Skip to main content
SpringerLink
Log in

Traditional Breeding, Genomics-Assisted Breeding, and Biotechnological Modification of Forest Trees and Short Rotation Woody Crops

  • Chapter
  • First Online:
Book cover Wood-Based Energy in the Northern Forests

Abstract

The use of woody biomass for biofuels is being pursued with both targeted harvests from natural forests and growth of Short Rotation Woody Crops (SRWCs) in plantations. Both native and exotic tree species can contribute to energy feedstocks, as managed, unmanaged, or native forests. However, although standing woody biomass may in total be considered sufficient to meet projected demands for energy in certain Northern regions, increases in productivity are often still required for woody biomass to become an economically and ecologically sustainable source of energy. Traditional plant breeding has been very successful in improving growth, tree volume, and various wood quality traits for the lumber and paper industries (Harfouche et al. 2012) for forest trees and for SRWCs. The rate of progress in tree breeding is limited by the long breeding cycle times of most tree species, however. Biotechnological approaches have great potential to augment and help advance tree improvement programs, through early, indirect selection of improved genotypes, propagation through tissue culture, or genetic engineering of traits such as flowering time or wood quality.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 149.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ahuja MR (2011) Fate of transgenes in the forest tree genome. Tree Genet Genomes 7:221–230

    Article  MathSciNet  Google Scholar 

  • Anterola AM, Lewis NG (2002) Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochemistry 61:221–294

    Article  Google Scholar 

  • Baginsky S, Hennig L, Zimmermann P, Gruissem W (2010) Gene expression analysis, proteomics, and network discovery. Plant Physiol 152:402–410

    Article  Google Scholar 

  • Baker AJ (1973) Effect of lignin on the in vitro digestibility of wood pulp. J Anim Sci 35:768–771

    Google Scholar 

  • Barakat A, Wall PK, DiLoreto S, dePamphilis CW, Carlson JE (2007) Conservation and divergence of microRNAs in Populus. BMC Genomics 8:481

    Article  Google Scholar 

  • Barakat A, Yassin NBM, Park JS, Choi A, Herr JR, Carlson JE (2011) Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants. Plant Sci 181:249–257

    Article  Google Scholar 

  • Bergante S, Facciotto G, Minotta G (2010) Identification of the main site factors and management intensity affecting the establishment of short-rotation-coppices (SRC) in northern Italy through stepwise regression analysis. Cent Eur J Biol 5:522–30

    Article  Google Scholar 

  • Bernard SM, Habash DZ (2009) The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling. New Phytol 182:608–620

    Article  Google Scholar 

  • Boerjan W (2005) Biotechnology and the domestication of forest trees. Curr Opin Biotechnol 16:159–166

    Article  Google Scholar 

  • Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546

    Article  Google Scholar 

  • Buchholz T, Volk TA (2011) Improving the profitability of willow crops—Identifying opportunities with a crop budget model. Bioenerg Res 4:85–95

    Article  Google Scholar 

  • Busov VB, Brunner AM, Meilan R, Filichkin S, Ganio L, Gandhi S, Strauss SH (2005) Genetic transformation: a powerful tool for dissection of adaptive traits in trees. New Phytol 167:9–18

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Campbell MM, Brunner AM, Jones HM, Strauss SH (2003) Forestry’s fertile crescent: the application of biotechnology to forest trees. Plant Biotechnol J 1:141–154

    Article  Google Scholar 

  • Chuck G, Cigan AM, Saeteurn K, Hake S (2007) The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat Genet 39:544–549

    Article  Google Scholar 

  • Cobb WR, Will RE, Daniels RF, Jacobson MA (2008) Aboveground biomass and nitrogen in four short-rotation woody crop species growing with different water and nutrient availabilities. For Ecol Manag 255:4032–4039

    Article  Google Scholar 

  • Cohen D, Bogeat-Triboulot M-B, Tisserant E, Balzergue S, Martin-Magniette M-L, Lelandais G, Ningre N, Renou J-P, Tamby J-P, Le Thiec D et al (2010) Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics 11:630

