genomes of Plants and Animals: 21st Stadler Genet Symp. Plenum, New York
Ohri D, Khoshoo TN (1986) Genome size in gymnosperms. Plant Syst Evol 153:119–131
Olsson T, Lindgren D, Li B (2001) Balancing genetic gain and relatedness in seed orchards. Silvae Genet 50:222–227
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
Ott J (1991) Analysis of Human Genetic Linkage. Johns Hopkins University Press, Baltimore, MD
Pacheco D, Díaz S, Osuna D, Bautista R, Claros MG, Cánovas FM, Cantón FR (2005) Identification of candidate genes conferring specific properties to distinct types of Pinus pinaster Ait. wood. IUFRO Tree Biotechnol, Pretoria, South Africa
Paiva J (2006) Phenotypic and molecular plasticity of wood forming tissues in maritime pine (Pinus pinaster Ait.). PhD thesis of Universidad Nova de Lisboa and Bordeaux 1
Paran I, Zamir D (2003) Quantitative traits in plants: beyond the QTL. Trends Genet 19:303–306
Park YS (2002) Implementation of conifer somatic embryogenesis in clonal forestry: technical requirements and deployment considerations. Ann For Sci 59:651–656
Paterson AH, Freeling M, Sasaki T (2005) Grains of knowledge: genomics of model cereals. Genome Res 15:1643–1650
Paul AD, Foster GS, Caldwell T, McRae J (1997) Parameters for height, diameter, and volume in a multilocation clonal study with loblolly pine. For Sci 43:87–98
Pavy N, Laroche J, Bousquet J, MacKay J (2005) Large-scale analysis of secondary xylem ESTs in pine. Plant Mol Biol 57:203224
Perlack RD, Wright LL, Turhollow AF, Graham RL, Stokes BJ, Erbach DC (2005) Biomass as a feedstock for a bioenergy and bioproducts industry: the technical feasibility of a billion-ton annual supply. Report No DOE/GO-102005-2135. US Dept of Energy/US Dept of Agri. http://www1.eere.energy.gov/biomass/pdfs/final_billionton_vision_report2.pdf
Peterson DG (2005) Reduced representation strategies and their application to plant genomes. In: Meksem K, Kahl G (eds) The Handbook of Genome Mapping: Genetic and Physical Mapping. Wiley, Weinheim, pp 307–335
Peterson DG, Chouvarine P, Thummasuwan S, Saha S, Mukherjee D, Carlson JE (2006) Exploring the pine genome using Cot filtration and 454 Life Sciences massively parallel shotgun sequencing. In: Plant & Animal Genomes XIV Conf, San Diego. http://www.intl-pag.org/pag/14/abstracts/PAG14_W376.html
Peterson DG, Nelson CD, Islam-Faridi MN, Main DS, Tomkins JP (2005) Accelerating pine genomics through development and utilization of molecular and cytogenetic resources. In: Plant & Animal Genomes XIII Conf, San Diego. http://www.intl-pag.org/pag/13/abstracts/PAG13_P515.html
Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH (2002) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12:795–807
Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin GG (2005) Comparative organisation of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol Ecol 14:689–701
Petit RJ, Vendramin GG (2007) Phylogeography of organelle DNA in plants: an introduction. In: Weiss S, Ferrand N (eds) Phylogeography of Southern European Refugia. Kluwer, Amsterdam, (in press)
Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7:275–291
Plomion C, Durel C-E (1996) Estimation of the average effects of specific alleles detected by the pseudo-testcross QTL mapping strategy. Gen Sel Evol 28:223–235
Plomion C, O’Malley DM (1996) Recombination rate differences for pollen parents and seed parents in pine. Heredity 77:341–350
Plomion C, Bahrman N, Durel CE, O’Malley DM (1995a) Genomic analysis in Pinus pinaster (Maritime pine) using RAPD and protein markers. Heredity 74:661–668
Plomion C, O’Malley DM, Durel CE (1995b) 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
