Biotechnology and the domestication of forest trees Wout ... › documents › master › BBFPS › boerjan... · Gene-mining of tree-speciﬁc processes The identiﬁcationofthe

Biotechnology and the domestication of forest treesWout Boerjan

Wood is one of the major renewable materials. To compensate

for the ever-increasing demand for wood and to reduce

pressure on native forests, more wood of higher quality will

need to be produced on less land by planting highly productive

trees. Biotechnology has shown great promise for forest

tree improvement and over the past 10 years this field has

flourished. Not only has the potential of transgenic trees with

optimized yield and quality traits been demonstrated in field

trials, but progress in genetical genomics and association

genetics promise quantum leaps forward for tree improvement.

Addresses

Department of Plant Systems Biology, Flanders Interuniversity Institute

for Biotechnology (VIB), Ghent University, Technologiepark 927,

B-9052 Gent, Belgium

Corresponding author: Boerjan, Wout ([email protected])

Current Opinion in Biotechnology 2005, 16:159–166

This review comes from a themed issue on

Plant biotechnology

Edited by Dirk Inze

Available online 12th March 2005

0958-1669/$ – see front matter

# 2005 Elsevier Ltd. All rights reserved.

DOI 10.1016/j.copbio.2005.03.003

IntroductionThe demand for wood is expected to grow by 20% in the

next decade, while the world’s forest cover declines at an

annual rate of 9.4 million hectares — a size comparable to

that of Portugal (http://www.fao.org/FO/SOFO/) [1].

These developments, together with increasing public con-

cern regarding the further exploitation of native forests

and loss of associated biodiversity (http://www.iucn.org)

[2], have fuelled research on the domestication process of

trees. Breeding of forest trees is a slow process mainly

because of the long generation intervals typical of most

forest trees and because many traits can only be properly

assessed at rotation age (see Glossary). One can distin-

guish two main avenues to accelerate domestication: one

is through geneticmodification, by introducing new genes

into already existing elite genotypes, and the other is

through the smart exploitation of genetic diversity in

breeding programs. Both strategies largely benefit from

a profound understanding of gene–function relationships

(Figure 1). This paper reviews accomplishments in the

forest biotechnology field over the past three years, and

gives an impression as to directions in which forest

biotechnology is likely to develop.

The tool boxBecause much of the typical biology of forest trees, such

as the seasonal cycles of growth and dormancy, phase

change, wood formation and long-term environmental

adaptation, are not easily studied in Arabidopsis thaliana,forest tree biotechnologists use a range of angiosperm and

gymnosperms tree species as experimental systems.

However, the genus Populus has been adopted by the

scientific community as the model of choice because it

offers numerous advantages, such as fast growth, facile

vegetative propagation, interspecific hybridization, ame-

nability to tissue culture and genetic transformation, and a

small genome size (�500 Mb) [3]). Large expressed

sequence tag (EST) collections of various tissues have

been assembled and have catalyzed the development of

microarrays with up to �23 000 spotted cDNAs [4–8]

(Table 1). A major breakthrough was the release of the

Populus trichocarpa genome sequence, the first available

sequence of a tree genome [9,10]. A draft annotation

based on four different software programs predicts

poplar to have �40 000 genes (Table 1) and gene-specific

oligonucleotide microarrays are expected for 2005, just a

few years after the first genome-wide Arabidopsis arraysbecame available. EST collections have also been made

for several other tree species, such as birch, pine [11],

eucalyptus [12], spruce, oak and acacia (Table 1).

In addition to the genome sequence and methods to

analyze the transcriptome, a comprehensive analysis of

phenotypes and biological processes will require meta-

bolomics, a tool that is generally much less well devel-

oped; only a few publications have reported metabolic

profiling in trees [13–16]. Research on the proteome of

forest tree tissues has also taken off [17,18�]. The pro-

teome of the wood-forming tissues has been analyzed in

maritime pine, revealing the identity of 175 proteins with

known function [18�,19].

The small genome size of poplar and its high transforma-

tion efficiency have allowed the construction of gene trap,

enhancer trap, and activation tagging libraries (see

Glossary) for gene discovery [20,21]. The isolation of a

gibberellic acid (GA) 2-oxidase that was overexpressed in

a dwarfed activation line represents the first successful

activation tagging of a developmental regulatory gene in

trees [21]. Also, transposon tagging (see Glossary) with

the maize Activator transposable element has revealed

several mutant phenotypes in poplar [22].

Genetic maps are available for a variety of tree species

and large simple sequence repeat (SSR) collections now

make it possible to compare maps and quantitative trait

www.sciencedirect.com Current Opinion in Biotechnology 2005, 16:159–166

locus (QTL) positions from different pedigrees, species

and genera. The largest SSR discovery program, based on

the poplar genome sequence, has resulted in over 4000

SSR primer combinations of which �500 have been

tested on 18 poplar and five willow species [23]

(Table 1). Syntheny and colinearity have been demon-

strated between the genomes of Populus and Arabidopsis[24] and between those of Pinus taeda and Pseudotsugamenziesii (Pinaceae) [25].

With the genome sequence at hand and RNA interfer-

ence technology established, a genome-wide knockout

collection of all poplar genes will be one of the next

milestones (Table 1). However, the establishment of

repositories for poplar genotypes poses different pro-

blems for storage as compared with Arabidopsis, becauseof their size and the fact that homozygous seeds cannot be

obtained. Several research groups are therefore evaluating

procedures for cryostorage of wild-type and transgenic

germplasm [26].