    Article  Google Scholar 

  • Coleman HD, Samuels AL, Guy RD, Mansfield SD (2008) Perturbed lignification impacts tree growth in hybrid poplar–a function of sink strength, vascular integrity, and photosynthetic assimilation. Plant Physiol 148:1229–1237

    Article  Google Scholar 

  • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Publ Group 12:499–510

    Google Scholar 

  • Demirbas A (2001) Relationships between lignin contents and heating values of biomass. Energ Convers Manage 42:183–188

    Article  Google Scholar 

  • Duguay J, Jamal S, Liu Z, Wang T-W, Thompson JE (2007) Leaf-specific suppression of deoxyhypusine synthase in Arabidopsis thaliana enhances growth without negative pleiotropic effects. Journal of Plant Physiology 164(4) 408–420

    Google Scholar 

  • Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, Chandrasegaran S (2005) Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res 33:5978–5990

    Article  Google Scholar 

  • Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, St Clair JB, Neale DB (2009) Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182:1289–1302

    Article  Google Scholar 

  • El-Khatib RT, Hamerlynck EP, Gallardo F, Kirby EG (2004) Transgenic poplar characterized by ectopic expression of a pine cytosolic glutamine synthetase gene exhibits enhanced tolerance to water stress. Tree Physiol 24:729–736

    Article  Google Scholar 

  • Ellis BE (2012) Bringing trees into the fuel line. New Phytol 194:1–3

    Article  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  Google Scholar 

  • Evenson RE, Gollin D (2003) Assessing the impact of the green revolution 1960 to 2000. Science 300(5620):758–762

    Article  Google Scholar 

  • Flachowsky H, Hanke MV, Peil A, Strauss SH, Fladung M (2009) A review on transgenic approaches to accelerate breeding of woody plants. Plant Breed 128:217–226

    Article  Google Scholar 

  • Fu J, Sampalo R, Gallardo F, Cánovas FM, Kirby EG (2003) Assembly of a cytosolic pine glutamine synthetase holoenzyme in leaves of transgenic poplar leads to enhanced vegetative growth in young plants. Plant Cell Environ 26:411–418

    Article  Google Scholar 

  • Goicoechea MM, Lacombe EE, Legay SS, Mihaljevic SS, Rech PP, Jauneau AA, Lapierre CC, Pollet BB, Verhaegen DD, Chaubet-Gigot NN et al (2005) EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis. Plant J 43:553–567

    Article  Google Scholar 

  • Grattapaglia D, Resende MDV (2011) Genomic selection in forest tree breeding. Tree Genet Genomes 7:241–255

    Article  Google Scholar 

  • Grattapaglia D, Plomion C, Kirst M, Sederoff RR (2009) Genomics of growth traits in forest trees. Curr Opin Plant Biol 12:148–156

    Article  Google Scholar 

  • Gstaiger M, Aebersold R (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 10:617–627

    Article  Google Scholar 

  • Hamanishi ET, Raj S, Wilkins O, Thomas BR, Mansfield SD, Plant AL, Campbell MM (2010) Intraspecific variation in the Populus balsamifera drought transcriptome. Plant Cell Environ 33:1742–1755

    Article  Google Scholar 

  • Harfouche A, Meilan R, Altman A (2011) Tree genetic engineering and applications to sustainable forestry and biomass production. Trends Biotechnol 29:9–17

    Article  Google Scholar 

  • Harfouche A, Meilan R, Kirst M, Morgante M, Boerjan W, Sabatti M, Scarascia MG (2012) Accelerating the domestication of forest trees in a changing world. Trends Plant Sci 17:64–72

    Article  Google Scholar 

  • Herr JR (2011) Bioenergy from trees. New Phytol 192:313–315

    Article  Google Scholar 

  • Hill WG (2012) Quantitative genetics in the genomics era. Curr Genomics 13:196–206

    Article  Google Scholar 

  • Hinchee M, Rottmann W, Mullinax L, Zhang C, Chang S, Cunningham M, Pearson L, Nehra N (2009) Short-rotation woody crops for bioenergy and biofuels applications. In Vitro Cell Dev Biol Plant 45:619–629