Plomion C, Durel C-E, O’Malley D (1996a) Genetic dissection of height in maritime pine seedlings raised under accelerated growth condition. Theor Appl Genet 93:849–858
Plomion C, Yani A, Marpeau A (1996b) Genetic determinism of ?3-carene in maritime pine using random amplified polymorphic DNA (RAPD) markers. Genome 39:1123–1127
Plomion C, Liu BH, O’Malley DM (1996c) Genetic analysis using trans dominant linked markers in an F2family. Theor Appl Genet 93:1083–1089
Plomion C, Costa P, Bahrman N, Frigerio JM (1997) Genetic Analysis of needle proteins in maritime pine. 1. Mapping dominant and codominant protein markers assayed on diploid tissue, in a haploid-based geneticmap. Silvae Genet 46:161–165
Plomion C, Hurme P, Frigerio J-M, Ridolphi M, Pot D, Pionneau C, Avila C, Gallardo F, David H, Neutlings G, Campbell M, Canovas FM, Savolainen O, Bodénès C, Kremer A (1999) Developing SSCP markers in two Pinus species. Mol Breed 5:21–31
Plomion C, Pionneau C, Brach J, Costa P, Baillères H (2000) Compression wood-responsive proteins in developing xylem of maritime pine (Pinus pinaster Ait.). Plant Physiol 123:959–969
Plomion C, LeProvost G, Pot D, Vendramin G, Gerber S, Decroocq S, Brach J, Raffin A, Pastuszka P (2001) Pollen contamination in a maritime pine polycross seed orchard and certification of improved seeds using chloroplast microsatellites. Can J For Res 31:1816–1825
Plomion C, Bahrman N, Costa P, Dubos C, Frigério J-M, Gerber S, Gion J-M, Lalanne C, Madur D, Pionneau C (2004) Proteomics for genetics and physiological studies in forest trees: application in maritime pine. In: Kumar S, Fladung M (eds) Molecular Genetics and Breeding of Forest Trees. Haworth, Binghamton, NY, pp 53–80
Pot D (2004) Déterminisme génétique de la qualité du bois chez le pinmaritime: du phénotype aux gènes. PhD thesis, University of Rennes I, ENSAR, France
Pot D, Chantre G, Rozenberg P, Rodrigues JC, Jones GL, Pereira H, Hannrup B, Cahalan C, Plomion C (2002) Genetic control of pulp and timber properties in maritime pine (Pinus pinaster Ait.). Ann For Sci 59:563–575
Pot D, McMillan L, Echt C, Le Provost G, Garnier-Géré P, Cato S, Plomion C (2005a) Nucleotide variation in genes involved in wood formation in two pine species. New Phytol 167:101–112
Pot D, Rodrigues J-C, Rozenberg P, Chantre G, Tibbits J, Cahalan C, Pichavant F, Plomion C (2005b) QTLs and candidate genes for wood properties in maritime pine (Pinus pinaster Ait.). Tree Genet Genom 2:10–26
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, UK, pp 49–68
Provan J, Soranzo N, Wilson NJ, Goldstein DB, Powell W (1999) A low mutation rate for chloroplast microsatellites. Genetics 153:943–947
Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J (2001) The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29:159–164
Quencez C, Bastien C (2001) Genetic variation within and between populations of Pinus sylvestris L. (Scots pine) for susceptibility to Melampsora pinitorqua Rostr. (pine twist rust). Heredity 86:36–44
Rabinowicz PD, Citek R, Budiman MA, Nunberg A, Bedell JA, Lakey N, O’Shaughnessy AL, Nascimento LU, McCombie WR, Martienssen RA (2005) Differential methylation of genes and repeats in land plants. Genome Res 15:1431–1440
Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, McCombie WR, Martienssen RA (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23:305–308
Rafalski A (1998) Randomly amplified polymorphic DNA (RAPD) analysis. In: Caetano-Anollés G, Gresshoff PM (eds) DNA Markers Protocols, Applications, and Overviews. Wiley-Liss, New York, pp 75–83
Rake AV, Miksche JP, Hall RB, Hansen KM (1980) DNA reassociation kinetics of four conifers. Can J Genet Cytol 22:69–79