Gene-mining of tree-specific processesThe identification of the genes that control traits relevant

to tree domestication is a challenging task, especially as

our knowledge on tree-specific processes is still scarce.

Yet, microarray and reverse genetics experiments are

beginning to shed light on the molecular basis of devel-

opmental processes that hallmark the typical biology of

forest trees. For example, wood formation is determined

by the activity of the vascular cambium, the meristem

that gives rise to radial growth of the trunk, and by the

length of the growing season. The most profound tran-

script profiling experiments in trees have focused on the

vascular cambium in poplar. Microarray analyses with

RNA prepared from tangential cryosections [27] have

revealed substantial differences in the transcriptomes

of the six anatomically homogeneous cell layers of the

cambial zone. These studies have provided sets of marker

genes for different stages of xylem and phloem differ-

160 Plant biotechnology

Glossary

Rotation age: The planned number of years between the

establishment or regeneration of a tree crop or stand and its final

cutting at a specified stage of maturity. Rotation times can be short

(e.g. 5–7 years) when poplar wood is used for pulp and paper or long

(e.g. 15 years) when poplar wood is used for veneer.

Gene/enhancer trapping: A method whereby the coding sequence

of a reporter gene without promoter, or with a minimal promoter, is

randomly inserted into the genome by transformation. Transgenic

plants are screened for reporter gene expression, and the tagged

gene/enhancer can be cloned.

Transposon tagging: A method whereby a transposable element is

randomly inserted into the genome. New transpositions of this

element into functional genes may cause phenotypic alterations

associated with loss of gene function.

Activation tagging: A method whereby a strong enhancer is

randomly inserted into the genome by transformation, resulting in

mutant plants with dominant phenotypes.

Ecotilling: A high-throughput method to identify allelic variants of a

given DNA sequence from germplasm collections. It allows the

detection of SNPs and indels and can be used for homozygous and

heterozygous organisms.

Figure 1

Marker-assisted selection

Genetic engineering

Candidate genes

DomesticationCurrent Opinion in Biotechnology

Transcript,metabolite andprotein profiling

Comparativegenomics and

genomeannotation

QTL, geneticalgenomics and

associationmapping

Annual and perennialmodel systems

Strategies that lead to candidate gene identification and their use in the domestication of forest trees. Genes that are involved in yield and quality

traits relevant to forest tree improvement are identified by different approaches. In addition to forest trees, candidate gene mining in annual plants

such as Arabidopsis can also be relevant for forest tree improvement. Transcript, metabolite and protein profiling identify genes that are involved

in a given process, but only suggest a role in that process. QTL mapping, genetical genomics and association genetics provide further support for the

involvement of a gene in a given trait. Comparative genomics and genome annotation allow genomic information to be compared from a range of

model systems, to identify candidate genes in a QTL, and to provide insight into gene family structure and gene regulation. Reverse genetics is

used to demonstrate the role of a candidate gene in the elaboration of a phenotype. If this phenotype is of benefit, two avenues can be followed:

either elite clones are genetically modified with the gene, or alleles of this gene that are associated with beneficial phenotypes are identified and

the genotypes harboring these alleles introduced in the breeding program.

Current Opinion in Biotechnology 2005, 16:159–166 www.sciencedirect.com

entiation and candidate regulators for cambial meristem

activity [28��]. The seasonal cycles of growth and dor-

mancy are another important aspect of tree biology that is

beginning to unveil its secrets. Dormancy is imposed on

all meristems at the end of the growing season and is

triggered by shortening of the day length. Transcript

profiling of active versus dormant cambial meristems

indicates an extensive remodelling of the cambial tran-

scriptome during dormancy and has identified potential

regulators governing these massive changes in gene

expression [29]. Dormancy induction of the apical mer-

istem is hallmarked by the formation of bud scales that

protect the embryonic leaves inside the bud. PtABI3 is a

transcription factor that is temporarily expressed in devel-

oping buds approximately two weeks after the critical day

length is perceived. Reverse genetics experiments have

shown that this factor has a role in the relative develop-

ment of embryonic leaves and bud scales during bud

formation, making PtABI3 the first transcription factor for

which a role in bud development has been established

[30].

The formation of reaction wood has also received a lot of

attention [5,6,17,31,32]. When a tree stem leans, angios-

perm trees make tension wood at the upper side, whereas

gymnosperms make compression wood at the under side

of the leaning trunk. These tissues differ from those of

upward growing trees both anatomically and chemically,

causing problems during wood processing. The predomi-

nant class of genes that is upregulated during tension

wood formation encode fasciclin-like arabinogalactan pro-

teins, some of which might have a specific function in the

synthesis of the gelatinous (G)-layer that is typical for

secondary walls in tension wood [5,31]. Analogous tran-

script and protein profiling studies in Populus spp., Pinusspp. and Eucalyptus spp. have identified genes differen-

tially expressed in early versus late wood [32,33], juvenile

versus mature wood [32], autumnal leaf senescence

[34,35�], developing xylem [12,36], wounding and viral

infection [37], water deficit [38], adventitious rooting [4],

chilling stress [39], and ectomycorrhizal symbiosis [40]. In

addition to profiling wild-type trees in a variety of devel-

opmental and environmental conditions, transcript profil-

ing of transgenic trees with improved growth provides an

interesting source of genes important for yield [7,41].

