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Genomic Selection for Crop Improvement pp 199–249Cite as

Status and Perspectives of Genomic Selection in Forest Tree Breeding

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Abstract

Trees have long life cycles and become reproductively active only after several years. The progress of tree breeding programs is therefore strongly dependent on the time needed to complete a breeding generation. Additionally, the uncertainties associated with conducting decade-long breeding programs can be high. The convergence of genomics and quantitative genetics has now established the paradigm of genomic selection as a way to accelerate breeding of complex traits. With the progressive accumulation of GS data for thousands of individuals across several unrelated populations, GS should also provide a potentially powerful framework to investigate the molecular underpinnings of complex traits. Genomic selection can increase the rate of genetic gain per unit time of a tree breeding program by radically reducing the generation interval and by increasing the selection intensity because many more young seedlings can be genotyped and their phenotypes predicted than the number of adult trees measured in field trials. Genomic selection has therefore become a hot topic in the tree genetics and breeding community worldwide in the last few years since the first perspectives based on simulations and experimental results were reported. In this chapter, a comprehensive discussion is presented, covering the main factors, both theoretical and practical, relevant to the application of GS to tree breeding, including those that have emerged from the recent flow of experimental studies in different forest tree species. Following a review of the basic insights and perspectives of GS, a detailed compilation is presented of all published experimental GS studies in forest trees to date, highlighting their main contributions to our current understanding of this new breeding approach. The conclusion summarizes the main lessons learned so far, condensed in a nine-point tentative roadmap for implementing GS in a tree breeding program.

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References

  • 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 

  • Arus P, Verde I, Sosinski B, Zhebentyayeva T, Abbott AG (2012) The peach genome. Tree Genet Genomes 8:531–547

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Bartholome J, Van Heerwaarden J, Isik F, Boury C, Vidal M, Plomion C, Bouffier L (2016) Performance of genomic prediction within and across generations in maritime pine. BMC Genomics 17:604

    Article  PubMed  PubMed Central  Google Scholar 

  • Bastiaansen JWM, Coster A, Calus MPL, van Arendonk JAM, Bovenhuis H (2012) Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures. Genet Sel Evol 44:3

    Article  PubMed  PubMed Central  Google Scholar 

  • Beaulieu J, Doerksen T, Clement S, Mackay J, Bousquet J (2014a) Accuracy of genomic selection models in a large population of open-pollinated families in white spruce. Heredity 113:343–352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beaulieu J, Doerksen TK, MacKay J, Rainville A, Bousquet J (2014b) Genomic selection accuracies within and between environments and small breeding groups in white spruce. BMC Genomics 15:1048

    Article  PubMed  PubMed Central  Google Scholar 

  • Beissinger TM, Hirsch CN, Sekhon RS, Foerster JM, Johnson JM, Muttoni G, Vaillancourt B, Buell CR, Kaeppler SM, de Leon N (2013) Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics 193:1073–1081

    Article  CAS  PubMed  PubMed Central  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 genome wide selection for quantitative traits in maize. Crop Sci 47:1082–1090

    Article  Google Scholar 

  • Berry DP, Kearney JF (2011) Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection. Animal 5:1162–1169

    Article  CAS  PubMed  Google Scholar 

  • Blondel M, Onogi A, Iwata H, Ueda N (2015) A ranking approach to genomic selection. PLoS One 10:e0128570

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Boichard D, Chung H, Dassonneville R, David X, Eggen A, Fritz S, Gietzen KJ, Hayes BJ, Lawley CT, Sonstegard TS, Van Tassell CP, PM VR, Viaud-Martinez KA, Wiggans GR, Consortium BL (2012) Design of a bovine low-density SNP array optimized for imputation. PLoS One 7:e34130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bouvet JM, Makouanzi G, Cros D, Vigneron P (2016) Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: prediction accuracy implications. Heredity 116:146–157

    Article  CAS  PubMed  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  PubMed Central  CAS  Google Scholar 

  • Burgueno J, de los Campos G, 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 