Rat Genome Sequencing Project Consortium (2004) Rat Genome Sequencing Project Consortium, Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493–521
Remington DL, O’Malley DM (2000a) Evaluation of major genetic loci contributing to inbreeding depression for survival and early growth in a selfed family of Pinus taeda. Evolution 54:1580–1589
Remington DL, O’Malley DM (2000b) Whole genome characterization of embryonic state inbreeding depression in a selfed loblolly pine family. Genetics 155:337–348
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
Ribeiro MM, Plomion C, Petit RJ, Vendramin GG, Szmidt AE (2001) Variation of chloroplast single-sequence repeats in Portuguese maritime pine (Pinus pinaster Ait.). Theor Appl Genet 102:97–103
Richardson BA., Brunsfeld SJ, Klopfenstein NB (2002) DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization of whitebark pine (Pinus albicaulis). Mol Ecol 11:215–227
Richardson DM, Rundel PW (1998) Ecology and biogeography of Pinus: an introduction. In: Richardson DM (ed) Ecology and Biogeography of Pinus. Cambridge University Press, Cambridge, UK, pp 3–46
Ritland K, Zhuang J, Ralph S, Ritland C, Bohlmann J (2006) Comparative conifer genomics and the new “Treenomix” program. In: Plant & Animal Genomes XIV Conf, San Diego, W12
Ritter E, Aragonés A, Markussen T, Acheré V, Espinel S, Fladung M, Wrobel S, Faivre-Rampant P, Jeandroz S, Favre JM (2002) Toward construction of an ultra high density linkage map for Pinus pinaster. Ann For Sci 59:637–643
Robledo-Arnuncio JJ, Collada C, Alía R, Gil L (2005) Genetic structure of montane isolates of Pinus sylvestris L. in a Mediterranean refugial area. J Biogeogr 32:595–605
Rosvall O, Lindgren D, Mullen TJ (1998) Sustainability, robustness and efficiency of a multi-generation breeding strategy based on within-family clonal selection. Silvae Genet 47:307–321
Rounsley S, Xiaoying L, Ketchum KA (1998) Large-scale sequencing of plant genomes. Curr Opin Plant Biol 1:136–141
Rozenberg P, Van Loo J, Hannrup B, Grabner M. 2002. Clonal variation of wood density record of cambium reaction to water deficit in Picea abies (L.) Karst. Ann For Sci 59:533–540
Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8:321–329
Rudin D, Ekberg I (1978) Linkage studies in Pinus sylvestris L. using macrogametophyte allozymes. Silvae Genet 27:1–12
Sanchez AC, Ilag LL, Yang D, Brar DS, Ausubel F, Khush GS, Yano M, Sasaki T, Li Z, Huang N (1999) Genetic and physical mappingof xa13, a recessive bacterial blight resistance gene in rice. Theor Appl Genet 98:1022–1028
Sánchez C, Vielva MJ, Vieitez AM, de Mier B, Abarca D, Díaz-Sala C (2005) Identification of genes related to adventitious rooting capacity in pine and chestnut. IUFRO Tree Biotechnol, Pretoria, South Africa
Sathyan P, Newton RJ, Loopstra CA (2005) Genes induced by WDS are differentially expressed in two populations of aleppo pine (Pinus halepensis). Tree Genet Genom 1:166–173
Sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552–560
Sax K, Sax HJ (1933) Chromosome numbers and morphology in the conifers. J Arnold Arbor 14:356–375
Saylor LC (1961) A karyotype analysis of selected species of Pinus. Silvae Genet 10:77–85
Saylor LC (1964) Karyotype analysis of Pinus-group Lariciones. Silvae Genet 13:165–170
Saylor LC (1972) Karyotype analysis of Pinus-subgenus Pinus. Silvae Genet 21:155–163
Saylor LC (1983) Karyotype analysis of the genus Pinus — subgenus Strobus. Silvae Genet 32:119–121
Schmidt A, Doudrick RL, Heslop-Harrison JS, Schmidt T (2000) The contribution of short repeats of low sequence complexity to large conifer genomes. Theor Appl Genet 101:7–14
Schmidt R (2002) Plant genome evolution: lessons from comparative genomics at the DNA level. Plant Mol Biol 48:21–37
