You have full text access to this OnlineOpen article
Forest-tree population genomics and adaptive evolution
Article first published online: 27 MAR 2006
DOI: 10.1111/j.1469-8137.2006.01686.x
Additional Information
How to Cite
González-Martínez, S. C., Krutovsky, K. V. and Neale, D. B. (2006), Forest-tree population genomics and adaptive evolution. New Phytologist, 170: 227–238. doi: 10.1111/j.1469-8137.2006.01686.x
Publication History
- Issue published online: 27 MAR 2006
- Article first published online: 27 MAR 2006
- Received: 21 December 2005 Accepted: 11 January 2006
References
- , . 2000. Magnitude and implications of gene flow in gene conservation reserves. In: YoungA, BoshierD, BoyleT, eds. Forest Conservation Genetics: Principles and Practice. Wallingford, UK: CABI Publishing, 215–224.
- , . 1981. Genetic adaptation and source specificity. In: HobbsSD, HelgersonOT, eds. Reforestation of Skeletal Soils. Corvallis, OR, USA: Forest Research Laboratory, Oregon State University, 78–85.
- . 2003. Community genetics: new insights into community ecology by integrating population genetics. Ecology 84: 543–544.
- , , , , . 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Research 12: 1805–1814.
- , . 2003. Functional markers in plants. Trends in Plant Science 8: 554–560.
- , , , , , , , , , , , , , , , , , , , , , . 2004. A transcriptional timetable of autumn senescence. Genome Biology 5: R24.
- , . 2004. Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology 13: 969–980.
- , . 1996. Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London B 263: 1619–1626.
- , . 2004. The Bayesian revolution in genetics. Nature Reviews Genetics 5: 251–261.
- , , , . 2001. Population genomics: genome-wide sampling of insect populations. Annual Review of Entomology 46: 441–469.
- , . 2000. Forest conservation genetics: limitations and future directions. In: YoungA, BoshierD, BoyleT, eds. Forest Conservation Genetics: Principles and Practice. Wallingford, UK: CABI Publishing, 289–297.
- , , , , . 2002. Genetic parameters and QTL analysis of δ13C and ring width in maritime pine. Plant, Cell & Environment 25: 945–953.
- , , , , , , , , , . 2003. Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL verification and candidate gene mapping. Genetics 164: 1537–1546.
- , , , , . 2004. Nucleotide variation and linkage disequilibrium in loblolly pine. Proceedings of the National Academy of Sciences, USA 101: 15255–15260.
- . 1979. Genecology of Douglas-fir in a watershed in the Oregon Cascades. Ecology 60: 1036–1050.
- , , , . 2003. Forestry's fertile crescent: the application of biotechnology to forest trees. Plant Biotechnology Journal 1: 141–154.
- , . 2001. Association study designs for complex diseases. Nature Reviews Genetics 2: 91–99.
- , , , , , , . 2004. Identification of QTLs affecting adaptive traits in Castanea sativa Mill. Plant, Cell & Environment 27: 1088–1101.
- , , , , , , . 2003. Comparative genome and QTL mapping between maritime and loblolly pines. Molecular Breeding 12: 185–195.
- , , , , , , , , , , , . 2004. Cross species transferability and mapping of genomic and cDNA SSRs in pines. Theoretical and Applied Genetics 109: 1204–1214.
- , , , , , . 2004a. QTL associations for density and diameter in Pinus radiata and the potential for marker-aided selection. Theoretical and Applied Genetics 108: 516–524.
- , , , , , , , . 2004b. Detection and verification of quantitative trait loci for resistance to Dothistroma needle blight in Pinus radiata. Theoretical and Applied Genetics 108: 1056–1063.
- . 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics 3: 43–52.
- , . 2003. Identification of water-deficit responsive genes in maritime pine (Pinus pinaster Ait.) roots. Plant Molecular Biology 51: 249–262.
- , , , , , , , . 2003. Identification and characterization of water-stress-responsive genes in hydroponically grown maritime pine (Pinus pinaster) seedlings. Tree Physiology 23: 169–179.
- , , , . 2002. Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Molecular Biology and Evolution 19: 179–188.
- . 1998. Evolutionary forces influencing variation among populations of Pinus sylvestris. Silva Fennica 32: 173184.
- , . 2003. Evolutionary and ecological functional genomics. Nature Reviews Genetics 4: 649–655.
