Bioenergy Trees

Special Feature Articles: Commentary Bringing trees into the fuel line Brian E. Ellis

Research reviews Towards optimizing wood development in bioenergy trees Kaisa Nieminen, Marcel Robischon, Juha Immanen and Ykä Helariutta

Cellulose factories: advancing bioenergy production from forest trees Eshchar Mizrachi, Shawn D. Mansfield and Alexander A. Myburg

Full papers Isoprene emission-free poplars – a chance to reduce the impact from poplar plantations on the atmosphere Katja Behnke, Rüdiger Grote, Nicolas Brüggemann, Ina Zimmer, Guanwu Zhou, Mudawi Elobeid, Dennis Janz, Andrea Polle and Jörg-Peter Schnitzler

The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus Eryang Li, Apurva Bhargava, Weiya Qiang, Michael C. Friedmann, Natascha Forneris, Rodney A. Savidge, Lee A. Johnson, Shawn D. Mansfield, Brian E. Ellis and Carl J. Douglas

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees Marcos D. V. Resende, Márcio F. R. Resende Jr, Carolina P. Sansaloni, Cesar D. Petroli, Alexandre A. Missiaggia, Aurelio M. Aguiar, Jupiter M. Abad, Elizabete K. Takahashi, Antonio M. Rosado, Danielle A. Faria, Georgios Pappas, Andrzej Kilian and Dario Grattapaglia

Salt stress induces the formation of a novel type of ‘pressure wood’ in two Populus species Dennis Janz, Silke Lautner, Henning Wildhagen, Katja Behnke, Jörg-Peter Schnitzler, Heinz Rennenberg, Jörg Fromm and Andrea Polle

CsRAV1 induces sylleptic branching in hybrid poplar Alicia Moreno-Cortés, Tamara Hernández-Verdeja, Paloma Sánchez-Jiménez, Pablo González-Melendi, Cipriano Aragoncillo and Isabel Allona

Designed for deconstruction – Poplar trees altered in cell wall lignification improve the efficacy of bioethanol production Shawn D. Mansfield, Kyu-Young Kang and Clint Chapple

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Introduction If there is to be a Holy Grail for the twenty-first century, the development of a true ‘bioeconomy’ to replace our current fossil fuel-based economy would seem to be a good candidate. Just as for the medieval seekers, the way to this Grail may be arduous and confused but the ultimate objective is unarguably one of immense importance. The 26th New Phytologist Symposium – Bioenergy trees – in May 2011 (http://www.newphytologist.org/bioenergy/default.htm) brought together a wide range of expertise to explore the current status of one potential strategy for reaching that goal: the large-scale use of forest biomass as a carbon and energy feedstock (Herr, 2011). The basic concept is simple; rather than relying upon petroleum, natural gas and coal – the products of solar energy captured by photosynthesizing plants hundreds of millions of years ago – we would harvest more recently synthesized photosynthetic products and convert these to industrially useful materials, most urgently to liquid fuels.

To this end, there are many strategies being pursued, but they fall into two broad categories. The first is to develop new or improved technologies for more efficiently processing existing feedstocks and the second, and the focus of the Bioenergy trees Symposium in Nancy (France), involves creation of novel biomass plant genotypes, either through genetic selection or genetic modification.

This Special Feature highlights a number of research reviews and articles that address some key biological questions: What is the biochemical basis of a particular biomass trait? What metabolic systems are engaged in supporting it?

Which genes control the relevant pathways and how are those genes themselves regulated? It is clear that the bioenergy trees planned for the future will have to be optimized for many different uses and for growth across a wide range of environments, but they will also need to be deployed in a socially responsible manner if we are to realize their full potential to contribute newly captured carbon and energy to the global economy.

Research review Towards optimizing wood development in bioenergy trees

Author for correspondence: Yk채 Helariutta Tel: +35 89 19 15 94 22 Email: yrjo.helariutta@helsinki.fi

Kaisa Nieminen, Marcel Robischon, Juha Immanen and Yk채 Helariutta

Summary New Phytologist (2011) doi: 10.1111/j.1469-8137.2011.04011.x

Key words: bioenergy, biofuel, biomass, tree breeding, wood formation, xylem development

To secure a sustainable energy source for the future, we need to develop an alternative to fossil fuels. Cellulose-based biofuel production has great potential for development into a sustainable and renewable energy source. The thick secondary walls of xylem cells provide a natural source of cellulose. As a result of the extensive production of wood through cambial activity, massive amounts of xylem cells can be harvested from trees. How can we obtain a maximal cellulose biomass yield from these trees? Thus far, tree breeding has been very challenging because of the long generation time.

