The economic and ecological importance of forest trees, as well as their unique biological features, has recently raised the level of interest in studies on their genomes, including sequencing of the entire poplar genome. However, cytogenetic studies have not moved in parallel with developments in genomics. This is especially true for hardwood species characterized by small genomes and relatively high numbers of small chromosomes. Molecular cytogenetic studies have mainly been focused on coniferous species, owing to the larger size of their chromosomes, and have been applied exclusively for chromosome identification and comparative karyotyping in an attempt to understand genome evolution and phylogenetic relationships. In this context, rRNA genes physical mapped by FISH reveal particularly useful chromosomal landmarks with variable distribution patterns between species. Here we present a contribution of DNA markers used for chromosome analysis, which already allowed a deeper characterization and understanding of the processes underlying genome diversity of forest trees. The use of advanced cytogenetic techniques and other potential important methods for genome analysis of forest trees is also discussed.

1.
Ahuja M: Recent advances in molecular genetics of forest trees. Euphytica 121:173–195 (2001).
2.
Ahuja M: Polyploidy in gymnosperms: Revisited. Silvae Genet 54:59–69 (2005).
3.
Ahuja M, Neale D: Origins of polyploidy in coast redwood (Sequoia sempervirens (d. Don) Endl.) and relationship of coast redwood to other genera of Taxodiaceae. Silvae Genet 51:93–100 (2002).
4.
Anamthawat-Jónsson K: Preparation of chromosomes from plant leaf meristems for karyotype analysis and in situ hybridization. Methods Cell Sci 25:91–95 (2004).
5.
Anamthawat-Jónsson K, Thórsson AT: Natural hybridisation in birch: Triploid hybrids between Betula nana and B. pubescens. Plant Cell Tiss Org Cult 75:99–107 (2003).
6.
Armstead I, Bollard A, Morgan W, Harper J, King I, et al: Genetic and physical analysis of a single Festuca pratensis chromosome segment substitution in Lolium perenne. Chromosoma 110:52–57 (2001).
7.
Barcaccia G, Meneghetti S, Albertini E, Triest L, Lucchin M: Linkage mapping in tetraploid willows: Segregation of molecular markers and estimation of linkage phases support an allotetraploid structure for Salix alba x Salix fragilis interspecific hybrids. Heredity 90:169–180 (2003).
8.
Barral G, Poggio L, Giberti G: Chromosome numbers and DNA content from Ilex argentina (Aquifoliaceae). Bol Soc Argent Bot 30:243–248 (1995).
9.
Barreneche T, Casasoli M, Russell K, Akkak A, Meddour H, et al: Comparative mapping between Quercus and Castanea using simple-sequence repeats (SSRs). Theor Appl Genet 108:558–566 (2004).
10.
Beech R, Strobeck C: Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca). Plant Mol Biol 22:887–892 (1993).
11.
Bellarosa R, Delre V, Schirone B, Maggini F: Ribosomal RNA genes in Quercus spp. (Fagaceae). Plant Syst Evol 172:127–139 (1990).
12.
Bennett M, Leitch I: Angiosperm DNA c-values database (release 5.0, dec. 2004) (2004). http://www.kew.org/cval/homepage.html
13.
Bennett M, Smith J, Heslop-Harrison J: Nuclear DNA amounts in angiosperms. Proc R Soc Lond B Biol Sci 216:179–199 (1982).
14.
Blakesley D, Allen A, Pellny T, Roberts A: Natural and induced polyploidy in Acacia dealbata Link. and Acacia mangium Willd. Ann Bot 90:391–398 (2002).
15.
Bobola M, Smith D, Klien A: Five major nuclear ribosomal repeats represent a large and variable fraction of the genomic DNA of Picea rubens and P. mariana. Mol Biol Evol 9:125–137 (1992).
16.
Borzan Z, Schlarbaum S: Cytogenetics of forest tree species, in Burley J, Evans J, Youngquist JA (eds): Encyclopedia of Forest Science, pp 204–214 (Elsevier, Oxford 2004).
17.
Brown G, Newton C, Carlson J: Organization and distribution of Sau3a tandem repeated DNA sequence in Picea (Pinaceae) species. Genome 41:560–565 (1998).