    Article  Google Scholar 

  • Karp A, Shield I (2008) Bioenergy from plants and the sustainable yield challenge. New Phytol 179:15–32

    Article  Google Scholar 

  • Kiernan BD, Volk TA, Tharakan PJ, Nowak CA, Phillipon SP, Abrahamson LP, White EH (2003) Clone-site testing and selections for scale-up plantings. SUNY College of Environmental Science and Forestry, Syracuse, NY. http://www.esf.edu/willow/reports.htm. Accessed 24 Jul 2013

  • Kopp RF (2000) Genetic improvement of Salix using traditional breeding and AFLP fingerprinting. Thesis, SUNY College of Environmental Science and Forestry, Syracuse, NY. pp 175

    Google Scholar 

  • Kopp RF, Smart LB, Maynard CA, Isebrands JG, Tuskan GA, Abrahamson LP (2001) The development of improved willow clones for eastern North America. Forest Chron 77:287–92

    Google Scholar 

  • Leplé J-C, Dauwe R, Morreel K, Storme V, Lapierre C, Pollet B, Naumann A, Kang K-Y, Kim H, Ruel K et al (2007) Downregulation of cinnamoyl-coenzyme A reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell 19:3669–3691

    Article  Google Scholar 

  • Lexer C, Stölting KN (2012) Whole genome sequencing (WGS) meets biogeography and shows that genomic selection in forest trees is feasible. New Phytol 196:652–654

    Article  Google Scholar 

  • Li B, Qin Y, Duan H, Yin W, Xia X (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot 62:3765–3779

    Article  Google Scholar 

  • Li X, Weng J-K, Chapple C (2008) Improvement of biomass through lignin modification. Plant J 54:569–581

    Article  Google Scholar 

  • Liang H, Frost CJ, Wei X, Brown NR, Carlson JE, Tien M (2008) A novel approach toward lignin modification to facilitate cellulosic ethanol production: introducing a tyrosine-rich cell wall peptide gene in poplar. Clean 36(8):662–668

    Google Scholar 

  • Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:14–14

    Article  Google Scholar 

  • Man H-M, Boriel R, El-Khatib R, Kirby EG (2005) Characterization of transgenic poplar with ectopic expression of pine cytosolic glutamine synthetase under conditions of varying nitrogen availability. New Phytol 167:31–39

    Article  Google Scholar 

  • Mansfield SD (2009) Solutions for dissolution–engineering cell walls for deconstruction. Curr Opin Biotechnol 20:286–294

    Article  Google Scholar 

  • Mead DJ (2005) Forests for energy and the role of planted trees. Crit Rev Plant Sci 24:407–421

    Article  Google Scholar 

  • Meyer RS, DuVal AE, Jensen HR (2012) Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. New Phytol 196:29–48

    Article  Google Scholar 

  • Mizrachi E, Mansfield SD, Myburg AA (2012) Cellulose factories: advancing bioenergy production from forest trees. New Phytol 194:54–62

    Article  Google Scholar 

  • Mosseler A, Zsuffa L, Stoehr MU, Kenney WA (1988) Variation in biomass production, moisture content, and specific gravity in some North American willows (Salix L.). Can J For Res 18:1535–40

    Article  Google Scholar 

  • Mosseler A, Papadopol CS (1989) Seasonal isolation as a reproductive barrier among sympatric Salix species. Can J Bot 67:2563–70

    Article  Google Scholar 

  • Mosseler A, Zsuffa L (1989) Sex expression and sex ratios in intra- and interspecific hybrid families of Salix L. Silvae Genet 38:12–17

    Google Scholar 

  • Mosseler A (1990) Hybrid performance and species crossability relationships in willows (Salix). Can J Bot 68:2329–38

    Google Scholar 

  • Neale DB (2007) Genomics to tree breeding and forest health. Curr Opin Genet Dev 17:539–544

