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Breeding Forest Trees by Genomic Selection: Current Progress and the Way Forward

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Genomics of Plant Genetic Resources

Abstract

A challenge common to all forest tree improvement programs is the long time interval of a breeding cycle. Moreover, the large size of trees, late trait expression and the extended time-lag between the breeding investment and the deployment of genetically improved material, make tree breeding a costly operation, more susceptible to changes in market demands, business objectives and climate change. The outlook of accelerating tree breeding and improving selection precision by marker assisted selection (MAS), thus became one of the driving principles of most forest tree genome projects. Although important advances were made in quantitative trait locus (QTL) mapping and association genetics, MAS did not make it in the ‘real tree breeding world’. Limitations of early genomic technologies, coupled to the genetic heterogeneity of tree species and an overoptimistic assessment of the architecture of complex traits in such phenotypically plastic perennial organisms, largely explain this outcome. The inability to ascertain and make use of individual QTLs has caused a paradigm shift from trying to dissect trait components and determine their individual effects, to dealing with the aggregate of whole-genome effects to predict phenotypes by Genomic Selection (GS). Given the rapidly growing interest of tree breeders on this theme, this chapter provides an update on the current status and upcoming perspectives of GS in forest tree breeding. After a brief explanation of the basic principles and the main factors that impact prediction accuracy, the perspectives and the encouraging experimental results of GS in forest trees are reviewed. Concerns raised by tree breeders about GS are then discussed by reviewing the current knowledge in other species, while attempting to provide a roadmap for upcoming research and operational applications of GS. The prospects of GS in tree breeding are very promising to increase genetic gain per unit time through improved estimation of breeding (parent selection) and genotypic (clone selection) values, reduction of generation time and optimization of genome-directed mate allocation. Furthermore, the progressive accumulation of huge genotype and corresponding phenotype datasets in GS will provide an exceptional ‘big data’ framework that should enhance our understanding of the connection between genome-wide elements and the observable phenotypic variation in complex traits.

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References

  • Albrecht T, Wimmer V, Auinger HJ, Erbe M et al (2011) Genome-based prediction of testcross values in maize. Theor Appl Genet 123:339–350

    Article  PubMed  Google Scholar 

  • Araujo JA, Borralho NMG, Dehon G (2012) The importance and type of non-additive genetic effects for growth in Eucalyptus globulus. Tree Genet Genomes 8:327–337

    Article  Google Scholar 

  • Assis T (2011) Hybrids and mini-cutting: a powerful combination that has revolutionized the Eucalyptus clonal forestry. BMC Proceedings 5:I18

    Google Scholar 

  • Assis TF, de Resende MDV (2011) Genetic improvement of forest tree species. Crop Breed Appl Biotechnol 11:44–49

    Article  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. Plos One 3(10):e3376

    Article  PubMed Central  PubMed  Google Scholar 

  • Bernardo R (2008) Molecular markers and selection for complex traits in plants: Learning from the last 20 years. Crop Sci 48:1649–1664

    Article  Google Scholar 

  • Bernardo R, Yu JM (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090

    Article  Google Scholar 

  • Bouvet JM, Saya A, Vigneron P (2009) Trends in additive, dominance and environmental effects with age for growth traits in Eucalyptus hybrid populations. Euphytica 165:35–54

    Article  Google Scholar 

  • Brondani RP, Williams ER, Brondani C, Grattapaglia D (2006) A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biol 6:20

    Article  PubMed Central  PubMed  Google Scholar 

  • Burgueno J, de los CG, Weigel K, Crossa J (2012) Genomic prediction of breeding values when modeling genotype x environment interaction using pedigree and dense molecular markers. Crop Sci 52:707–719

    Article  Google Scholar 

  • Coster A, Bastiaansen JWM, Calus MPL, van Arendonk JAM et al (2010) Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance. Genet Sel Evol 42:9

    Google Scholar 

  • Crossa J, de los CG, Perez P, Gianola D et al (2010) Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186:713–406

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Daetwyler HD, Villanueva B, Bijma P, Woolliams JA (2007) Inbreeding in genome-wide selection. J Anim Breed Genet 124:369–376

    Article  CAS  PubMed  Google Scholar 

  • Daetwyler HD, Villanueva B, Woolliams JA (2008) Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS One 3:e3395

    Article  PubMed Central  PubMed  Google Scholar 

  • Daetwyler HD, Hickey JM, Henshall JM, Dominik S et al (2010) Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population. Anim Prod Sci 50:1004–1010

    Article  Google Scholar 

  • Denis M, Bouvet J-M (2013) Efficiency of genomic selection with models including dominance effect in the context of Eucalyptus breeding. Tree Genet Genomes 9:37–51