  • Chancerel E, Lepoittevin C, Le Provost G, Lin YC, Jaramillo-Correa JP, Eckert AJ, Wegrzyn JL, Zelenika D, Boland A, Frigerio JM, Chaumeil P, Garnier-Gere P, Boury C, Grivet D, Gonzalez-Martinez SC, Rouze P, Van de Peer Y, Neale DB, Cervera MT, Kremer A, Plomion C (2011) Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics 12:368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charlier C, Coppieters W, Rollin F, Desmecht D, Agerholm JS, Cambisano N, Carta E, Dardano S, Dive M, Fasquelle C, Frennet JC, Hanset R, Hubin X, Jorgensen C, Karim L, Kent M, Harvey K, Pearce BR, Simon P, Tama N, Nie H, Vandeputte S, Lien S, Longeri M, Fredholm M, Harvey RJ, Georges M (2008) Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet 40:449–454

    Article  CAS  PubMed  Google Scholar 

  • Chen C, Mitchell SE, Elshire RJ, Buckler ES, El-Kassaby YA (2013) Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform. Tree Genet Genomes 9:1537–1544

    Article  Google Scholar 

  • Coster A, Bastiaansen JWM, Calus MPL, van Arendonk JAM, Bovenhuis H (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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J (2012) Targeted enrichment strategies for next-generation plant biology. Am J Bot 99:291–311

    Article  CAS  PubMed  Google Scholar 

  • Crossa J, de los Campos G, Perez P, Gianola D, Burgueno J, Araus JL, Makumbi D, Singh RP, Dreisigacker S, Yan JB, Arief V, Banziger M, Braun HJ (2010) Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186:713–724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daetwyler HD, Calus MPL, Pong-Wong R, de los Campos G, Hickey JM (2013) Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking. Genetics 193:347–365

    Article  PubMed  PubMed Central  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  PubMed Central  CAS  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 Rev Genet 12:499–510

    Article  CAS  PubMed  Google Scholar 

  • de los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MPL (2013) Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics 193:327–345

    Article  PubMed Central  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  Google Scholar 

  • Dillen S, Storme V, Marron N, Bastien C, Neyrinck S, Steenackers M, Ceulemans R, Boerjan W (2008) Genomic regions involved in productivity of two interspecific poplar families in Europe. 1. Stem height, circumference and volume. Tree Genet Genomes 5:147–164

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eckert AJ, Pande B, Ersoz ES, Wright MH, Rashbrook VK, Nicolet CM, Neale DB (2009) High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.) Tree Genet Genomes 5:225–234

    Article  Google Scholar 

  • Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, Gonzalez-Martinez SC, Neale DB (2010) Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda l., Pinaceae). Genetics 185:969–982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • El-Dien OG, Ratcliffe B, Klapste J, Chen C, Porth I, El-Kassaby YA (2015) Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing. BMC Genomics 16:370

    Article  CAS  Google Scholar 

  • El-Kassaby YA, Lstiburek M (2009) Breeding without breeding. Genet Res 91:111–120

    Article  Google Scholar 

  • Esfandyari H, Sorensen AC, Bijma P (2015) Maximizing crossbred performance through purebred genomic selection. Genet Sel Evol 47:16

    Article  PubMed  PubMed Central  Google Scholar 

  • Freeman JS, Potts BM, Downes GM, Pilbeam D, Thavamanikumar S, Vaillancourt RE (2013) Stability of quantitative trait loci for growth and wood properties across multiple pedigrees and environments in Eucalyptus globulus. New Phytol 198:1121–1134

    Article  CAS  PubMed  Google Scholar 

  • Geraldes A, Difazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N, Porth I, Mckown AD, Skyba O, Li E, Fujita M, Klapste J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wasteneys GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QCB, Ehlting J, Douglas CJ, Tuskan GA (2013) A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour 13:306–323

    Article  CAS  PubMed  Google Scholar 

  • Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao YJ, Tam A, Wang SC, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ (2011) SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour 11:81–92

    Article  CAS  PubMed  Google Scholar 

  • Gion JM, Carouche A, Deweer S, Bedon F, Pichavant F, Charpentier JP, Bailleres H, Rozenberg P, Carocha V, Ognouabi N, Verhaegen D, Grima-Pettenati J, Vigneron P, Plomion C (2011) Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus. BMC Genomics 12:301