Currently, new breeding possibilities are emerging through the development of highthroughput technologies in molecular genetics. What potential does our current knowledge on the regulation of cambial activity provide for the domestication of optimal bioenergy trees? We examine the hormonal and molecular regulation of wood development with the aim of identifying the key regulatory aspects. We describe traits, including stem morphology and xylem cell dimensions, that could be modified to enhance wood production. Finally, we discuss the potential of novel marker-assisted tree breeding technologies.

Research review Cellulose factories: advancing bioenergy production from forest trees

Author for correspondence: Alexander A. Myburg Tel: +27 01 24 20 49 45 Email: zander.myburg@fabi.up.ac.za

Eshchar Mizrachi, Shawn D. Mansfield and Alexander A. Myburg

Summary New Phytologist (2011) doi: 10.1111/j.1469-8137.2011.03971.x

Key words: bioenergy, cellulose, Eucalyptus, hemicellulose, Populus, sucrose, systems genetics

Fast-growing, short-rotation forest trees, such as Populus and Eucalyptus, produce large amounts of cellulose-rich biomass that could be utilized for bioenergy and biopolymer production. Major obstacles need to be overcome before the deployment of these genera as energy crops, including the effective removal of lignin and the subsequent liberation of carbohydrate constituents from wood cell walls. However, significant opportunities exist to both select for and engineer the structure and interaction of cell wall biopolymers, which could afford a means to improve processing and product development. The molecular underpinnings and regulation of cell wall carbohydrate biosynthesis are rapidly being elucidated, and are providing tools to strategically develop and guide the targeted modification required to adapt forest trees for the emerging bioeconomy. Much insight has already been gained from the perturbation of individual genes and pathways, but it is not known to what extent the natural variation in the sequence and expression of these same genes underlies the inherent variation in wood properties of field-grown trees. The integration of data from next-generation genomic technologies applied in natural and experimental populations will enable a systems genetics approach to study cell wall carbohydrate production in trees, and should advance the development of future woody bioenergy and biopolymer crops.

Isoprene emission-free poplars – a chance to reduce the impact from poplar plantations on the atmosphere Katja Behnke, Rüdiger Grote, Nicolas Brüggemann, Ina Zimmer, Guanwu Zhou, Mudawi Elobeid, Dennis Janz, Andrea Polle and Jörg-Peter Schnitzler

Summary Author for correspondence: Jörg-Peter Schnitzler Tel: +49 89 3187 2413 Email: jp.schnitzler@helmholtzmuenchen.de

New Phytologist (2011) doi: 10.1111/j.1469-8137.2011.03979.x

Key words: biomass production, modelling, non-isoprene emitting, outdoor conditions, Populus × canescens

• Depending on the atmospheric composition, isoprene emissions from plants can have a severe impact on air quality and regional climate. For the plant itself, isoprene can enhance stress tolerance and also interfere with the attraction of herbivores and parasitoids.

• Here, we tested the growth performance and fitness of Populus × canescens in which isoprene emission had been knocked down by RNA interference technology (PcISPS-RNAi plants) for two growing seasons under outdoor conditions.

• Neither the growth nor biomass yield of the PcISPS-RNAi poplars was impaired, and they were even temporarily enhanced compared with control poplars. Modelling of the annual carbon balances revealed a reduced carbon loss of 2.2% of the total gross primary production by the absence of isoprene emission, and a 6.9% enhanced net growth of PcISPS-RNAi poplars. However, the knock down in isoprene emission resulted in reduced susceptibility to fungal infection, whereas the attractiveness for herbivores was enhanced.

• The present study promises potential for the use of non- or low-isoprene-emitting poplars for more sustainable and environmentally friendly biomass production, as reducing isoprene emission will presumably have positive effects on regional climate and air quality.