Scotti I, Burelli A, Cattonaro F, Chagné D, Fuller J, Hedley PE, Jansson G, Lalanne C, Madur D, Neale D, Plomion C, Powell W, Troggio M, Morgante M (2005) Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (P. abies karst). Tree Genet Genom 1:93–102
Scotti-Saintagne C, Bodénès C, Barreneche T, Bertocchi E, Plomion C, Kremer A (2004) Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L. Theor Appl Genet 109:1648–1659
Sewell MM, Bassoni DL, Megraw RA, Wheeler NC, Neale DB (2000) Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). I. Physical wood properties. Theor Appl Genet 101:1273–1281
Sewell MM, Davis MF, Tuskan GA, Wheeler NC, Elam CC, Bassoni DL, Neale DB (2002). Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). II. Chemical wood properties. Theor Appl Genet 104:214–222
Sewell MM, Neale DB (2000) Mapping quantitative traits in forest trees. In: Jain SM, Minocha SC (eds) Molecular Biology of Woody Plants. Kluwer, Dordrecht, pp 407–433
Sewell MM, Sherman BK, Neale DB (1999) A consensus map for loblolly pine (Pinus taeda L.). I. Construction and in etegration if individual linkage maps from two outbred three-generation pedigrees. Genetics 151:321–330
Shelbourne CJA (1992) Genetic gains from different kinds of breeding population and seed or plant production populations. S Afr For J 160:49–65
Shelbourne CJA (2000) Some insights on hybrids in forest tree improvement. In: Dungey HS, Dieters MJ, Nikles DG (Compl) Hybrid Breeding and Genetics of Forest Trees. Proc QFRI/CRC-SPF Symp, 9–14 April 2000, Noosa, Queensland, Australia. Dept of Pri Indus, Brisbane, pp 53–62
Shelbourne CJA, Apiolaza LA, Jayawickrama KJS, Sorensson CT (1997) Developing breeding objectives for radiata pine in New Zealand. In: Burdon R, Moore JM (eds) “IUFRO’ 97 Genetics of Radiata Pine”, Proc IUFRO Conf 1–4 Dec and workshop 5 Dec, Rotorua, New Zealand. FRI Bull 203:60–168
Shepherd M, Cross M, Dieters MJ, Henry R (2003) Genetic maps for Pinus elliottii var. elliottii and P. caribaea var. hondurensis using AFLP and microsatellite markers. Theor App Genet 106:1409–1419
Shepherd M, Cross M, Dieters MJ, Henry R (2002b) Branch architecture QTL for Pinus elliottii var. elliottii × Pinus caribea var. hondurensis hybrids. Ann For Sci 59:617–625
Shepherd M, Cross M, Maguire TL, Dieters MJ, Williams CG, Henry RJ (2002a) Transpecific microsatellites for hard pines. Theor Appl Genet 104:819–827
Shoulders E (1984) The case for planting longleaf pine. Proc of the Southern Silvicultural Res Conf, 7–8 Nov 1984, Atlanta, GA, pp 255–260
Smith DN, Devey M (1994) Occurrence and inheritance of microsatellites in Pinus radiata. Genome 37:977–983
Soranzo N, Alia R, Provan J, Powell W (2000) Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations. Mol Ecol 9:1205–1211
Sorensson CT, Shelbourne CJA (2005) Clonal forestry. In: Colley M (ed) Forestry Handbook. NZ Inst of Foresters, pp 92–96
Springer NM, Xu X, Barbazuk WB (2004) Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiol 136:3023–3033
Stelzer HE, Goldfarb B (1997) Implementing clonal forestry in the southeastern United States: SRIEG satellite workshop summary. Can J For Res 27:442–446
Stirling B, Yang ZK, Gunter LE, Tuskan GA, Bradshaw HD (2003) Comparative sequence analysis between orthologous regions of the Arabidopsis and Populus genomes reveals substantial synteny and microcollinearity. Can J For Res 33:2245–2251
Strabala TJ (2004) Expressed sequence tag databases from forestry tree species. In: Kumar S, Fladung M (eds) Molecular Genetics and Breeding of Forest Trees. Haworth, Binghamton, NY, pp 19–52
Strauss SH, Doerksen AH (1990) Restriction fragment analysis of pine phylogeny. Evolution 44:1081–1096