- , , , , , , . 2002. Leaf stomatal and epidermal cell development: identification of putative quantitative trait loci in relation to elevated carbon dioxide concentration in poplar. Tree Physiology 22: 633–640.
- . 2002. Applications of selective neutrality tests to molecular ecology. Molecular Ecology 11: 1245–1262.
- . 2004. Genetic predisposition to cancer – insights from population genetics. Nature Reviews Genetics 5: 764–772.
- , , . 2002. Introduction to Conservation Genetics. Cambridge, UK: Cambridge University Press.
- , , , , , , . 2000. Quantitative trait loci and candidate gene mapping of bud set and bud flush in Populus. Genetics 154: 837–845.
- , , . 2003. Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Molecular Ecology 12: 1195–1206.
- . 2002. Microarrays in ecology and evolution: a preview. Molecular Ecology 11: 17–24.
- , , , , . 2004. English elm is a 2000-year-old Roman clone. Nature 431: 1053.
- , , , , , , , , , , , , . 2004. Genetic resources in maritime pine (Pinus pinaster Aiton): molecular and quantitative measures of genetic variation and differentiation among maternal lineages. Forest Ecology and Management 197: 103–115.
- , , , , . 2006. DNA sequence variation and selection of tag SNPs at candidate genes for drought-stress response in Pinus taeda L. Genetics. (In press.)
- . 2004. Integrating genomics into eucalyptus breeding. Genetics Molecular Research 3: 369–379.
- , , , , , , , . 2005. Genomics applied to the study of adaptation in pine species. Investigación Agraria: Sistemas y Recursos Forestales 14: 292–306.
- , . 2004. Molecular markers from the transcribed/expressed region of the genome in higher plants. Functional and Integrative Genomics 4: 139–162.
- , , . 2005. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology 57: 461–485.
- . 2004. Response of forest trees to global environmental changes. Forest Ecology and Management 197: 323–335.
- , . 2000. Gene flow in forest trees. In: YoungA, BoshierD, BoyleT, eds. Forest Conservation Genetics: Principles and Practice. Wallingford, UK: CABI Publishing, 81–90.
- , , . 1992. Factors influencing levels of genetic diversity in woody plant species. New Forests 6: 95–124.
- , . 2005. Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics 6: 95–108.
- . 2005. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169: 945–953.
- , . 2002. Association mapping in plant populations. In: KangMS, ed. Quantitative Genetics, Genomics and Plant Breeding. Wallingford, UK: CABI Publishing, 59–68.
- , , , . 2003. DNA sequence variation in BpMADS2 gene in two populations of Betula pendula. Molecular Ecology 12: 369–384.
- , , , , . 2001a. Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. I. Timing of vegetative bud flush. Theoretical and Applied Genetics 102: 1142–1151.
- , , , , , , . 2001b. Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. II. Spring and fall cold-hardiness. Theoretical and Applied Genetics 102: 1152–1158.
- , , , , , . 2003. Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas fir. III. Quantitative trait loci-by-environment interactions. Genetics 165: 1489–1506.
- , , , . 2003. DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics 164: 1547–1559.
- , , , , , , . 1996. Do molecular markers reflect patterns of differentiation in adaptive traits of conifers? Theoretical and Applied Genetics 93: 215–221.
- , , , , , . 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 Physiology 135: 2368–2378.
- . 2000. Methods to detect selection in populations with applications to the human. Annual Review of Genomics and Human Genetics 1: 539–559.
- , . 2005a. Forest genomics and new molecular genetic approaches to measuring and conserving adaptive genetic diversity in forest trees. In: GeburekT, TurokJ, eds. Conservation and Management of Forest Genetic Resources in Europe. Zvolen, Slovakia: Arbora Publishers, 369–390. http://www.fao.org/DOCREP/003/X6884E/X6884E00.HTM
- , . 2005b. Nucleotide diversity and linkage disequilibrium in cold hardiness and wood quality related candidate genes in Douglas-fir. Genetics 171: 2029–2041.
- . 2001. From library screening to microarray technology: strategies to determine gene expression profiles and to identify differentially regulated genes in plants. Annals of Botany 87: 139–155.
- . 2001. Methods for genotyping single nucleotide polymorphism. Annual Review of Genomics and Human Genetics 2: 235–258.
- , , , . 2005. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6: 1–12. http://www.biomedcentral.com/1471-2164/6/23
- , . 1990. Genetic structure of Norway spruce (Picea abies): concordance of morphological and allozymic variation. Evolution 44: 38–53.