Furthermore, the annual plant Arabidopsis, which pro-

duces secondary xylem from the vascular cambium when

grown under short-day conditions, is an excellent model

system to identify candidate genes for wood formation

[42,43].

Transcript and protein profiling data provide insight into

the complex developmental programs that make up a tree

and lead to the identification of interesting targets for

further functional analysis by reverse genetics. The

challenge is to extract from these complex datasets the

genes that can effectively be used to improve a given trait.

One way of achieving this is to select those genes that also

form the basis of phenotypic variation in natural popula-

tions, by using strategies such as genetical genomics

[44��] and association genetics [45] (see below).

Towards application by genetic modificationGenetic modification remains an important avenue to

accelerate the domestication of forest trees, despite the

public debate. The main advantage is that the genetic

Forest tree biotechnology Boerjan 161

Table 1

Forest tree genomics databases.

Species Feature Link

Eucalyptus spp.; Picea spp.; Pinus spp.

Robinia spp., Populus spp. EST http://web.ahc.umn.edu/biodata/

Picea spp.; Populus spp. EST http://www.arborea.ulaval.ca/en/

Pinus spp. EST http://www.pierroton.inra.fr/Lignome/

EST http://pinetree.ccgb.umn.edu/

EST http://fungen.botany.uga.edu/Projects/Pine/Pine.htm

EST http://cbi.labri.fr/outils/SAM/COMPLETE/index.php

EST http://www.cbc.umn.edu/ResearchProjects/Pine/DOE.pine/index.html

Protein database http://cbi.labri.fr/outils/protic/ProticDB.php

Populus spp. EST http://Poppel.fysbot.umu.se

EST http://www.populus.db.umu.se

EST http://sputnik.btk.fi/project?name=Populus%20euphratica

EST http://www.aspendb.mtu.edu/

EST http://mycor.nancy.inra.fr/poplardb/index.html

Microarray analysis http://www.upscbase.db.umu.se/

Genome sequence http://genome.jgi-psf.org/Poptr1/Poptr1.home.html

SSR resource http://www.ornl.gov/sci/ipgc/ssr_resource.htm

Science Plan http://www.ornl.gov/sci/ipgc/the_populus_genome_science_plan.pdf

All forest tree species General http://dendrome.ucdavis.edu/index.html


constitution of the elite clone can be maintained, whereas

in classical tree breeding programs it is lost with every

new cross and inbred lines cannot be obtained because of

inbreeding depression. A second key argument is that

transformation circumvents the long generation times

that are typical for most forest trees.

The largest effort in genetic engineering has been

devoted to modifying the amounts and composition of

lignin in trees to improve lignin extractability during

pulping [46]. The deployment of such transgenic trees

could enhance the capacity of the pulpmill while decreas-

ing chemical costs and, importantly, reducing the ecolo-

gical impact on the environment. Overexpression of

ferulate-5-hydroxylase (F5H) in poplar results in a less

condensed lignin and in significant improvements in

lignin extractability and bleaching, whereas fiber quality

remained equal or was even better [47]. Similarly, down-

regulation of cinnamyl alcohol dehydrogenase (CAD), the

enzyme catalyzing the last step in the biosynthesis of the

monolignols, improves wood quality for chemical pulp-

ing, as demonstrated with wood harvested from four-year

old field trials; fewer chemicals were needed to remove

lignin from the pulp and a higher pulp yield was obtained

[48�]. By co-transforming poplar with two different con-

structs — one aimed at increasing F5H expression and

the other at reducing 4-coumarate CoA-ligase expression

— the combined effect expected for the single transfor-

mations was obtained: lignin amount was reduced and

compensated for by more cellulose, and lignin was less

condensed [49]. This work demonstrated the potential of

modifying one genotype simultaneously for multiple

traits by stacking transgenes, a strategy that could cir-

cumvent numerous generations of conventional breeding

[50].

Besides quality, yield is one of the most important traits

and several genes involved in different processes have

been shown to impact on growth in transgenic poplar.

Overexpression of a cytosolic pine glutamine synthase

(GS), a key enzyme involved in nitrogen assimilation,

increases height by 41% and stem diameter by 36%, as

measured for three-year old, field-grown transgenic

poplars [51�]. Enhanced growth and cellulose production

and reduced lignin have been obtained through the

constitutive overexpression of an Aspergillus xylogluca-

nase in poplar. Xyloglucanases break the xyloglucan

cross-links between cellulose microfibrils, promoting cell

expansion [52]. Similarly, overexpression of the Arabidop-sis endoglucanase CEL1 gene in poplar increases height,

leaf size, stem diameter, and cellulose/hemicellulose

content [53]. Remarkably, overexpression of a horserad-

ish peroxidase in poplar enhances height growth by 25%

and stem volume by 30%, and increases oxidative stress

resistance. Here, the enhanced growth rate is possibly

caused by altered ascorbate/dehydroascorbate levels that

are thought to play an important role in cell division and

elongation [54]. Genetic engineering in trees has also

focused on pathogen and pest resistance [55–59], bior-

emediation [60], the acceleration and prevention of flow-

ering [61,62] and herbicide resistance [63]).