Strauss SH, Lande R, Namkoong G (1992) Limitations of molecular marker-aided selection in forest tree breeding. Can J For Res 22:1050–1061
Stromberg LD, Dudley JD, Rufener GK (1994) Comparing conventional early generation selection with molecular marker assisted selection in maize. Crop Sci 34:1221–1225
Stuber CW, Polacco M, Senior ML (1999) Synergy of empirical breeding, marker-assisted selection, and genomics to increase crop yield. Crop Sci 39:1571–1583
Syring J, Willyard A, Cronn R, Liston A (2005) Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. Am J Bot 92:2086–2100
Syvanen AC (2001) Accessing genetic variation. Genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942
Szmidt AE, Muona O (1989) Linkage relationships of allozyme loci in Pinus sylvestris. Heredity 111:91–97
Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203
Telfer EJ, Echt CS, Nelson CD, Wilcox PL (2006) Comparative mapping in Pinus radiata and P. taeda reveals co-location of wood density-related QTL. In: Plant & Animal Genome XIV Conf, San Diego
Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM, Neale DB (2001) Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theor Appl Genet 102:664–675
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Thiellement H, Plomion C, Zivy M (2001) Proteomics as a tool for plant genetics and breeding. In:Dunn MJ, Pennington S (eds) Proteomics: from protein sequence to function. BIOS, Oxford, pp 289–309
Thoday JM (1961) Location of polygenes. Nature 191:368–370
Thumma BR, Nolan MF, Evans R, Moran GF (2005) Polymorphisms in Cinnamoyl CoA Reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171:1257–1265
Travis SE, Ritland K, Whitham TG, Keim P (1998) A genetic linkage map of pinyon pine (Pinus edulis) based on amplified fragment length polymorphisms. Theor Appl Genet 97:871–880
Tulsieram LK, Glaubitz JC, Kiss G, Carlson JE (1992) Single tree genetic linkage mapping in conifers using haploid DNA from megagametophytes. Bio/Technology 10:686–690
Tuskan GA, DiFazio SP, Teichmann T (2004) Poplar genomics is getting popular: the impact of the poplar genome project on tree research. Plant Biol (Stuttg) 6:2–4
Van der Burgh J (1973) Hölzer der nierderrheinischen Braunkohlenformation. 2. Hölzer der Braunkohlengruben ‚Maria Theresia ‘zu Herzogenrath, ‚Zukunft West ‘zu Eschweiler und ‚Victor ‘(Zülpich Mitte) zu Zülpich. Nebst einer systematisch-anatomischen Bearbeitung der Gattung Pinus L. Rev Palaeobot Palynol 15:73–275
van Tienderen PH, de Haan AA, van der Linden CG, Vosman B (2002) Biodiversity assessment using markers for ecologically important traits. Trends Ecol Evol 17:577–582
van Zyl L, von Arnold S, Bozhkov P, Chen Y, Egertsdotter U, MacKay J, Sederoff R, Weir B, Shen J, Sun Y-H, Whetten R, Zelena L, Clapham D (2002) Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. taeda, P. sylvestris or Picea abies. Comp Funct Genom 3:306–318
Verhaegen D, Plomion C, Poitel M, Costa P, Kremer A (1998) Quantitative trait disscetion analysis in Eucalyptus using RAPD markers: 2. linkage disequilibrium in a factorial design between E. urophylla and E. Grandis. For Genet 5:61–69
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Wahlenberg WG (1946) Longleaf Pine. Charles Lathrop Pack Forestry Foundation, Washington, DC
Wakamiya I, Price HJ, Messina MG, Newton RJ (1996) Pine genome size diversity and water relations. Physiol Planta 96:13–20
Walker S, Haines R, Dieters M (1996) Beyond 2000. In: Dieters MJ, Matheson AC, Nikles DG, Harwood CE (eds) Clonal Forestry in Queensland. Queensland For Res Inst. Tree Improvement for Sustainable Tropical Forestry. QFRIIUFRO Conf, Caloundra, Queensland, Australia, 27 Oct–1 Nov 1996, vol 2, pp 351–354