- , , , , , , , , , , , , . 2004. Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Molecular Biology 54: 461–470.
- , , . 2000. AFLP mapping and detection of quantitative trait loci (QTLs) for economically important traits in Pinus sylvestris: a preliminary study. Molecular Breeding 6: 451–458.
- , , . 2001. Detection of quantitative trait loci in Pinus sylvestris L. across years. Euphytica 121: 117–122.
- , . 1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175–195.
- , , , . 2004. Microsatellites within genes: structure, function, and evolution. Molecular Biology and Evolution 21: 991–1007.
- . 2000. Variation in woody plants: molecular markers, evolutionary processes and conservation biology. In: JainSM, MinochaSC, eds. Molecular Biology of Woody Plants Forestry Sciences, Vol. 64. Dordrecht, the Netherlands: Kluwer Academic, 341–374.
- , . 1999. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Research 9: 720–731.
- , , , , . 2003. The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics 4: 981–994.
- , , , . 2003. Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution 18: 189–197.
- , , , . 2004. The effects of human population structure on large genetic association studies. Nature Genetics 36: 512–517.
- , , , . 2002. Sampling within the genome for measuring within-population diversity: trade-offs between markers. Molecular Ecology 11: 1145–1156.
- , , , , , , , , , . 2003. Identification of QTLs controlling growth, chemical and physical wood property traits in Pinus pinaster (Ait.). Silvae Genetica 52: 8–15.
- . 2001. Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nature Reviews Genetics 2: 370–381.
- , . 2002. Adaptive population divergence: markers, QTL and traits. Trends in Ecology and Evolution 17: 285–291.
- , , . 1988. Multivariate analysis of allozyme variation patterns in coastal Douglas-fir from southwest Oregon. Canadian Journal of Forest Research 18: 181–187.
- , . 2004. Genetic variation in piñon pine, Pinus edulis, associated with summer precipitation. Molecular Ecology 13: 1259–1264.
- , , . 1998. Variation in allozymes and stomatal size in pinyon (Pinus edulis, Pinaceae), associated with soil moisture. American Journal of Botany 85: 1262–1265.
- , , , , , . 2003. Development and characterization of microsatellite markers for Cryptomeria japonica D. Don. Theoretical and Applied Genetics 106: 751–758.
- . 2002. Strategies to protect biological diversity and the evolutionary processes that sustain it. Systematic Biology 51: 238–254.
- . 2001. Forest genetics: pattern and complexity. Canadian Journal of Forest Research 31: 623–632.
- , , . 1998. The breeding structure of a tropical keystone plant resource. Nature 391: 685–687.
- , . 2004. Association genetics of complex traits in conifers. Trends in Plant Science 9: 325–330.
- , , . 2002. Molecular dissection of the quantitative inheritance of wood property traits in loblolly pine. Annals of Forest Science 5: 595–605.
- , , , , . 1999. Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends in Ecology and Evolution 14: 140–145.
- , . 2000. Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspectives in Plant Ecology, Evolution and Systematics 3: 93–114.
- , , . 1999. Population genetics, molecular markers and the study of dispersal in plants. Journal of Ecology 87: 551–568.
- , , , , , , , , , , , . 2004. Investigating the utility of combining Φ29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray genotyping. BMC Biotechnology 4: 15. http://www.biomedcentral.com/1472-6750/4/15
- , ed. 1998. Molecular Dissection of Complex Traits. New York, USA: CRC Press.
- , , . 2002. Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Molecular Biology and Evolution 7: 1143–1153.
- , . 2004. Molecular basis for the evolution of xylem lignification. Current Opinion in Plant Biology 7: 737–742.
- , , , , , , , , , , , , , , , , . 2003. Glacial refugia: hotspots but not melting pots of genetic divesity. Science 300: 1563–1565.
- , , , , , . 2005. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology 14: 689–701.
- . 2004. Déterminisme Génétique de la Qualité du Bois chez le Pin Maritime, du Phénotype aux Gènes. PhD Thesis. Rennes, France: ENSA.
- , , , , , , , , . 2002. Genetic control of pulp and timber properties in maritime pine (Pinus pinaster Ait.). Annals of Forest Science 59: 563–575.
- , , , , , , . 2005. Nucleotide variation in genes involved in wood formation in two pine species. New Phytologist 167: 101–112.
- , . 2004. Regulatory SNPs in complex diseases: their identification and functional validation. Expert Reviews in Molecular Medicine 6: 1–15.