    Google Scholar 

  • Dillen S, Storme V, Marron N, Bastien C et al (2008) Genomic regions involved in productivity of two interspecific poplar families in Europe. 1. Stem height, circumference and volume. Tree Genet Genomes5:147–164

    Google Scholar 

  • Echt CS, Saha S, Krutovsky KV, Wimalanathan K et al (2011) An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genet 12:17

    Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA et al (2011) A robust, simple genotyping-by-sequencing (GbS) approach for high diversity species. Plos One 6:e19379

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Faria DA, Tanno P, Reis A, Martins A et al (2012) Genotyping-by-Sequencing (GbS) the highly heterozygous genome of Eucalyptus provides large numbers of high quality genome-wide SNPs Plant and Animal Genome Conference XX, San Diego, p P0521

    Google Scholar 

  • Gion JM, Carouche A, Deweer S, Bedon F et al (2011) Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus. BMC Genomics 12:301

    Article  PubMed Central  PubMed  Google Scholar 

  • Goddard M (2009) Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136:245–257

    Article  PubMed  Google Scholar 

  • Goddard ME, Hayes BJ (2009) Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet 10:381–391

    Article  CAS  PubMed  Google Scholar 

  • Grattapaglia D, Kirst M (2008) Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytol 179:911–929

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Grattapaglia D, Chaparro J, Wilcox P, Mccord S et al (1992) Mapping in woody plants with RAPD markers: applications to breeding in forestry and horticulture. Proceedings of the Symposium “Applications of RAPD Technology to Plant Breeding”. Crop Science Society of America, American Society of Horticultural Science, American Genetic Association, pp 37–40

    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  CAS  PubMed  Google Scholar 

  • Grattapaglia D, de Alencar S, Pappas G (2011) Genome-wide genotyping and SNP discovery by ultra-deep Restriction-Associated DNA (RAD) tag sequencing of pooled samples of E. grandis and E. globulus. BMC Proceedings 5:P45

    Google Scholar 

  • Greenwood MS, Adams GW, Gillespie M (1991) Stimulation of flowering by grafted black spruce and white spruce—a comparative-study of the effects of gibberellin a4/7, cultural treatments, and environment. Can J For Res 21:395–400

    Article  CAS  Google Scholar 

  • Habier D, Fernando RL, Dekkers JCM (2009) Genomic Selection using low-density marker panels. Genetics 182:343–353

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Haley CS, Visscher PM (1998) Strategies to utilize marker-quantitative trait loci associations. J Dairy Sci 81:85–97

    Article  CAS  PubMed  Google Scholar 

  • Hammami H, Rekik B, Gengler N (2009) Genotype by environment interaction in dairy cattle. Biotechnol Agron Soc 13:155–164

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Hasan O, Reid JB (1995) Reduction of generation time in Eucalyptus globulus. Plant Growth Regul 17:53–60

    CAS  Google Scholar 

  • Hayes B, Goddard M (2010) Genome-wide association and genomic selection in animal breeding. Genome 53:876–883

    Article  CAS  PubMed  Google Scholar 

  • Hayes BJ, Bowman PJ, Chamberlain AC, Verbyla K et al (2009a) Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet Sel Evol 41:51

    Article  Google Scholar 

  • Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009b) Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92:433–443

    Article  CAS  Google Scholar 

  • Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12

    Article  CAS  Google Scholar 

  • Heslot N, Yang HP, Sorrells ME, Jannink JL (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52:146–160

    Article  Google Scholar 

  • Hu ZQ, Li YG, Song XH, Han YP et al (2011) Genomic value prediction for quantitative traits under the epistatic model. BMC Genet 12:15

    Article  PubMed Central  PubMed  Google Scholar 

  • Hudson CJ, Freeman JS, Kullan AR, Petroli CD et al (2012) A reference linkage map for Eucalyptus. BMC Genomics 13:240

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ibanz-Escriche N, Fernando RL, Toosi A, Dekkers JCM (2009) Genomic selection of purebreds for crossbred performance. Genet Sel Evol 41:12

    Article  Google Scholar 

  • Iwata H, Hayashi T, Tsumura Y (2011) Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica. Tree Genet Genomes 7:747–758

    Article  Google Scholar 

  • Jannink JL (2010) Dynamics of long-term genomic selection. Genet Sel Evol 42:35

    Article  PubMed Central  PubMed  Google Scholar 

  • Jannink JL, Zhong SQ, Dekkers JCM, Fernando RL (2009) Factors affecting accuracy from Genomic Selection in populations derived from multiple inbred lines: a barley case study. Genetics 182:355–364

    Article  PubMed Central  PubMed  Google Scholar 

  • Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177

    Article  CAS  PubMed  Google Scholar 

  • Kizilkaya K, Fernando RL, Garrick DJ (2010) Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J Anim Sci 88:544–551