Walter R, Epperson BK (2001) Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations. Mol Ecol 10:103–111
Wang XR, Szmidt AE, Nguyen HN (2000) The phylogenetic position of the endemic flat-needle pine Pinus krempfii (Pinaceae) from Vietnam based on PCR-RFLP analysis of chloroplast DNA. Plant Syst Evol 220:21–36
Wang XR, Szmidt AE, Savolainen O (2001) Genetic composition and diploid hybrid speciation of a high mountain pine, Pinus densata, native to the Tibetan plateau. Genetics 159:337–346
Wang XT, Tsumara Y, Yoshimaru H, Nagasaka K, Szmidt A (1999) Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcL, matK, rpl20-rps18 spacer, and trnV intron sequences. Am J Bot 86:1742–1753
Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res 30:103–105
Watkinson JI, Sioson AA, Vasquez-Robinet C, Shukla M, Kumar D, Ellis M, Heath LS, Ramakrishnan N, Chevone B, Watson LT, van Zyl L, Egertsdotter U, Sederoff RR, Grene R, et al (2003) Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine. Plant Physiol 133:1702–1716
Wei RP, Lindgren D, Yeh FC (1997) Expected gain and status number following restricted individual and combined-index selection. Genome 40:1–8
Weng C, Kubisiak TL, Nelson CD, Stine M (2002) Mapping quantitative trait loci controlling early growth in a (longleaf pine × slash pine) × slash pine BC1 family. Theor Appl Genet104:852–859
Weng C, Kubisiak TL, Stine M (1998) SCAR markers in a longleaf pine × slash pine F1 family. For Genet 5:239–247
Whetten R, Sun Y, Zhang Y Sederoff RR (2001) Functional genomics and cell wall biosynthesis in loblolly pine. Plant Mol Biol 47:275–291
Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, van Heeringen S, Karamycheva S, Bennetzen JL, San Miguel P, Lakey N, Bedford J, Yuan Y, Budiman MA, Resnick A, van Aken S, Utterback T, Riedmuller S, Williams SM, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302:2118–2120
Wilcox PL (1995) Genetic dissection of fusiform rust resistance. PhD Thesis, Dept of Forestry, North Carolina State University, Raleigh, NC
Wilcox PL (1997) Linkage groups, map length, and recombination in Pinus radiata. In: Burdon RD, Moore JM (eds) “IUFRO’ 97 Genetics of Radiata Pine”, Proc IUFRO Conf 1–4 Dec and workshop 5 Dec, Rotorua, New Zealand. FRI Bull 20
Wilcox PL, Burdon RD (2006) Application of association genetics to coniferous forest trees. In: Proc 13th Australasian Plant Breed Conf, Christchurch, New Zealand pp 651–659, http://www.apbc.org.nz
Wilcox PL, Amerson HV, Kuhlman EG, Liu B-H, O’Malley DM, Sederoff RR (1996) Detection of a major gene for resistance to fusiform rust disease in loblolly pine by genomic mapping. Proc Natl Acad Sci USA 93:3859–3864
Wilcox PL, Richardson TE, Carson SD (1997) Nature of quantitative trait variation in Pinus radiata: insights from QTL detection experiments. In: Burdon RD, Moore JM (eds) “IUFRO’ 97 Genetics of Radiata Pine”, Proc IUFRO Conf 1–4 Dec and workshop 5 Dec, Rotorua, New Zealand. FRI Bull 203:304–312
Wilcox PL, Richardson TE, Corbet GE, Ball RD, Lee JR, Djorovic A, Carson SD (2001a) Framework Linkage Maps of Pinus radiata D. Don based on pseudotestcross markers. For Genet 8:109–117
Wilcox PL, Carson SD, Richardson TE, Ball RD, Horgan GP, Carter P (2001b) Benefit-cost analysis of DNA marker-based selection in progenies of Pinus radiata seed orchard parents. Can J For Res 31:2213–2224
Wilcox PL, Echt CS, Cato SA, McMillan LK, Kumar S, Ball RD, Burdon RD, Pot D (2003) Gene assisted selection — a new paradigm for selection in forest tree species? In: Plant & Animal Genomes XI Conf, San Diego
Wilcox PL, Cato S, McMillan L, Power M, Ball RD, Burdon RD, Echt CS (2004) Patterns of linkage disequilibrium in Pinus radiata. In: Plant & Animal Genome XII Conf, San Diego, W89. http://www.intlpag.org/12/abstracts/W22_PAG12_89.html