    Article  PubMed  PubMed Central  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 (2014) Breeding forest trees by genomic selection: current progress and the way forward. Chapter 26. In: Tuberosa R, Graner A, Frison E (eds) Advances in genomics of plant genetic resources. Springer, New York, pp 652–682

    Google Scholar 

  • Grattapaglia D, Chaparro J, Wilcox P, Mccord S, Werner D, Amerson H, Mckeand S, Bridgwater F, Whetten R, O'malley D, Sederoff RR (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, de Alencar S, Pappas G (2011a) 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 Proc 5:P45

    Article  PubMed Central  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, Resende MDV (2011) Genomic selection in forest tree breeding. Tree Genet Genomes 7:241–255

    Article  Google Scholar 

  • Grattapaglia D, Resende MDV, Resende M, Sansaloni C, Petroli C, Missiaggia A, Takahashi E, Zamprogno K, Kilian A (2011b) Genomic selection for growth traits in Eucalyptus: accuracy within and across breeding populations. BMC Proc 5:O16

    Article  PubMed Central  Google Scholar 

  • Grattapaglia D, Ribeiro VJ, Rezende GD (2004) Retrospective selection of elite parent trees using paternity testing with microsatellite markers: an alternative short term breeding tactic for Eucalyptus. Theor Appl Genet 109:192–199

    Article  CAS  PubMed  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic-linkage maps of Eucalyptus-grandis and Eucalyptus-urophylla using a pseudo-testcross – mapping strategy and RAPD markers. Genetics 137:1121–1137

    CAS  PubMed  PubMed Central  Google Scholar 

  • Grattapaglia D, Silva OB, Kirst M, de Lima BM, Faria DA, Pappas GJ (2011c) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biol 11:65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grattapaglia D, Vaillancourt R, Shepherd M, Thumma B, Foley W, Külheim C, Potts B, Myburg A (2012) Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus. Tree Genet Genomes 3:463–508

    Article  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 (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389–2397

    CAS  PubMed  PubMed Central  Google Scholar 

  • Habier D, Fernando RL, Dekkers JCM (2009) Genomic selection using low-density marker panels. Genetics 182(1):343–353

    Google Scholar 

  • Habier D, Fernando RL, Garrick DJ (2013) Genomic BLUP decoded: a look into the black box of genomic prediction. Genetics 194:597–607

    Article  CAS  PubMed  PubMed Central  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 

  • Harfouche A, Meilan R, Kirst M, Morgante M, Boerjan W, Sabatti M, Mugnozza GS (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 BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009a) Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92:433–443

    Article  CAS  PubMed  Google Scholar 

  • Hayes BJ, Visscher PM, Goddard ME (2009b) Increased accuracy of artificial selection by using the realized relationship matrix. Genet Res 91:47–60

    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, Jannink JL, Sorrells ME (2015) Perspectives for genomic selection applications and research in plants. Crop Sci 55:1–12

    Article  Google Scholar 

  • Heslot N, Rutkoski J, Poland J, Jannink JL, Sorrells ME (2013) Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity. PLoS One 8:e74612

    Article  CAS  PubMed  PubMed Central  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 

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

    Article  CAS  Google Scholar 

  • Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S (2008) Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European aspen (Populus tremula, Salicaceae). Genetics 178:2217–2226

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Isik F, Bartholome J, Farjat A, Chancerel E, Raffin A, Sanchez L, Plomion C, Bouffier L (2016) Genomic selection in maritime pine. Plant Sci 242:108–119

    Article  CAS  PubMed  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  PubMed Central  CAS  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  PubMed Central  CAS  Google Scholar 

  • Jarquin D, Crossa J, Lacaze X, Du Cheyron P, Daucourt J, Lorgeou J, Piraux F, Guerreiro L, Perez P, Calus M, Burgueno J, de los Campos G (2014) A reaction norm model for genomic selection using high-dimensional genomic and environmental data. Theor Appl Genet 127:595–607

    Article  PubMed  Google Scholar 

  • Jia Y, Jannink JL (2012) Multiple-trait genomic selection methods increase genetic value prediction accuracy. Genetics 192:1513–1522

    Article  PubMed  PubMed Central  Google Scholar 

  • Jonas E, de Koning DJ (2013) Does genomic selection have a future in plant breeding? Trends Biotechnol 31:497–504