Although many reports on gene silencing in annual model

plants have raised concerns over the stability of transgene

expression during the long-term deployment of trans-

genic trees, results from field trial experiments seem to

suggest that transgene expression is stable over succes-

sive years [49,59,63,64]. Therefore, the variability of

transgene expression is of minor concern for commercial

applications of transgenic trees [65]. Worldwide, over 210

field trials with transgenic trees exist, mostly restricted to

the genera Populus, Pinus, Liquidambar and Eucalyptus[66]. Only China has reported the commercial release of

transgenic poplar, with approximately 1.4 million insect-

resistant trees planted on 300–500 ha [59,66].

Towards marker-aided selectionA second strategy to speed-up domestication of forest

trees is based on the more efficient exploitation of genetic

diversity in the germplasm. Over the past few decades,

genetic maps have been made for many tree species and

QTLs have been mapped for a range of agronomically

important traits, such as wood properties, with the aim of

using genetic markers linked to QTLs to follow the trait

in breeding programs [67]. However, the potential of

marker-assisted selection (MAS) in forest tree breeding

is limited, because linkage between a trait and a linked

marker decreases with each generation owing to genetic

recombination, unless the marker is in the gene itself.

Map-based cloning is difficult to achieve in outbreeding

species that have long generation times and large gen-

omes. Currently, there are no examples of genes that have

been positionally cloned from any forest tree, even for

traits showing Mendelian segregation such as resistance

to Melampsora spp. [68–71].

Several strategies are currently used to identify the genes

underlying QTLs. One is the candidate gene approach in

which genes assumed to be involved in the trait are

genetically mapped and associations with QTLs for that

trait analyzed. For example, 18 candidate genes involved

in lignin biosynthesis and cell-wall structure have been

mapped in loblolly pine, and several co-located with wood

property QTLs [67]. However, the large linkage gener-

ated in artificial crosses does not allow any firm conclu-

sions to be made as to the role of the candidate gene in

determining the trait.

A second strategy combines a QTL analysis of pheno-

types with a QTL analysis of gene expression levels

(eQTL) in amapping pedigree, a strategy called genetical

genomics. The first such approach in forest trees has been

carried out in an interspecific Eucalyptus backcross popu-lation, where QTLs for diameter growth co-localized with



eQTLs for lignin-related genes, suggesting that growth

and lignin characteristics are controlled by the same loci

[44��]. None of the lignin-related genes themselves

mapped at the growth QTL, except for the gene encoding

S-adenosyl-L-methionine synthetase (SAMS). Downre-

gulation of SAMS in maize results in reduced lignin

content, hence SAMS is a good candidate regulator of

both lignin formation and growth in eucalyptus. A similar

strategy to identify candidate genes for yield was followed

at the proteome level in maritime pine, where a QTL for

biomass production was found to co-localize with the GSgene and a protein quantity QTL (PQTL) that controls

the abundance of GS [18�]. Still, these candidate genes

could remain associated with the trait merely because of

linkage in the mapping pedigree.

The lack of resolution in mapping candidate genes and

QTL alleles can be overcome by association genetics,

using natural populations in which the long evolutionary

history has broken up the linkage between markers and

genes [45]. A prerequisite is the presence of large allelic

variation in the population. Sequencing alleles in a range

of candidate genes in eucalyptus, pine and aspen demon-

strate that such variants, including single nucleotide

polymorphisms (SNPs) and indels, can readily be found

[72,73,74��,75]. In the loblolly pine germplasm, linkage

disequilibrium (LD) decays in the order of the physical

length of a gene, and in European aspen LD extends only

a few hundred base pairs, indicating the potential of

association genetics to identify genes responsible for

variation in the trait [74��,75].

ConclusionsIn the space of just a few years, forest tree biotechnology

has developed into a cutting-edge scientific discipline in

which aspects of plant biology that are not easily studied

in Arabidopsis have been tackled. The first long-term field

trials with transgenic trees have shown the potential to

tailor yield and quality traits, and these traits are stably

maintained after successive years in the field. Studies on

LD in several forest tree species suggest that association

genetics might become an efficient tool to identify the

genes determining traits and that MAS in forest trees will

become increasingly more feasible. The annotation of the


Figure 2

Improved trees

Candidate genes

Field evaluation

RNAi in transgenic trees

CrossPhenotypic evaluation

Phenotypic evaluation of offspring

Current Opinion in Biotechnology

Gene mining inmodel systems

Ecotilling in natural provenancesfor heterozygous null mutants

General scheme to accelerate tree improvement by marker-assisted selection, based on the knowledge generated from transgenic plants.

Candidate genes involved in a process important for tree productivity or quality are identified (see Figure 1). The function of these candidate

genes is analyzed by reverse genetics in trees. Transgenic trees with promising phenotypes are further evaluated in field trials. Genes that

correspond to improved traits upon downregulation in transgenic trees are ideal candidates to identify the corresponding loss of function alleles

from natural germplasm, for example, by Ecotilling (see Glossary) [76]. Trees heterozygous for the null allele are crossed and the phenotypes

of the homozygous null, heterozygous null and normal progenies evaluated. Depending on the end-use, the improved genotypes can either be

deployed as such or incorporated into the breeding program. The red stars mark trees that are heterozygous for a null allele in a candidate gene.