- , . 2003. Merging ecology, molecular evolution, and functional genetics. Molecular Ecology 12: 1109–1112.
- , . 2004. Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends in Genetics 20: 103–111.
- , , , . 1999. Genetic responses to climate in Pinus contorta: niche breadth, climate change and reforestation. Ecological Monographs 69: 375–407.
- , , . 2001. Physiological plasticity, evolution, and impacts of a changing climate on Pinus contorta. Climatic Change 50: 355–376.
- , , , . 2001. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293: 2242–2245.
- , , . 2005. QTL analyses of drought tolerance and growth for a Salix dasyclados×Salix viminalis hybrid in contrasting water regimes. Theoretical and Applied Genetics 110: 537–549.
- , . 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics 3: 380–390.
- , , , , , , , . 2004. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5: 1–9. http://www.biomedcentral.com/1471-2164/5/99
- , , , , , , . 2004. A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.). Theoretical and Applied Genetics 108: 433–441.
- , , , , . 2005. A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169: 1601–1615.
- , , , , , . 2000. Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences. Genome 43: 41–46.
- , , , , , . 2004a. Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L. Theoretical and Applied Genetics 109: 1648–1659.
- , , , , , , , . 2004b. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics 168: 1615–1626.
- , , , , , , , . 2001. Monitoring the expression patterns of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13: 61–71.
- , . 2000. Mapping quantitative traits in forest trees. In: JainSM, MinochaSC, eds. Molecular Biology of Woody Plants. Forestry Sciences Vol. 64. Dordrecht, the Netherlands: Kluwer Academic, 407–423.
- , , , , , , . 2002. Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.). II. Chemical wood properties. Theoretical and Applied Genetics 104: 214–222.
- , . 2004. Measuring pollen flow in forest trees: a comparison of alternative approaches. Forest Ecology and Management 197: 21–38.
- , , . 1993. Transmission test for linkage disequilibrium, the insulin gene region and insulin-dependent diabetes mellitus, IDDM. American Journal of Human Genetics 52: 506–516.
- . 2005. Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology 14: 671–688.
- , , , , , , . 2004. Identification of quantitative trait loci for wood and fibre properties in two full-sib pedigrees of Eucalyptus globulus. Theoretical and Applied Genetics 109: 856–864.
- , , . 2002. An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix. Theoretical and Applied Genetics 105: 277–288.
- , , . 2003. Mapping of quantitative trait loci controlling timing of bud flush in Salix. Hereditas 138: 172–178.
- , , . 2004. Mapping of quantitative trait loci (QTLs) affecting autumn freezing resistance and phenology in Salix. Theoretical and Applied Genetics 108: 1335–1342.
- , , , , , . 2004. Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Canadian Journal of Forest Research 34: 85–93.
- , , . 2005. Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution 22: 1067–1076.
- , . 2005. Connections between species diversity and genetic diversity. Ecology Letters 8: 767–781.
- , , . 2001. Interpretation of variation across marker loci as evidence of selection. Genetics 158: 1811–1823.
- , , , . 2005. Genome–wide association studies: theoretical and practical concerns. Nature Reviews Genetics 6: 109–118.
- , , , , , , , , , , , , , . 2003. Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine. Plant Physiology 133: 1702–1716.
- , , , . 2002. Mapping quantitative trait loci controlling early growth in a (longleaf pine × slash pine) × slash pine BC1 family. Theoretical and Applied Genetics 104: 852–859.
- , , , , , , . 2005. Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. IV. Cold-hardiness QTL verification and candidate gene mapping. Molecular Breeding 15: 145–156.
- , , , , , , , , , , , . 2003. Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 84: 559–573.
- , , , , , , , , , , . 2003. Quantitative trait loci for growth trajectories in Populus. Genetical Research 81: 51–64.
- , , , . 2004. Seasonal changes in gene expression at the sapwood–heartwood transition zone of black locust (Robinia pseudoacacia) revealed by cDNA microarray analysis. Tree Physiology 24: 461–474.
- , . 2005. Seasonal variation in gene expression for loblolly pine (Pinus taeda) from different geographical regions. Tree Physiology 25: 1063–1073.
- , , , . 2003. Marker trait association for autumn cold acclimation and growth rhythm in Pinus sylvestris. Scandinavian Journal of Forest Research 18: 29–38.

1469-8137/asset/NPH_left.gif?v=1&s=08bb9ae88048d5716b3d3495e7b2fcfe48536ab2)