    Article  Google Scholar 

  • Neale DB, Ingvarsson PK (2008) Population, quantitative and comparative genomics of adaptation in forest trees. Curr Opin Plant Biol 11:149–155

    Article  Google Scholar 

  • Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nat Publ Group 12:111–122

    Google Scholar 

  • Nilsson R, Bernfur K, Gustavsson N, Bygdell J, Wingsle G, Larsson C (2010) Proteomics of plasma membranes from poplar trees reveals tissue distribution of transporters, receptors, and proteins in cell wall formation. Mol Cell Proteomics 9:368–387

    Article  Google Scholar 

  • Patzlaff AA, McInnis SS, Courtenay AA, Surman CC, Newman LJL, Smith CC, Bevan MWM, Mansfield SS, Whetten RWR, Sederoff RRR et al (2003) Characterisation of a pine MYB that regulates lignification. Plant J 36:743–754

    Article  Google Scholar 

  • Polle A, Altman A, Jiang X (2006) Towards Genetic Engineering for drought tolerance in trees. Pages 275–297. From “Tree Transgenesis” Edited by M Fladung & D Ewald, Springer (Berlin, Heidelberg)

    Google Scholar 

  • Qiu QQ, Ma TT, Hu QQ, Liu BB, Wu YY, Zhou HH, Wang QQ, Wang JJ, Liu JJ (2011) Genome-scale transcriptome analysis of the desert poplar, Populus euphratica. Tree Physiol 31:452–461

    Article  Google Scholar 

  • Quesada T, Gopal V, Cumbie WP, Eckert AJ, Wegrzyn JL, Neale DB, Goldfarb B, Huber DA, Casella G, Davis JM (2010) Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.). Genetics 186:677–686

    Article  Google Scholar 

  • Resende MFR, Muñoz P, Acosta JJ, Peter GF, Davis JM, Grattapaglia D, Resende MDV, Kirst M (2012) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytol 193:617–624

    Article  Google Scholar 

  • Riemenschneider DE, Berguson WE, Dickmann DI, Hall RB, Isebrands JG, Mohn CA, Stanosz GR, Tuskan GA (2001) Poplar breeding and testing strategies in the north-central US: demonstration of potential yield and consideration of future research needs. Forest Chron 77:245–53

    Google Scholar 

  • Shani ZZ, Dekel MM, Roiz LL, Horowitz MM, Kolosovski NN, Lapidot SS, Alkan SS, Koltai HH, Tsabary GG, Goren RR et al (2006) Expression of endo-1,4-beta-glucanase (cel1) in Arabidopsis thaliana is associated with plant growth, xylem development and cell wall thickening. Plant Cell Rep 25:1067–1074

    Article  Google Scholar 

  • Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotech 26:1135–1145

    Article  Google Scholar 

  • Simmons BA, Loque D, Blanch HW (2008) Next-generation biomass feedstocks for biofuel production. Genome Biol 9:242

    Article  Google Scholar 

  • Sims REH, Venturi P (2004) All-year-round harvesting of short rotation coppice Eucalyptus compared with the delivered costs of biomass from more conventional short season, harvesting systems. Biomass Bioenergy 26:27–37

    Article  Google Scholar 

  • Smart LB, Cameron KD (2008) Genetic improvement of willow (Salix spp.) as a dedicated bioenergy crop. In: Vermerris WE (ed) Genetic improvement of bioenergy crops. Springer Science, New York, NY, pp 347–76

    Google Scholar 

  • Smart LB, Cameron KD (2011) Shrub willow (Salix spp.) bioenergy crops. In: Kole C, Joshi S, Shonnard D (eds) Handbook of bioenergy crop plants. Taylor and Francis, Boca Raton, FL, In press

    Google Scholar 

  • Smart LB, Volk TA, Lin J, Kopp RF, Phillips IS, Cameron KD, White EH, Abrahamson LP (2005) Genetic improvement of shrub willow (Salix spp.) crops for bioenergy and environmental applications in the United States. Unasylva 56:51–55