(The picture is an aerial photograph of the field trial of transgenic poplar modified in lignin biosynthesis at Jealott’s Hill, UK [48�]; Picturecourtesy of Syngenta.)


poplar genome sequence will make this an ideal species

for association studies, because the full set of genes in a

QTL region is easily accessible. A straightforward sce-

nario for MAS is to identify (from the germplasm) geno-

types that are heterozygous null for genes that result in

improved quality traits upon downregulation in trans-

genic plants, and to use these as parents in the breeding

program (Figure 2). Unintentionally, examples have

already become available: CAD deficiency in transgenic

poplar improves pulping characteristics [48�] and natural

cad null mutants in loblolly pine [73], having similarly

improved characteristics for lignin extraction, are widely

used in commercial plantations. The appealing corollary

of association genetics is that it argues for a maximal

conservation of genetic diversity in the germplasm, a

welcome driving force in the protection of nature.

References and recommended readingPapers of particular interest, published within the annual period ofreview, have been highlighted as:

� of special interest�� of outstanding interest

1. Fenning TM, Gershenzon J: Where will the wood come from?Plantation forests and the role of biotechnology.Trends Biotechnol 2002, 20:291-296.

2. Wimp GM, Young WP, Woolbright SA, Keim P, Whitham TG:Conserving plant genetic diversity for dependent animalcommunities. Ecol Lett 2004, 7:776-780.

3. Taylor G: Populus: Arabidopsis for forestry. Do we need amodel tree? Ann Bot 2002, 90:681-689.

4. Kohler A, Delaruelle C, Martin D, Encelot N, Martin F: The poplarroot transcriptome: analysis of 7000 expressed sequencetags. FEBS Lett 2003, 542:37-41.

5. Dejardin A, Leple J-C, Lesage-Descauses M-C, Costa G, Pilate G:Expressed sequence tags from poplar wood tissues – acomparative analysis from multiple libraries. Plant Biol 2004,6:55-64.

6. Pilate G, Dejardin A, Laurans F, Leple J-C: Tension woodas a model for functional genomics of wood formation.New Phytol 2004, 164:63-72.

7. Ranjan P, Kao Y-Y, Jiang H, Joshi CP, Harding SA, Tsai C-J:Suppression subtractive hybridization-mediatedtranscriptome analysis from multiple tissues of aspen(Populus tremuloides) altered in phenylpropanoidmetabolism. Planta 2004, 219:694-704.

8. Sterky F, Bhalerao RR, Unneberg P, Segerman B, Nilsson P,Brunner AM, Charbonnel-Campaa L, Jonsson Lindvall J, Tandre K,Strauss SH et al.: A Populus EST resource for plant functionalgenomics. Proc Natl Acad Sci USA 2004, 101:13951-13956.

9. Brunner AM, Busov VB, Strauss SH: Poplar genome sequence:functional genomics in an ecologically dominant plantspecies. Trends Plant Sci 2004, 9:49-56.

10. Tuskan GA, DiFazio SP, Teichmann T: Poplar genomics isgetting popular: the impact of the poplar genome project ontree research. Plant Biol 2004, 6:2-4.

11. Kirst M, Johnson AF, Baucom C, Ulrich E, Hubbard K, Staggs R,Paule C, Retzel E, Whetten R, Sederoff R: Apparent homology ofexpressed genes from wood-forming tissues of loblollypine (Pinus taeda L.) with Arabidopsis thaliana. Proc Natl AcadSci USA 2003, 100:7383-7388.

12. Paux E, Tamasloukht M, Ladouce N, Sivadon P, Grima-Pettenati J:Identification of genes preferentially expressed duringwood formation in Eucalyptus. Plant Mol Biol 2004,55:263-280.

13. Jonsson P, Gullberg J, Nordstrom A, Kusano M, Kowalczyk M,Sjostrom M, Moritz T: A strategy for identifying differences inlarge series of metabolomic samples analyzed by GC/MS.Anal Chem 2004, 76:1738-1745.

14. Morreel K, Ralph J, Kim H, Lu F, Goeminne G, Ralph S, Messens E,Boerjan W: Profiling of oligolignols reveals monolignolcoupling conditions in lignifying poplar xylem. Plant Physiol2004, 136:3537-3549.

15. Morreel K, Ralph J, Lu F, Goeminne G, Busson R, Herdewijn P,Goeman JL, Van der Eycken J, Boerjan W, Messens E: Phenolicprofiling of caffeic acid O-methyltransferase-deficient poplarreveals novel benzodioxane oligolignols. Plant Physiol 2004,136:4023-4036.

16. Morris CR, Scott JT, Chang H-m, Sederoff RR, O’Malley D,Kadla JF: Metabolic profiling: a new tool in the studyof wood formation. J Agric Food Chem 2004,52:1427-1434.

17. Plomion C, Pionneau C, Bailleres H: Analysis of proteinexpression along the normal to tension wood gradient inEucalyptus gunnii. Holzforschung 2003, 57:353-358.

18.�

Plomion C, Bahrman N, Costa P, Dubos C, Frigerio J-M, Gion J-M,Lalanne C, Madur D, Pionneau C, Gerber S: Proteomics forgenetic and physiological studies in forest trees: application inmaritime pine. In Molecular Genetics and Breeding of ForestTrees. Edited by Kumar S, Fladung M. New York: Food ProductsPress; 2004:53-79.