18.
Cai Q, Zhang D, Liu Z-l, Wang X-R: 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 (2006).
19.
Caperta AD, Neves N, Morais-Cecílio L, Malhó R, Viegas W: Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci. J Cell Sci 115:2839–2846 (2002).
20.
Castilho A, Heslop-Harrison J: Physical mapping of 5S and 18S-25S rDNA and repetitive DNA sequences in Aegilops umbellulata. Genome 38:91–96 (1995).
21.
Chase M, Knapp S, Cox A, Clarkson J, Butsko Y, et al: Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Ann Bot 92:107–127 (2003).
22.
Cheng Z, Presting G, Buell C, Wing R, Jiang J: High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157:1749–1757 (2001).
23.
Clausen K, Kung F, Bey C, Daniels RA: Variation in white ash. Silvae Genet 30:93–97 (1982).
24.
Datson P, Murray B: Ribosomal DNA locus evolution in Nemesia: Transposition rather than structural rearrangement as the key mechanism? Chromosome Res 14:845–857 (2006).
25.
de Bustos A, Cuadrado A, Soler C, Jouve N: Physical mapping of repetitive DNA sequences and 5S and 18S-26S rDNA in five wild species of the genus Hordeum. Chromosome Res 4:491–499 (1996).
26.
Devey M, Sewell M, Uren T, Neale D: Comparative mapping in loblolly pine and radiata pine using RFLP and microsatellite markers. Theor Appl Genet 99:656–662 (1999).
27.
Doudrick R, Heslop-Harrison J, Nelson C, Schmidt T, Nance W, Schwarzacher T: Karyotype of slash pine (Pinus elliottii var. elliottii) using patterns of fluorescence in situ hybridization and fluorochrome banding. J Hered 86:289–296 (1995).
28.
Dubcovsky J, Dvorak J: Ribosomal RNA multigene loci: Nomads of the Triticeae genomes. Genetics 140:1367–1377 (1995).
29.
Fominaya A, Linares C, Loarce Y, Ferrer E: Microdissection and microcloning of plant chromosomes. Cytogenet Genome Res 109:8–14 (2005).
30.
Fransz P, Jong JD, Lysak M, Castiglione M, Schubert I: Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc Natl Acad Sci USA 99:14584–14589 (2002).
31.
Fuchs J, Brandes A, Schubert I: Telomere sequence localization and karyotype evolution in higher plants. Plant Syst Evol 196:227–241 (1995).
32.
Hair J: The chromosomes of the Cupressaceae. New Zea J Bot 6:277–284 (1968).
33.
Hall A, Kettler G, Preuss D: Dynamic evolution at pericentromeres. Genome Res 16:355–364 (2006).
34.
Hasterok R, Marasek A, Donnison I, Armstead I, Thomas A, et al: Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173:349–362 (2006).
35.
Hayashi M, Miyahara A, Sato S, Kato T, Yoshikawa M, et al: Construction of a genetic linkage map of the model legume Lotus japonicus using an intraspecific F2 population. DNA Res 8:301–310 (2001).
36.
Hizume M, Shibata F, Matsusaki Y, Kondo T: Chromosomal localization of telomere sequence repeats in five gymnosperm species. Chromosome Sci 4:39–42 (2000).
37.
Hizume M, Shibata F, Maruyama Y, Kondo T: Cloning of DNA sequences localized on proximal fluorescent chromosome bands by microdissection in Pinus densiflora Sieb. & Zucc. Chromosoma 110:345–351 (2001).
38.
Hizume M, Shibata F, Matsusaki Y, Garajova Z: Chromosome identification and comparative karyotypic analyses of four Pinus species. Theor Appl Genet 105:491–497 (2002).
39.
Islam-Faridi M, Nelson C, Kubisiak T: Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L.). Genome 50:241–251 (2007).
40.
Jacobs M, Gardner R, Murray B: Cytological characterization of heterochromatin and rDNA in Pinus radiata and P. taeda. Plant Syst Evol 223:71–79 (2000).
41.
Jiang J, Gill B: Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057–1068 (2006).