    Article  CAS  PubMed  Google Scholar 

  • Jonas E, de Koning DJ (2015) Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs. Front Genet 6:49

    Article  PubMed  PubMed Central  Google Scholar 

  • Junghans DT, Alfenas AC, Brommonschenkel SH, Oda S, Mello EJ, Grattapaglia D (2003) Resistance to rust (Puccinia psidii Winter) in eucalyptus: mode of inheritance and mapping of a major gene with RAPD markers. Theor Appl Genet 108:175–180

    Article  CAS  PubMed  Google Scholar 

  • Kerr RJ, Dieters MJ, Tier B (2004) Simulation of the comparative gains from four different hybrid tree breeding strategies. Can J For Res 34:209–220

    Article  Google Scholar 

  • Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 888:67–89

    Article  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 

  • Lambeth C, Lee BC, O'Malley D, Wheeler NC (2001) Polymix breeding with parental analysis of progeny: an alternative to full-sib breeding and testing. Theor Appl Genet 103:930–943

    Article  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

  • Lepoittevin C, Frigerio JM, Garnier-Gere P, Salin F, Cervera MT, Vornam B, Harvengt L, Plomion C (2010) In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species? PLoS One 5:e11034

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lima BM (2014) Bridging genomics and quantitative genetics of Eucalyptus: genome-wide prediction and genetic parameter estimation for growth and wood properties using high-density SNP data. Genetics Dep. University of São Paulo, Piracicaba, SP, Brazil, pp 93. Available in English at http://www.teses.usp.br/teses/disponiveis/11/11137/tde-25062014-25085814/pt-br.php

  • Lin Z, Hayes BJ, Daetwyler HD (2014) Genomic selection in crops, trees and forages: a review. Crop Pasture Sci 65:1177–1191

    Article  Google Scholar 

  • Liu HM, Sorensen AC, Meuwissen THE, Berg P (2014) Allele frequency changes due to hitch-hiking in genomic selection programs. Genet Sel Evol 46:8

    Article  PubMed  PubMed Central  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 

  • Lorenz AJ, Chao SM, Asoro FG, Heffner EL, Hayashi T, Iwata H, Smith KP, Sorrells ME, Jannink JL (2011) Genomic selection in plant breeding: knowledge and prospects. Adv Agron 110:77–123

    Article  Google Scholar 

  • MacLeod IM, Hayes BJ, Goddard ME (2014) The Effects of demography and long-term selection on the accuracy of genomic prediction with sequence data. Genetics 198 (4):1671–1684

    Google Scholar 

  • Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TPL, Sonstegard TS, Van Tassell CP (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4:e5350

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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

    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  PubMed Central  Google Scholar 

  • Moser G, Tier B, Crump RE, Khatkar MS, Raadsma HW (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  PubMed Central  CAS  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 

  • Munoz PR, Resende MFR, Gezan SA, Resende MDV, de los Campos G, Kirst M, Huber D, Peter GF (2014) Unraveling additive from nonadditive effects using genomic relationship matrices. Genetics 198:1759–1768

    Article  PubMed  PubMed Central  Google Scholar 

  • Murray C, Huerta-Sanchez E, Casey F, Bradley DG (2010) Cattle demographic history modelled from autosomal sequence variation. Philos T R Soc B 365:2531–2539

    Article  CAS  Google Scholar 

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

    Book  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 

  • 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 

  • Nejati-Javaremi A, Smith C, Gibson JP (1997) Effect of total allelic relationship on accuracy of evaluation and response to selection. J Anim Sci 75:1738–1745

    Article  CAS  PubMed  Google Scholar 

  • Neves LG, Davis JM, Barbazuk WB, Kirst M (2014) A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping. G3 Genes Genom Genet 4:29–37

    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  PubMed Central  Google Scholar 

  • Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9:312

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Novaes E, Osorio L, Drost DR, Miles BL, Boaventura-Novaes CRD, Benedict C, Dervinis C, Yu Q, Sykes R, Davis M, Martin TA, Peter GF, Kirst M (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 

  • Pan J, Wang BS, Pei ZY, Zhao W, Gao J, Mao JF, Wang XR (2015) Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers. Mol Ecol Resour 15:711–722