The first example in maritime pine of a PQTL for GS that co-localizes withtheGS gene and aQTL for biomass. Together with the paper by Kirst et al.[44��], it strongly suggests that expression profiling in mapping popula-tions is a good strategy to identify candidate genes that determinequantitative traits.

19. Gion J-M, Lalanne C, Le Provost G, Ferry-Dumazet H, Paiva J,Chaumeil P, Frigerio J-M, Brach J, Barre A, de Daruvar A et al.:The proteome of maritime pine wood forming tissue.Proteomics 2005, in press.

20. Groover A, Fontana JR, Dupper G, Ma C, Martienssen R,Strauss S, Meilan R: Gene and enhancer trap tagging ofvascular-expressed genes in poplar trees. Plant Physiol 2004,134:1742-1751.

21. Busov VB, Meilan R, Pearce DW, Ma C, Rood SB, Strauss SH:Activation tagging of a dominant gibberellin catabolism gene(GA 2-oxidase) from poplar that regulates tree stature.Plant Physiol 2003, 132:1283-1291.

22. Fladung M, Deutsch F, Honicka H, Kumar S: T-DNA andtransposon tagging in aspen. Plant Biol 2004, 6:5-11.

23. Tuskan GA, Gunter LE, Yang ZK, Yin T, Sewell MM, DiFazio SP:Characterization of microsatellites revealed by genomicsequencing of Populus trichocarpa. Can J For Res 2004,34:85-93.

24. Stirling B, Yang ZK, Gunter LE, Tuskan GA, Bradshaw HD Jr:Comparative sequence analysis between orthologous regionsof the Arabidopsis and Populus genomes reveals substantialsynteny and microcollinearity. Can J For Res 2003,33:2245-2251.

25. Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB:Comparative mapping in the Pinaceae. Genetics 2004,168:447-461.

26. Tsai C-J, Hubscher SL: Cryopreservation in Populus functionalgenomics. New Phytol 2004, 164:73-81.

27. Uggla C, Sundberg B: Sampling of cambial region tissues forhigh resolution analysis. In Wood Formation in Trees: CellularandMolecular Biology Techniques. Edited by Chaffey NJ. London:Taylor & Francis; 2002:215-228.

28.��

Schrader J, Nilsson J, Mellerowicz E, Berglund A, Nilsson P,Hertzberg M, Sandberg G: A high-resolution transcript profileacross the wood-forming meristem of poplar identifiespotential regulators of cambial stem cell identity. Plant Cell2004, 16:2278-2292.

This paper is exemplary in that it applies cutting edge technology tounravel the biology of a poorly understood tissue typical for perennialplants. By cryosectioning of the vascular cambium [27], single-cell layers



were obtained from which RNA was prepared for microarray hybridiza-tions. Transcript profiling reveals different transcriptomes for the sixanatomically similar cambial cell layers.

29. Schrader J, Moyle R, Bhalerao R, Hertzberg M, Lundeberg J,Nilsson P, Bhalerao RP: Cambial meristem dormancy intrees involves extensive remodelling of the transcriptome.Plant J 2004, 40:173-187.

30. Rohde A, Prinsen E, De Rycke R, Engler G, Van Montagu M,Boerjan W: ABI3 impinges on growth and differentiation ofembryonic leaves during bud set in poplar. Plant Cell 2002,14:1885-1901.

31. Lafarguette F, Leple J-C, Dejardin A, Laurans F, Costa G,Lesage-Descauses M-C, Pilate G: Poplar genes encodingfasciclin-like arabinogalactan proteins are highly expressedin tension wood. New Phytol 2004, 164:107-121.

32. Le Provost G, Paiva J, Pot D, Brach J, Plomion C: Seasonalvariation in transcript accumulation in wood-forming tissuesof maritime pine (Pinus pinaster Ait.) with emphasis on a cellwall glycine-rich protein. Planta 2003, 217:820-830.

33. Egertsdotter U, van Zyl LM, Mackay J, Peter G, Kirst M, Clark C,Whetten R, Sederoff R: Gene expression during formation ofearlywood and latewood in loblolly pine: expression profiles of350 genes. Plant Biol 2004, 6:654-663.

34. Bhalerao R, Keskitalo J, Sterky F, Erlandsson R, Bjorkbacka H,Jonsson Birve S, Karlsson J, Gardestrom P, Gustafsson P,Lundeberg J, Jansson S: Gene expression in autumn leaves.Plant Physiol 2003, 131:430-442.

35.�

Andersson A, Keskitalo J, Sjodin A, Bhalerao R, Sterky F, Wissel K,Tandre K, Aspeborg H,Moyle R, Ohmiya Y et al.:A transcriptionaltimetable of autumn senescence. Genome Biol 2004,5:R24.1-R24.13.

This paper reports the changes in gene expression during autumn leafsenescence. The work is special in that the samples are derived fromoutdoor-grown trees and thus reflect both developmental and environ-mental cues. Such studies are essential to understand the full biology oftrees in their natural environment.

36. Lorenz WW, Dean JFD: SAGE profiling and demonstration ofdifferential gene expression along the axial developmentalgradient of lignifying xylem in loblolly pine (Pinus taeda).Tree Physiol 2002, 22:301-310.