42.
Kamm A, Doudrick R, Heslop-Harrison J, Schmidt T: The genomic and physical organization of tyl-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 (1996).
43.
Karvonen P, Karjalainen M, Savolainen O: Ribosomal RNA genes in scots pine (Pinus sylvestris L.): Chromosomal organization and structure. Genetica 88:59–68 (1993).
44.
Lim K, Matyášek R, Lichtenstein C, Leitch A: Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma 109:245–258 (2000).
45.
MacPherson P, Filion W: Karyotype analysis and the distribution of constitutive heterochromatin in five species of pinus. J Hered 72:193–198 (1981).
46.
Martins C, Ferreira I, Oliveira C, Foresti F, Galetti PM Jr: A tandemly repetitive centromeric DNA sequence of the fish Hoplias malabaricus (Characiformes: Erythrinidae) is derived from 5S rDNA. Genetica 127:133–141 (2006).
47.
Morais-Cecílio L, Delgado M, Jones R, Viegas W: Painting rye B chromosomes in wheat: Interphase chromatin organization, nucleolar disposition and association in plants with two, three or four Bs. Chromosome Res 4:195–200 (1996).
48.
Morais-Cecílio L, Delgado M, Jones R, Viegas W: Modification of wheat rDNA loci by rye B chromosomes: A chromatin organization model. Chromosome Res 8:341–351 (2000).
49.
Murray B, Friensen N, Heslop-Harrison J: Molecular cytogenetic analysis of Podocarpus and comparison with other gymnosperm species. Ann Bot 89:483–489 (2002).
50.
Murray B, Leitch I, Bennett M: Gymnosperm DNA c-values database (release 3.0, dec. 2004) (2004). (http://www.kew.org/cval/homepage.html)
51.
Nakamura M, Fukui K: A chromosome-oriented approach to genome analysis in a woody plant – Sequoiadendron giganteum (Lindl.) Buchholz, in Borzan Z, Schlarbaum S (eds): Cytogenetic Studies of Forest Trees and Shrub Species, pp 89–102 (Univ Zagreb, Zagreb 1997).
52.
Ohri D, Ahuja M: Giemsa C-banding in Fagus sylvatica L., Betula pendula Roth and Populus tremula L. Silvae Genet 40:72–75 (1991).
53.
Pedrosa-Harand A, de Almeida CC, Mosiolek M, Blair M, Schweizer D, Guerra M: Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theor Appl Genet 112:924–933 (2006).
54.
Petit R, Hampe A: Some evolutionary consequences of being a tree. Annu Rev Ecol Evol Syst 37:187–214 (2006).
55.
Poke F, Vaillancourt R, Potts B, Reid J: Genomic research in eucalyptus. Genetica 125:79–101 (2005).
56.
Prado E, Faivre-Rampant P, Schneider C, Darmency M: Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species. Genome 39:1020–1026 (1996).
57.
Pruitt R, Meyerowitz E: Characterization of the genome of Arabidopsis thaliana. J Mol Biol 187:169–183 (1986).
58.
Raskina O, Belyayev A, Nevo E: Activity of the En/Spm-like transposons in meiosis as a base for chromosome repatterning in a small, isolated, peripheral population of Aegilops speltoides Tausch. Chromosome Res 12:153–161 (2004).
59.
Rocheta M, Cordeiro J, Oliveira M, Miguel C: Pprt1: The first complete gypsy-like retrotransposon isolated in Pinus pinaster. Planta 225:551–562 (2007).
60.
Rogers D: Inheritance of allozymes from seed tissues of the hexaploid gymnosperm, Sequoia sempervirens (d. Don) Endl. (coast redwood). Heredity 78:166–175 (1997).
61.
Rogers S, Bendich A: Ribosomal RNA genes in plants: Variability in copy number and in the intergenic spacer. Plant Mol Biol 9:509–520 (1987).
62.
Särkilahti E: Micropropagation of a mature colchicine-polyploid and irradiation-mutant of Betula pendula Roth. Tree Physiol 4:173–179 (1988).
63.