CsRAV1 induces sylleptic branching in hybrid poplar

Alicia Moreno-Cortés, Tamara Hernández-Verdeja, Paloma Sánchez-Jiménez, Pablo González-Melendi, Cipriano Aragoncillo and Isabel Allona

Summary Author for correspondence: Isabel Allona Tel: +34 913364543 Email: isabel.allona@upm.es

• Sylleptic branching in trees may increase significantly branch number, leaf area and the general growth of the tree, particularly in its early years. Although this is a very important trait, so far little is known about the genes that control this process.

New Phytologist (2012) doi: 10.1111/j.1469-8137.2011.04023.x

• This article characterizes the Castanea sativa RAV1 gene, homologous to Arabidopsis TEM genes, by analyzing its circadian behavior and examining its winter expression in chestnut stems and buds. Transgenic hybrid poplars over-expressing CsRAV1 or showing RNA interference down-regulated PtaRAV1 and PtaRAV2 expression were produced and analyzed.

Key words: bioenergy, chestnut, CsRAV1, hybrid poplar, sylleptic branching, transcriptional repressors

• Over-expression of the CsRAV1 gene induces the early formation of sylleptic branches in hybrid poplar plantlets during the same growing season in which the lateral buds form.

Only minor growth differences and no changes in wood anatomy are produced.

• The possibility of generating trees with a greater biomass by manipulating the CsRAV1 gene makes CsRAV1 transgenic plants promising candidates for bioenergy production

Designed for deconstruction – Poplar trees altered in cell wall lignification improve the efficacy of bioethanol production Shawn D. Mansfield, Kyu-Young Kang and Clint Chapple

Summary Author for correspondence: Shawn D. Mansfield Tel: +1 60 48 22 01 96 Email: shawn.mansfield@ubc.ca

New Phytologist (2012) doi: 10.1111/j.1469-8137.2011.04031.x

Key words: bioethanol, hydrolysis, lignin, monomer composition, organosolv, poplar, steam explosion

• There is a pressing global need to reduce the increasing societal reliance on petroleum and to develop a bio-based economy. At the forefront is the need to establish a sustainable, renewable, alternative energy sector. This includes liquid transportation fuel derived from lignocellulosic plant materials. However, one of the current limiting factors restricting the effective and efficient conversion of lignocellulosic residues is the recalcitrance of the substrate to enzymatic conversion.

• In an attempt to assess the impact of cell wall lignin on recalcitrance, we subjected poplar trees engineered with altered lignin content and composition to two potential industrial pretreatment regimes, and evaluated the overall efficacy of the bioconversion to ethanol process.

• It was apparent that total lignin content has a greater impact than monomer ratio (syringyl : guaiacyl) on both pretreatments. More importantly, low lignin plants showed as much as a 15% improvement in the efficiency of conversion, with near complete hydrolysis of the cellulosic polymer.

• Using genomic tools to breed or select for modifications in key cell wall chemical and/or ultrastructural traits can have a profound effect on bioenergy processing. These techniques may therefore offer means to overcome the current obstacles that underpin the recalcitrance of lignocellulosic substrates to bioconversion.

The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus Eryang Li, Apurva Bhargava, Weiya Qiang, Michael C. Friedmann, Natascha Forneris, Rodney A. Savidge, Lee A. Johnson, Shawn D. Mansfield, Brian E. Ellis and Carl J. Douglas

Summary Author for correspondence: Carl J. Douglas Tel: +1 60 48 22 26 18 Email: carl.douglas@ubc.ca

• The formation of secondary cell walls in cell types such as tracheary elements and fibers is a defining characteristic of vascular plants. The Arabidopsis transcription factor KNAT7 is a component of a transcription network that regulates secondary cell wall biosynthesis, but its function has remained unclear.

New Phytologist (2012) doi: 10.1111/j.1469-8137.2011.04016.x

• We conducted anatomical, biochemical and molecular phenotypic analyses of Arabidopsis knat7 loss-of-function alleles, KNAT7 over-expression lines and knat7 lines expressing poplar KNAT7.

Key words: homeodomain protein, lignin, poplar, repression, secondary cell wall, transcription factor, xylem

• KNAT7 was strongly expressed in concert with secondary wall formation in Arabidopsis and poplar. Arabidopsis knat7 loss-of-function alleles exhibited irregular xylem phenotypes, but also showed increased secondary cell wall thickness in fibers. Increased commitment to secondary cell wall biosynthesis was accompanied by increased lignin content and elevated expression of secondary cell wall biosynthetic genes. KNAT7 overexpression resulted in thinner interfascicular fiber cell walls.