    Article  CAS  PubMed  Google Scholar 

  • de Koning DJ, McIntyre L (2012) Setting the standard: a special focus on Genomic Selection in GENETICS and G3. Genetics 190:1151–1152

    Article  PubMed Central  PubMed  Google Scholar 

  • Kumar S, Bink MCAM, Volz RK, et al (2012a) Towards genomic selection in apple (Malus domestica Borkh.) breeding programmes: Prospects, challenges and strategies. Tree Genet Genomes 8:1–14

    Article  Google Scholar 

  • Kumar S, Chagne D, Bink MCAM, Volz RK et al (2012b) Genomic Selection for fruit quality traits in apple (Malus domestica Borkh.). PLoS One 7:e36674

    Article  CAS  Google Scholar 

  • Lee M (2006) The phenotypic and genotypic eras of plant breeding. In: Lamkey KR, Lee M (eds) Plant breeding: the Arnel R Hallauer international symposium Blackwell Publishing, Ames, pp 213–217

    Google Scholar 

  • Legarra A, Robert-Granie C, Manfredi E, Elsen JM (2008) Performance of genomic selection in mice. Genetics 180:611–618

    Article  PubMed Central  PubMed  Google Scholar 

  • Long N, Gianola D, Rosa GJM, Weigel KA (2011) Long-term impacts of genome-enabled selection. J Appl Genet 52:467–480

    Article  PubMed  Google Scholar 

  • Lorenzana RE, Bernardo R (2009) Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet 120:151–161

    Article  PubMed  Google Scholar 

  • Lorenz AJ, Chao SM, Asoro FG, Heffner EL et al (2011) Genomic Selection in Plant Breeding: Knowledge and Prospects. Adv Agron 110(110):77–123

    Article  Google Scholar 

  • Luan T, Woolliams JA, Lien S, Kent M et al (2009) The accuracy of genomic selection in Norwegian red cattle assessed by cross-validation. Genetics 183:1119–1126

    Article  PubMed Central  PubMed  Google Scholar 

  • McKeand SE, Bridgwater FE (1998) A strategy for the third breeding cycle of loblolly pine in the Southeastern US. Silvae Genetica 47:223–234

    Google Scholar 

  • Meilan R (1997) Floral induction in woody angiosperms. New For 14:179–202

    Article  Google Scholar 

  • Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    CAS  PubMed Central  PubMed  Google Scholar 

  • Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13:85–96

    CAS  Google Scholar 

  • Moser G, Tier B, Crump RE et al (2009) A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers. Genet Sel Evol 41:56

    Article  PubMed Central  PubMed  Google Scholar 

  • Muir WM (2007) Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J Anim Breed Genet 124:342–355

    Article  CAS  PubMed  Google Scholar 

  • Myles S, Chia JM, Hurwitz B, Simon C et al (2010) Rapid genomic characterization of the genus Vitis. Plos One 5:e8219

    Article  PubMed Central  PubMed  Google Scholar 

  • Nakaya A, Isobe SN (2012) Will genomic selection be a practical method for plant breeding? Ann Bot (Lond) 110:1303–1316

    Article  Google Scholar 

  • Namkoong G, Kang HC, Brouard JS (1988) Tree Breeding: principles and strategies. Springer Verlag, New York

    Book  Google Scholar 

  • Neale DB, Williams CG (1991) Restriction-Fragment-Length-Polymorphism mapping in conifers and applications to forest genetics and tree improvement. Can J For Res 21:545–554

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Nielsen HM, Sonesson AK, Yazdi H, Meuwissen THE (2009) Comparison of accuracy of genome-wide and BLUP breeding value estimates in sib based aquaculture breeding schemes. Aquaculture 289:259–264

    Article  CAS  Google Scholar 

  • Nirea KG, Sonesson AK, Woolliams JA, Meuwissen THE (2012) Effect of non-random mating on genomic and BLUP selection schemes. Genet Sel Evol 44:11

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Novaes E, Osorio L, Drost DR, Miles BL, Boaventura-Novaes CRD et al (2009) Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels. New Phytol 182:878–890

    Article  CAS  PubMed  Google Scholar 

  • Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pryce JE, Daetwyler HD (2012) Designing dairy cattle breeding schemes under genomic selection: a review of international research. Anim Prod Sci 52:107–114

    Article  Google Scholar 

  • Rae A, Pinel M, Bastien C, Sabatti M et al (2008) QTL for yield in bioenergy Populus: identifying G × E interactions from growth at three contrasting sites. Tree Genet Genomes 4:97–112

    Article  Google Scholar 

  • Raymond CA, Schimleck LR (2002) Development of near infrared reflectance analysis calibrations for estimating genetic parameters for cellulose content in Eucalyptus globulus. Can J For Res 32:170–176