Scalfi M, Troggio M, Piovani P, Leonardi S, Magnaschi G, et al: A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.). Theor Appl Genet 108:433–441 (2004).
64.
Schmidt A, Doudrick R, Heslop-Harrison J, Schmidt T: The contribution of short repeats of low sequence complexity to large conifer genomes. Theor Appl Genet 100:7–14 (2000).
65.
Schubert V, Kim YM, Berr A, Fuchs J, Meister A, et al: Random homologous pairing and incomplete sister chromatid alignment are common in angiosperm interphase nuclei. Mol Genet Genomics 278:167–176 (2007).
66.
Schweizer D: Reverse fluorescent chromosome banding with chromomycin and DAPI. Chromosoma 58:307–324 (1976).
67.
Sewell M, Sherman B, Neale D: A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics 151:321–330 (1999).
68.
Shibata F, Matsusaki Y, Hizume M: AT-rich sequences containing Arabidopsis-type telomere sequence and their chromosomal distribution in Pinus densiflora. Theor Appl Genet 110:1253–1258 (2005).
69.
Siljak-Yakovlev S, Cerbah M, Coulaud J, Stoian V, Brown S, et al: Nuclear DNA content, base composition, heterochromatin and rDNA in Picea omorika and Picea abies. Theor Appl Genet 104:505–512 (2002).
70.
Sterck L, Rombauts S, Jansson S, Sterky F, Rouzé P, van de Peer Y: EST data suggest that poplar is an ancient polyploid. New Phytol 167:165–170 (2005).
71.
Stupar R, Song J, Tek A, Cheng Z, Dong F, Jiang J: Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats. Genetics 162:1435–1444 (2002).
72.
Suchankova P, Kubalakova M, Kovarova P, Bartos J, Cihalikova J, et al: Dissection of the nuclear genome of barley by chromosome flow sorting. Theor Appl Genet 113:651–659 (2006).
73.
Tagashira N, Kondo K: Chromosome phylogeny of Zamia and Ceratozamia by means of Robertosonian changes detected by fluorescence in situ hybridization (FISH) technique of rDNA. Plant Syst Evol 227:145–155 (2001).
74.
Taketa S, Ando H, Takeda K, van Bothmer R: Detection of Hordeum marinum genome in three polyploid Hordeum species and cytotypes by genomic in situ hybridization. Hereditas 130:185–188 (1999).
75.
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, et al: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604 (2006).
76.
Uchida W, Matsunaga S, Sugiyama R, Kawano S: Interstitial telomere-like repeats in the Arabidopsis thaliana genome. Genes Genet Syst 77:63–67 (2002).
77.
Vaio M, Speranza P, Valls J, Guerra M, Mazzella C: Localization of the 5S and 45S rDNA sites and cpDNA sequence analysis in species of the Quadrifaria group of Paspalum (Poaceae, Paniceae). Ann Bot 96:191–200 (2005).
78.
Vega M, Abbo S, Feldman M, Levy A: Chromosome painting in plants: In situ hybridization with a DNA probe from a specific microdissected chromosome arm of common wheat. Proc Natl Acad Sci USA 91:12041–12045 (1994).
79.
Vischi M, Jurman I, Bianchi G, Morgante M: Karyotype of Norway spruce by multicolor FISH. Theor Appl Genet 107:591–597 (2003).
80.
Wendel J, Schnabel A, Seelanan T: Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc Natl Acad Sci USA 92:280–284 (1995).
81.
Zhang X, Wessler SR: Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci USA 101:5589–5594 (2004).
82.
Zimmer E, Jupe E, Walbot V: Ribosomal gene structure, variation, and inheritance in maize and its ancestors. Genetics 120:1125–1136 (1988).
83.
Ziolkowski P, Sadowski J: FISH-mapping of rDNAs and Arabidopsis BACs on pachytene complements of selected Brassicas. Genome 45:189–197 (2002).
84.
Zoldos V, Papes D, Cerbah M, Panaud O, Besendorfer V, Siljak-Yakovlev S: Molecular-cytogenetic studies of ribosomal genes and heterochromatin reveal conserved genome organization among 11 Quercus species. Theor Appl Genet 99:969–977 (1999).
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