37. Smith CM, Rodriguez-Buey M, Karlsson J, Campbell MM: Theresponse of the poplar transcriptome to wounding andsubsequent infection by viral pathogen. New Phytol 2004,164:123-136.

38. Dubos C, Plomion C: Identification of water-deficit responsivegenes inmaritime pine (Pinus pinasterAit.) roots. Plant Mol Biol2003, 51:249-262.

39. Renaut J, Lutts S, Hoffmann L, Hausman J-F: Responses ofpoplar to chilling temperatures: proteomic and physiologicalaspects. Plant Biol 2004, 6:81-90.

40. Martin F, Duplessis S, Kohler A, Tagu D: Exploring thetranscriptome of the ectomycorrhizal symbiosis. In MolecularGenetics and Breeding of Forest Trees. Edited by Kumar S,Fladung M. New York: Food Products Press; 2004:81-109.

41. Israelsson M, Eriksson ME, Hertzberg M, Aspeborg H, Nilsson P,Moritz T: Changes in gene expression in the wood-formingtissue of transgenic hybrid aspen with increased secondarygrowth. Plant Mol Biol 2003, 52:893-903.

42. Chaffey N, Cholewa E, Regan S, Sundberg B: Secondary xylemdevelopment in Arabidopsis: a model for wood formation.Physiol Plant 2002, 114:594-600.

43. Ko J-H, Han K-H, Park S, Yang J: Plant body weight-inducedsecondary growth in Arabidopsis and its transcriptionphenotype revealed by whole-transcriptome profiling.Plant Physiol 2004, 135:1069-1083.

44.��

Kirst M, Myburg AA, De Leon JPG, Kirst ME, Scott J, Sederoff R:Coordinated genetic regulation of growth and lignin revealedby quantitative trait locus analysis of cDNA microarray data inan interspecific backcross of eucalyptus. Plant Physiol 2004,135:2368-2378.

The first paper describing a genetical genomics approach in forest treesto identify candidate genes for growth. The study was carried out in aninterspecific Eucalyptus backcross population, in which QTLs for growthco-localized with QTLs for mRNA abundance of lignin biosynthesis genesand associated methylation pathways. SAMS turned out to be an inter-esting candidate gene for further functional analysis.

45. Neale DB, Savolainen O: Association genetics of complex traitsin conifers. Trends Plant Sci 2004, 9:325-330.

46. Baucher M, Petit-Conil M, Boerjan W: Lignin: geneticengineering and impact on pulping. Crit Rev Biochem Mol Biol2003, 38:305-350.

47. Huntley SK, Ellis D, Gilbert M, Chapple C, Mansfield SD:Significant increases in pulping efficiency in C4H-F5H-transformed poplars: improved chemical savings andreduced environmental toxins. J Agric Food Chem 2003,51:6178-6183.

48.�

Pilate G, Guiney E, Holt K, Petit-Conil M, Lapierre C, Leple J-C,Pollet B, Mila I, Webster EA, Marstorp HG et al.: Field and pulpingperformances of transgenic trees with altered lignification.Nat Biotechnol 2002, 20:607-612.

This paper reports data from four-year old field trial experiments, carriedout in two countries, with transgenic poplar modified in lignin biosynth-esis. The data show that wood from poplars downregulated for CADrequires fewer chemicals to extract a given amount of lignin from the pulp,which could have both economic and environmental benefits. Impor-tantly, no adverse phenotypes on plant growth and health were noticedduring the four-year period in the field.

49. Li L, Zhou Y, Cheng X, Sun J, Marita JM, Ralph J, Chiang V:Combinatorial modification of multiple lignin traits in treesthrough multigene cotransformation. Proc Natl Acad Sci USA2003, 100:4939-4944.

50. Halpin C, Boerjan W: Stacking transgenes in forest trees.Trends Plant Sci 2003, 8:363-365.

51.�

Jing ZP, Gallardo F, Pascual MB, Sampalo R, Romero J, Torres deNavarra A, Canovas DM: Improved growth in a field trial oftransgenic hybrid poplar overexpressing glutaminesynthetase. New Phytol 2004, 164:137-145.

Overexpression of a pine cytosolic GS enhances height growth by 41%and stem diameter by 36% in three-year old, field-grown transgenicpoplar. The paper demonstrates that single genes can have profoundeffects on yield, without obvious adverse effects on health.

52. Park YW, Baba K, Furuta Y, Iida I, Sameshima K, Arai M, Hayashi T:Enhancement of growth and cellulose accumulation byoverexpression of xyloglucanase in poplar. FEBS Lett 2004,564:183-187.

53. Shani Z, Dekel M, Tsabary G, Goren R, Shoseyov O: Growthenhancement of transgenic poplar plants by overexpressionof Arabidopsis thaliana endo-1,4-b-glucanase (Cel1).Mol Breed 2004, 14:321-330.

54. Kawaoka A, Matsunaga E, Endo S, Kondo S, Yoshida K,Shinmyo A, Ebinuma H: Ectopic expression of a horseradishperoxidase enhances growth rate and increases oxidativestress resistance in hybrid aspen. Plant Physiol 2003,132:1177-1185.

55. Genissel A, Leple J-C, Millet N, Augustin S, Jouanin L, Pilate G:High tolerance against Chrysomela tremulae of transgenicpoplar plants expressing a synthetic cry3Aa gene fromBacillus thuringiensis spp. tenebrionis. Mol Breed 2003,11:103-110.