    Google Scholar 

  • Strauss SH, Brunner AM, Busov VB, Ma C, Meilan R (2004) Ten lessons from 15 years of transgenic Populus research. Forestry 77:455–465

    Article  Google Scholar 

  • Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604

    Article  Google Scholar 

  • van der Graaff E, Laux T, Rensing SA (2009) The WUS homeobox-containing (WOX) protein family. Genome Biol 10:248

    Article  Google Scholar 

  • Vanholme R, Morreel K, Darrah C, Oyarce P, Grabber JH, Ralph J, Boerjan W (2012) Metabolic engineering of novel lignin in biomass crops. New Phytol 196:978–1000

    Article  Google Scholar 

  • Villar E, Klopp C, Noirot C, Novaes E, Kirst M, Plomion C, Gion J-M (2011) RNA-Seq reveals genotype-specific molecular responses to water deficit in Eucalyptus. BMC Genomics 12:538–538

    Article  Google Scholar 

  • Wang Z-Y, Brummer EC (2012) Is genetic engineering ever going to take off in forage, turf and bioenergy crop breeding? Ann Bot 110:1317–1325

    Article  Google Scholar 

  • Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai C-J, Neale DB (2010) Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytol 188:515–532

    Article  Google Scholar 

  • Weng J-K, Li X, Bonawitz ND, Chapple C (2008) Emerging strategies of lignin engineering and degradation for cellulosic biofuel production. Curr Opin Biotechnol 19:7–7

    Article  Google Scholar 

  • Yokawa K, Kagenishi T, Baluška F (2013) Root photomorphogenesis in laboratory-maintained Arabidopsis seedlings. Trends Plant Sci 18(3):117–119

    Article  Google Scholar 

  • Yordanov YSY, Regan SS, Busov VV (2010) Members of the lateral organ boundaries domain transcription factor family are involved in the regulation of secondary growth in Populus. Plant Cell 22:3662–3677

    Article  Google Scholar 

  • Zalesny RS, Hall RB, Zalesny JA, McMahon BG, Berguson WE, Stanosz GR (2009) Biomass and genotype x environment interactions of Populus energy crops in the Midwestern United States. Bioenerg Res 2:106–22

    Article  Google Scholar 

  • Zawaski C, Kadmiel M, Ma C, Gai Y, Jiang X, Strauss SH, Busov VB (2011) Short internodes-like genes regulate shoot growth and xylem proliferation in Populus. New Phytol 191:678–691

    Article  Google Scholar 

  • Zhu X, Pattathil S, Mazumder K, Brehm A, Hahn MG, Dinesh-Kumar SP, Joshi CP (2010) Virus-induced gene Silencing offers a functional genomics platform for studying plant cell wall formation. Molecular Plant 3(5):818–833

    Google Scholar 

  • Zsuffa L (1988) A review of the progress in selecting and breeding North American Salix species for energy plantations at the Faculty of Forestry, University of Toronto, Canada. International Energy Agency willow breeding symposium, Uppsala, Sweden, 41–51

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The Department of Ecosystem Science and Management, The Schatz Center for Tree Genetics, Pennsylvania State University, 321 Forest Resources Building, University Park, PA, 16802, USA

    Joshua R. Herr Ph.D. & John E. Carlson Ph.D.

Authors
  1. Joshua R. Herr Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John E. Carlson Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Joshua R. Herr Ph.D. .

Editor information

Editors and Affiliations

  1. Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, USA

    Michael Jacobson

  2. Department of Agricultural and Biological Engineering, Pennsylvania State University, University Park, Pennsylvania, USA

    Daniel Ciolkosz

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Herr, J.R., Carlson, J.E. (2013). Traditional Breeding, Genomics-Assisted Breeding, and Biotechnological Modification of Forest Trees and Short Rotation Woody Crops. In: Jacobson, M., Ciolkosz, D. (eds) Wood-Based Energy in the Northern Forests. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9478-2_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-9478-2_5

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4614-9477-5

  • Online ISBN: 978-1-4614-9478-2

  • eBook Packages: EnergyEnergy (R0)

Publish with us

Policies and ethics

Search

Navigation