Wilcox PL, Echt CS, Burdon RD (2007) Gene-assisted selection: applications of association genetics for forest tree breeding. In: Oraguzie N, Rikkerink EHA, Gardiner SA, Nihal De Silva H (eds) Association Mapping in Plants. Springer, Berlin Heidelberg New York, pp 211–247
Williams CG, Neale DB (1992) Conifer wood quality and marker-aided selection: a case study. Can J For Res 22:1009–1017
Williams C, Megraw RA (1993) Juvenile-mature relationships for wood density in Pinus taeda. Can J For Res 24:714–722
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
Williams CG, Zhou Y, Hall SE (2001) A chromosomal region promoting outcrossing in a conifer. Genetics 159:1283–1289
Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22:506–519
Wu H (2002) Study of early selection in tree breeding. 4. Efficiency of marker aided early selection (MAES). Silvae Genet 51:261–269
Wu J, Krutovskii KV, Strauss SH (1999) Nuclear DNA diversity, population differentiation, and phylogenetic relationship in the Californian closed-cone pines based on RAPD and allozyme markers. Genome 42:893–908
Wu R, Ma C-X, Casella G (2002) Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics 160:779–792.
Yan HH, Mudge J, Kim DJ, Shoemaker RC, Cook DR, Young ND (2004) Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47:141–155
Yang SH, Loopstra CA (2005) Seasonal variation in gene expression for loblolly pines (Pinus taeda) from different geographical regions. Tree Physiol 25:1063–107325(8)
Yazdani R, Nilsson JE, Plomion C, Mathur G (2003) Marker trait association for autumn cold acclimatation and growth rhythm in Pinus sylvestris. Scand J For Res 18:29–38
Yazdani R, Yeh FC, Rimsha J (1995) Genomicmapping of Pinus sylvestris (L.) using random amplified polymorphic DNA markers. For Genet 2:109–116
Yin TM, Huang MR, Wang MX, Zhu LH, Zhai WX (1997) Construction of molecular linkage map in masson pine using RAPD markers and megagametophytes from a single tree. Acta Bot Sin 39:607–612
Yin TM, Wang XR, Andersson B, Lerceteau-Köhler E (2003) Nearly complete maps of Pinus sylvestris L. (Scots pine) constructed by AFLP marker analysis in a full-sib family. Theor Appl Genet 106:1075–1083
Yuan Y, SanMiguel PJ, Bennetzen JL (2003) High-Cot sequence analysis of the maize genome. Plant J 34:249–255
Zeng ZB (1993a) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90:10972–10976
Zeng ZB (1993b) Precision mapping of quantitative trait loci. Genetics 136:1457–1468
Zeng ZB, Liu J, Stam LF, Kao CH, Mercer JM, Cathy CL (2000) Genetic architecture of a morphological shape difference between two drosophila species. Genetics 154:299–310
Zhang H-B, Wu C (2001) BACs as tools for genome sequencing. Plant Physiol Biochem 39:195–209
Zheng Y, Ennos R, Wang HR, Zheng YQ, Wang HR (1994) Provenance variation and genetic parameters in a trial of Pinus caribaea Morelet var. bahamensis Barr and Golf. For Genet 1:165–174
Zhou Y, Bui T, Auckland L, Williams CG (2002) Undermethylation as a Source of microsatellites in large plant genomes. Genome 34:91–99
Zhou Y, Gwaze DP, Reyes-Valdes MH, Biu T, Williams CG (2003) No clustering for linkage map based on low-copy and undermethylated microsatellites. Genome 46:809–816
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Plomion, C. et al. (2007). Pines. In: Kole, C. (eds) Forest Trees. Genome Mapping and Molecular Breeding in Plants, vol 7. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-34541-1_2
Download citation
DOI: https://doi.org/10.1007/978-3-540-34541-1_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-34540-4
Online ISBN: 978-3-540-34541-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)