    Article  CAS  PubMed  Google Scholar 

  • Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA (2012) Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol Ecol 21:2991–3005

    Article  CAS  PubMed  Google Scholar 

  • Pavy N, Gagnon F, Rigault P, Blais S, Deschenes A, Boyle B, Pelgas B, Deslauriers M, Clement S, Lavigne P, Lamothe M, Cooke JEK, Jaramillo-Correa JP, Beaulieu J, Isabel N, Mackay J, Bousquet J (2013) Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners. Mol Ecol Resour 13:324–336

    Article  CAS  PubMed  Google Scholar 

  • Pavy N, Parsons LS, Paule C, MacKay J, Bousquet J (2006) Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 7:174

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pavy N, Pelgas B, Beauseigle S, Blais S, Gagnon F, Gosselin I, Lamothe M, Isabel N, Bousquet J (2008) Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics 9:1–17

    Article  CAS  Google Scholar 

  • Pelgas B, Bousquet J, Beauseigle S, Isabel N (2005) A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae. Theor Appl Genet 111:1466–1488

    Article  CAS  PubMed  Google Scholar 

  • Perez-Enciso M, Rincon JC, Legarra A (2015) Sequence- vs. chip-assisted genomic selection: accurate biological information is advised. Genet Sel Evol 47:43

    Article  PubMed  PubMed Central  Google Scholar 

  • Plomion C, Bartholome J, Lesur I, Boury C, Rodriguez-Quilon I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, de Miguel M, de Maria N, Cervera MT, Bagnoli F, Isik F, Vendramin GG, Gonzalez-Martinez SC (2016) High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Mol Ecol Resour 16:574–587

    Article  CAS  PubMed  Google Scholar 

  • Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome 5:92–102

    Article  CAS  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, Street N, Tucker J, Dixon C, Marron N, Dillen S, Taylor G (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 

  • Ratcliffe B, El-Dien OG, Klapste J, Porth I, Chen C, Jaquish B, El-Kassaby YA (2015) A comparison of genomic selection models across time in interior spruce (Picea engelmannii x glauca) using unordered SNP imputation methods. Heredity 115:547–555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Resende MDV, Resende MFR, Sansaloni CP, Petroli CD, Missiaggia AA, Aguiar AM, Abad JM, Takahashi EK, Rosado AM, Faria DA, Pappas GJ, Kilian A, Grattapaglia D (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  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Resende MFR, Munoz P, Resende MDV, Garrick DJ, Fernando RL, Davis JM, Jokela EJ, Martin TA, Peter GF, Kirst M (2012c) Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.) Genetics 190:1503–1510

    Article  PubMed  PubMed Central  Google Scholar 

  • Rezende GDSP, Resende MDV, Assis TF (2014) Eucalyptus breeding for clonal forestry. In: Fenning T (ed) Challenges and opportunities for the world’s forests in the 21st century. Springer Science+Business Media, Dordrecht, pp 393–424

    Chapter  Google Scholar 

  • Riedelsheimer C, Endelman JB, Stange M, Sorrells ME, Jannink JL, Melchinger AE (2013) Genomic predictability of interconnected biparental maize populations. Genetics 194:493–503

    Article  PubMed  PubMed Central  Google Scholar 

  • Rincent R, Laloe D, Nicolas S, Altmann T, Brunel D, Revilla P, Rodriguez VM, Moreno-Gonzalez J, Melchinger A, Bauer E, Schoen CC, Meyer N, Giauffret C, Bauland C, Jamin P, Laborde J, Monod H, Flament P, Charcosset A, Moreau L (2012) Maximizing the reliability of genomic selection by optimizing the calibration set of reference individuals: comparison of methods in two diverse groups of maize inbreds (Zea mays L.) Genetics 192:715–728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saatchi M, McClure MC, McKay SD, Rolf MM, Kim J, Decker JE, Taxis TM, Chapple RH, Ramey HR, Northcutt SL, Bauck S, Woodward B, Dekkers JCM, Fernando RL, Schnabel RD, Garrick DJ, Taylor JF (2011) Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation. Genet Sel Evol 43:40

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed Central  Google Scholar 

  • Schilling MP, Wolf PG, Duffy AM, Rai HS, Rowe CA, Richardson BA, Mock KE (2014) Genotyping-by-sequencing for populus population genomics: an assessment of genome sampling patterns and filtering approaches. PLoS One 9:95292