• Taken together with data demonstrating that KNAT7 is a transcriptional repressor, we hypothesize that KNAT7 is a negative regulator of secondary wall biosynthesis, and functions in a negative feedback loop that represses metabolically inappropriate commitment to secondary wall formation, thereby maintaining metabolic homeostasis.

The conservation of the KNAT7 regulatory module in poplar suggests new ways to manipulate secondary cell wall deposition for improvement of bioenergy traits in this tree.

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees Marcos D. V. Resende, Márcio F. R. Resende Jr, Carolina P. Sansaloni, Cesar D. Petroli, Alexandre A. Missiaggia, Aurelio M. Aguiar, Jupiter M. Abad, Elizabete K. Takahashi, Antonio M. Rosado, Danielle A. Faria, Georgios Pappas, Andrzej Kilian and Dario Grattapaglia

Summary Author for correspondence: Dario Grattapaglia Tel: +55 61 34484652 Email: dario@cenargen.embrapa.br

• Genomic selection (GS) is expected to cause a paradigm shift in tree breeding by improving its speed and efficiency. By fitting all the genome-wide markers concurrently, GS can capture most of the ‘missing heritability’ of complex traits that quantitative trait locus (QTL) and association mapping classically fail to explain. Experimental support of GS is now required.

New Phytologist (2012) doi: 10.1111/j.1469-8137.2011.04038.x

• The effectiveness of GS was assessed in two unrelated Eucalyptus breeding populations with contrasting effective population sizes (Ne = 11 and 51) genotyped with > 3000 DArT markers. Prediction models were developed for tree circumference and height growth, wood specific gravity and pulp yield using random regression best linear unbiased predictor (BLUP).

Key words: applied genomics, DArT, effective population size, Eucalyptus, genome-wide selection (GWS), genomic selection (GS), tree breeding

• Accuracies of GS varied between 0.55 and 0.88, matching the accuracies achieved by conventional phenotypic selection. Substantial proportions (74–97%) of trait heritability were captured by fitting all genome-wide markers simultaneously. Genomic regions explaining trait variation largely coincided between populations, although GS models predicted poorly across populations, likely as a result of variable patterns of linkage disequilibrium, inconsistent allelic effects and genotype × environment interaction.

• GS brings a new perspective to the understanding of quantitative trait variation in forest trees and provides a revolutionary tool for applied tree improvement. Nevertheless population-specific predictive models will likely drive the initial applications of GS in forest tree breeding.

Salt stress induces the formation of a novel type of ‘pressure wood’ in two Populus species Dennis Janz, Silke Lautner, Henning Wildhagen, Katja Behnke, Jörg-Peter Schnitzler, Heinz Rennenberg, Jörg Fromm and Andrea Polle

Summary Author for correspondence: Andrea Polle Tel: +49 551393480 Email: apolle@gwdg.de

New Phytologist (2011) doi: 10.1111/j.1469-8137.2011.03975.x

Key words: arabinogalactan protein, biomass, carbohydrate, fasciclin-like protein, phloem, salt transcriptome, wood, xylem

• Salinity causes osmotic stress and limits biomass production of plants. The goal of this study was to investigate mechanisms underlying hydraulic adaptation to salinity.

• Anatomical, ecophysiological and transcriptional responses to salinity were investigated in the xylem of a salt-sensitive (Populus × canescens) and a salt-tolerant species (Populus euphratica).

• Moderate salt stress, which suppressed but did not abolish photosynthesis and radial growth in P. × canescens, resulted in hydraulic adaptation by increased vessel frequencies and decreased vessel lumina. Transcript abundances of a suite of genes (FLA, COB-like, BAM, XET, etc.) previously shown to be activated during tension wood formation, were collectively suppressed in developing xylem, whereas those for stress and defense-related genes increased. A subset of cell wall-related genes was also suppressed in salt-exposed P. euphratica, although this species largely excluded sodium and showed no anatomical alterations. Salt exposure influenced cell wall composition involving increases in the lignin : carbohydrate ratio in both species.

• In conclusion, hydraulic stress adaptation involves cell wall modifications reciprocal to tension wood formation that result in the formation of a novel type of reaction wood in upright stems named ‘pressure wood’. Our data suggest that transcriptional co-regulation of a core set of genes determines reaction wood composition.