56. Gill RIS, Ellis BE, Isman MB: Tryptamine-induced resistance intryptophan decarboxylase transgenic poplar and tobaccoplants against their specific herbivores. J Chem Ecol 2003,29:779-793.

57. Tang W, Tian Y: Transgenic loblolly pine (Pinus taeda L.) plantsexpressing a modified d-endotoxin of Bacillus thuringiensiswith enhanced resistance to Dendrolimus punctatus Walkerand Crypyothelea formosicola Staud. J Exp Bot 2003,54:835-844.

58. Mentag R, Luckevich M, Morency M-J, Seguin A: Bacterialdisease resistance of transgenic hybrid poplar expressing thesynthetic antimicrobial peptide D4E1. Tree Physiol 2003,23:405-411.



59. Wang L, Han Y, Hu J: Transgenic forest trees for insectresistance. In Molecular Genetics and Breeding of Forest Trees.Edited by Kumar S, Fladung M. New York: Food Products Press;2004:243-261.

60. Che D, Meagher RB, Heaton ACP, Lima A, Rugh CL, Merkle SA:Expression of mercuric ion reductase in Eastern cottonwood(Populus deltoides) confers mercuric ion reductase andresistance. Plant Biotechnol J 2003, 1:311-319.

61. Skinner JS, Meilan R, Ma C, Straus SH: The Populus PTDpromoter imparts floral-predominant expression and enableshigh levels of floral-organ ablation in Populus, Nicotiana andArabidopsis. Mol Breed 2003, 12:119-132.

62. Brunner AM, Nilsson O: Revisiting tree maturation and floralinitiation in the poplar functional genomics era. New Phytol2004, 164:43-51.

63. Meilan R, Auerbach DJ, Ma C, DiFazio SP, Strauss SH:Stability of herbicide resistance and GUS expression intransgenic hybrid poplars (Populus sp.) during four years offield trials and vegetative propagation. HortScience 2002,37:277-280.

64. Hawkins S, Leple J-C, Cornu D, Jouanin L, Pilate G: Stability oftransgene expression in poplar: a model forest tree species.Ann For Sci 2003, 60:427-438.

65. Strauss SH, Brunner AM, Busov VB, Ma C, Meilan R: Ten lessonsfrom 15 years of transgenic Populus research. Forestry 2004,77:455-465.

66. Food and Agricultural Organization: Preliminary review ofbiotechnology in forestry, including genetic modification,(Forest Genetic Resources Working Papers, FRG/59E). Rome:FAO; 2004.

67. Brown GR, Bassoni DL, Gill GP, Fontana JR, Wheeler NC,Megraw RA, Davis MF, Sewell MM, Tuskan GA, Neale DB:Identification of quantitative trait loci influencing woodproperty traits in loblolly pine (Pinus taeda L.). III. QTLverification and candidate gene mapping. Genetics 2003,164:1537-1546.

68. Stirling B, Newcombe G, Vrebalov J, Bosdet I, Bradshaw HD Jr:Suppressed recombination around the MXC3 locus, a major

gene for resistance to poplar leaf rust. Theor Appl Genet 2001,103:1129-1137.

69. Zhang J, Steenackers M, Storme V, Neyrinck S, Van Montagu M,Gerats T, Boerjan W: Fine mapping and identification ofnucleotide-binding site/leucine-rich repeat sequences at theMER locus in Populus deltoides ‘S9-2’. Phytopathology 2001,91:1069-1073.

70. Lescot M, Rombauts S, Zhang J, Aubourg D, Mathe C, Jansson S,Rouze P, Boerjan W: Annotation of a 95-kb Populus deltoidesgenomic sequence reveals a disease resistance gene clusterand novel class I and class II transposable elements.Theor Appl Genet 2004, 109:10-22.

71. Yin T-M, DiFazio SP, Gunter LE, Jawdy SS, BoerjanW, Tuskan GA:Genetic and physical mapping of Melampsora rust resistancegenes in Populus and characterization of linkagedisequilibrium and flanking genomic sequence. New Phytol2004, 164:95-105.

72. Poke FS, Vaillancourt RE, Elliott RC, Reid JB: Sequence variationin two lignin biosynthesis genes, cinnamoyl CoA reductase(CCR) and cinnamyl alcohol dehydrogenase 2 (CAD2).Mol Breed 2003, 12:107-118.

73. Gill GP, Brown GR, Neale DB: A sequence mutation in thecinnamyl alcohol dehydrogenase gene associated withaltered lignification in loblolly pine. Plant Biotechnol J 2003,1:253-258.

74.��

Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB: Nucleotidediversity and linkage disequilibrium in loblolly pine. Proc NatlAcad Sci USA 2004, 101:15255-15260.

This paper shows that LD in loblolly pine declines in the order of a gene,indicating that association genetics in forest trees may be the strategy ofchoice to identify genes that determine complex traits.

75. Ingvarsson PK: Nucleotide polymorphism and linkagedisequilibrium within and among natural populations ofEuropean aspen (Populus tremula L. Salicaceae). Genetics2005, 169:945-953.

76. Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA,Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff S: Efficientdiscovery of DNA polymorphisms in natural populations byEcotilling. Plant J 2004, 37:778-786.



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