    Article  CAS  Google Scholar 

  • Silva-Junior OB, Faria DA, Grattapaglia D (2015) A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing 240 Eucalyptus tree genomes across 12 species. New Phytol 206:1527–1540

    Article  CAS  PubMed  Google Scholar 

  • Silva-Junior OB, Grattapaglia D (2015) Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis. New Phytol 208:830–845

    Article  CAS  PubMed  Google Scholar 

  • Solberg TR, Sonesson AK, Woolliams JA, Odegard J, Meuwissen THE (2009) Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect. Genetics Selection Evolution 41 (1):53

    Google Scholar 

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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stirling B, Newcombe G, Vrebalov J, Bosdet I, Bradshaw HD (2001) Suppressed recombination around the MXC3 locus, a major gene for resistance to poplar leaf rust. Theor Appl Genet 103:1129–1137

    Article  CAS  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 

  • Telfer EJ, Stovold GT, Li YJ, Silva OB, Grattapaglia DG, Dungey HS (2015) Parentage reconstruction in Eucalyptus nitens using SNPs and microsatellite markers: a comparative analysis of marker data power and robustness. PLoS One 10:e0130601

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Van Eenennaam AL, Weigel KA, Young AE, Cleveland MA, Dekkers JCM (2014) Applied animal genomics: results from the field. Annu Rev Anim Biosci 2:105–139

    Article  PubMed  Google Scholar 

  • VanRaden PM (2008) Efficient methods to compute genomic predictions. J Dairy Sci 91:4414–4423

    Article  CAS  PubMed  Google Scholar 

  • White TL, Adams WT, Neale DB (2007) Forest genetics. CABI Publishing, Cambridge, MA, p 682

    Book  Google Scholar 

  • Wilcox PL, Amerson HV, Kuhlman EG, Liu BH, O'Malley DM, Sederoff RR (1996) Detection of a major gene for resistance to fusiform rust disease in loblolly pine by genomic mapping. Proc Natl Acad Sci U S A 93:3859–3864

    Article  CAS  PubMed  PubMed Central  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  PubMed Central  Google Scholar 

  • Zapata-Valenzuela J, Isik F, Maltecca C, Wegrzyn J, Neale D, McKeand S, Whetten R (2012) SNP markers trace familial linkages in a cloned population of Pinus taeda – prospects for genomic selection. Tree Genet Genomes 6:1307–1318

    Article  Google Scholar 

  • Zapata-Valenzuela J, Whetten RW, Neale D, McKeand S, Isik F (2013) Genomic estimated breeding values using genomic relationship matrices in a cloned population of loblolly pine. G3 Genes Genom Genet 3:909–916

    Google Scholar 

  • Zeng J, Toosi A, Fernando RL, Dekkers JCM, Garrick DJ (2013) Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action. Genet Sel Evol 45:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhou LC, Holliday JA (2012) Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture. BMC Genomics 13:703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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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. Special thanks to all my students, collaborators, and colleagues worldwide working in genomic prediction and forest tree breeding with whom I have had the privilege to share and discuss several of the ideas presented in this chapter.

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Authors and Affiliations

  1. EMBRAPA Genetic Resources and Biotechnology – EPqB, 70770-910, Brasilia, DF, Brazil

    Dario Grattapaglia

  2. Universidade Católica de Brasília- SGAN, 916 modulo B, Brasília, DF, 70790-160, Brazil

    Dario Grattapaglia

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  1. Dario Grattapaglia
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Correspondence to Dario Grattapaglia .

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Editors and Affiliations

  1. Center of Excellence in Genomics, Research Program - Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India

    Rajeev K. Varshney

  2. Center of Excellence in Genomics, Research Program - Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India

    Manish Roorkiwal

  3. Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA

    Mark E. Sorrells

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Grattapaglia, D. (2017). Status and Perspectives of Genomic Selection in Forest Tree Breeding. In: Varshney, R., Roorkiwal, M., Sorrells, M. (eds) Genomic Selection for Crop Improvement. Springer, Cham. https://doi.org/10.1007/978-3-319-63170-7_9

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