    Article  Google Scholar 

  • Resende MDV, de Assis TF(2008) Seleção recorrente recíproca entre populações sintéticas multi-espécies (SRR-PSME) de eucalipto. Pesquisa Florestal Brasileira 57:57–60

    Google Scholar 

  • Resende MDV, Resende MFR, Sansaloni CP, Petroli CD et al (2012a) Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytol 194:116–128

    Article  Google Scholar 

  • de Roos APW, Hayes BJ, Goddard ME (2009) Reliability of genomic predictions across multiple populations. Genetics 183:1545–1553

    Article  PubMed Central  PubMed  Google Scholar 

  • Resende MFR, Munoz P, Acosta JJ, Peter GF et al (2012b) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytol 193:617–624

    Article  Google Scholar 

  • Resende MFR, Munoz P, Resende MDV, Garrick DJ et al (2012c) Accuracy of genomic selection methods in a standard data set of Loblolly Pine (Pinus taeda L.). Genetics 190:1503–1510

    Article  Google Scholar 

  • Riedelsheimer C, Czedik-Eysenberg A, Grieder C, Lisec J et al (2012) Genomic and metabolic prediction of complex heterotic traits in hybrid maize. Nat Genet 44:217–220

    Article  CAS  PubMed  Google Scholar 

  • Sansaloni C, Petroli C, Jaccoud D, Carling J et al (2011) Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proceedings 5:P54

    Google Scholar 

  • Sewell MM, Sherman BK, Neale DB (1999) 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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Silva JCE, Wellendorf H, Borralho NMG (2000) Prediction of breeding values and expected genetic gains in diameter growth, wood density and spiral grain from parental selection in Picea abies (L.) KARST. Silvae Genetica 49:102–109

    Google Scholar 

  • Solberg TR, Sonesson AK, Woolliams JA et al (2009) Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect. Genet Sel Evol 41:53

    Article  PubMed Central  PubMed  Google Scholar 

  • Sonesson AK, Meuwissen THE (2009) Testing strategies for genomic selection in aquaculture breeding programs. Genet Sel Evol 41:37

    Article  PubMed Central  PubMed  Google Scholar 

  • Strauss SH, Lande R, Namkoong G (1992) Limitations of molecular-marker-aided selection in forest tree breeding. Can J For Res 22:1050–1061

    Article  CAS  Google Scholar 

  • Sved JA (1971) Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol 2:125–141

    Article  CAS  PubMed  Google Scholar 

  • Thumma BR, Southerton SG, Bell JC, Owen JV et al (2010) Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens. Tree Genet Genomes 6:305–317

    Article  Google Scholar 

  • Toro MA, Varona L (2010) A note on mate allocation for dominance handling in genomic selection. Genet Sel Evol 42:33

    Article  PubMed Central  PubMed  Google Scholar 

  • Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF et al (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247–252

    Article  CAS  PubMed  Google Scholar 

  • VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS et al (2009) Invited review: Reliability of genomic predictions for North American Holstein bulls. J Dairy Sci 92:16–24

    Article  CAS  PubMed  Google Scholar 

  • White TL, Adams WT, Neale DB (2007) Forest Genetics. CABI Publishing

    Google Scholar 

  • Williams CG (1988) Accelerated short-term genetic testing for Loblolly Pine families. Can J For Res 18:1085–1089

    Article  Google Scholar 

  • Williams CG, Neale DB (1992) Conifer wood quality and marker-aided selection—a case-study. Can J For Res 22:1009–1017

    Article  Google Scholar 

  • Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159

    CAS  PubMed Central  PubMed  Google Scholar 

  • Xu SZ, Jia ZY (2007) Genomewide analysis of epistatic effects for quantitative traits in barley. Genetics 175:1955–1963

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zapata-Valenzuela J, Isik F, Maltecca C, Wegrzyn J et al (2012) SNP markers trace familial linkages in a cloned population of Pinus taeda – prospects for genomic selection. Tree Genet Genomes 8:1307–1318

    Google Scholar 

  • Zhao YS, Gowda M, Liu WX, Wurschum T et al (2012) Accuracy of genomic selection in European maize elite breeding populations. Theor Appl Genet 124:769–776

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by CNPq grant 577047/2008-6, PRONEX-FAP-DF grant “NEXTREE” 2009/00106-8, EMBRAPA Macroprogram 2 grant 02.07.01.004 and a CNPq research fellowship to DG.

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Grattapaglia, D. (2014). Breeding Forest Trees by Genomic Selection: Current Progress and the Way Forward. In: Tuberosa, R., Graner, A., Frison, E. (eds) Genomics of Plant Genetic Resources. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7572-5_26

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