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  • Allison DB, Fernandez JR, Heo M, Zhu S, Etzel C, Beasley TM, Amos CI. 2002. Bias in estimates of quantitative-trait-locus effect in genome scans: demonstration of the phenomenon and a method-of-moments procedure for reducing bias. American Journal of Human Genetics 70: 575585.
  • Astle W, Balding DJ. 2009. Population structure and cryptic relatedness in genetic association studies. Statistical Science 24: 451471.
  • Aulchenko YS, de Koning D-J, Haley C. 2007. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177: 577585.
  • Brachi B, Morris G, Borevitz J. 2011. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biology 12: 232.
  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 26332635.
  • Brown DM, Zeef LAH, Ellis J, Goodacre R, Turner SR. 2005. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17: 22812295.
  • Carroll A, Somerville C. 2009. Cellulosic biofuels. Annual Review of Plant Biology 60: 165182.
  • Chang VS, Holtzapple MT. 2000. Fundamental factors affecting biomass enzymatic reactivity. Applied Biochemistry and Biotechnology 84–6: 537.
  • Cronk QCB. 2005. Plant eco-devo: the potential of poplar as a model organism. New Phytologist 166: 3948.
  • Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. 2010. Rare variants create synthetic genome-wide associations. Plos Biology 8: e1000294.
  • Dillon SK, Nolan M, Li W, Bell C, Wu HX, Southerton SG. 2010. Allelic variation in cell wall candidate genes affecting solid wood properties in natural populations and land taces of Pinus radiata. Genetics 185: 14771487.
  • Dinus RJ. 2000. Genetic modification of short rotation poplar biomass feedstock for efficient conversion to ethanol: bioenergy feedstock development program. Oak Ridge, TN, USA: Oak Ridge National Laboratory, Environmental Sciences Division.
  • Donaldson LA, Knox JP. 2012. Localization of cell wall polysaccharides in normal and compression wood of Radiata Pine: relationships with lignification and microfibril orientation. Plant Physiology 158: 642653.
  • Eckenwalder JE. 1996. Systematics and evolution of Populus. National Research Council of Canada. Ottawa, ON, Canada: NRC Research Press.
  • Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. 2010. Missing heritability and strategies for finding the underlying causes of complex disease. Nature Reviews Genetics 11: 446450.
  • Eyueboglu B, Pfister K, Haberer G, Chevalier D, Fuchs A, Mayer KFX, Schneitz K. 2007. Molecular characterisation of the STRUBBELIG-RECEPTOR FAMILY of genes encoding putative leucine-rich repeat receptor-like kinases in Arabidopsis thaliana. BMC Plant Biology 7: 16.
  • Falconer DS. 1981. Introduction to quantitative genetics. London, UK: Longman.
  • Gao X, Stamier J, Martin ER. 2008. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genetic Epidemiology 32: 361369.
  • Geraldes A, Difazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N et al. 2013. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Molecular Ecology Resources 13: 306323.
  • Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I et al. 2011. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Molecular Ecology Resources 11(Suppl 1): 8192.
  • Gonzalez-Martinez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB. 2007. Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175: 399409.
  • Gorshkova T, Brutch N, Chabbert B, Deyholos M, Hayashi T, Lev-Yadun S, Mellerowicz EJ, Morvan C, Neutelings G, Pilate G. 2012. Plant fiber formation: state of the art, recent and expected progress, and open questions. Critical Reviews in Plant Sciences 31: 201228.
  • Grattapaglia D, Resende MDV. 2011. Genomic selection in forest tree breeding. Tree Genetics and Genomes 7: 241255.
  • Guerra FP, Wegrzyn JL, Sykes R, Davis MF, Stanton BJ, Neale DB. 2013. Association genetics of chemical wood properties in black poplar (Populus nigra). New Phytologist 197: 162176.
  • Guillot G, Mortier F, Estoup A. 2005. GENELAND: a computer package for landscape genetics. Molecular Ecology Notes 5: 712715.
  • Hamberger B, Ellis M, Friedmann M, Souza CDA, Barbazuk B, Douglas CJ. 2007. Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene families. Canadian Journal of Botany-Revue Canadienne De Botanique 85: 11821201.
  • Hatakeyama H, Hatakeyama T. 2010. Lignin structure, properties, and applications. Biopolymers: Lignin, Proteins, Bioactive Nanocomposites 232: 163.
  • Hussey SG, Mizrachi E, Spokevicius AV, Bossinger G, Berger DK, Myburg AA. 2011. SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus. BMC Plant Biology 11: 173.
  • Ingvarsson PK. 2005. Nucleotide polymorphism and linkage disequilbrium within and among natural populations of European Aspen (Populus tremula L., Salicaceae). Genetics 169: 945953.
  • Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S. 2008. Nucleotide polymoirphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 22172226.
  • Keller SR, Levsen N, Olson MS, Tiffin P. 2012. Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L. Molecular Biology and Evolution 29: 31433152.
  • Ko JH, Han KH. 2004. Arabidopsis whole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth. Plant Molecular Biology 55: 433453.
  • Ko JH, Kim H-T, Hwang I, Han K-H. 2012. Tissue-type-specific transcriptome analysis identifies developing xylem-specific promoters in poplar. Plant Biotechnology Journal 10: 587596.
  • Kremer A. 2011. Missing heritability and missing Fst of candidate genes: why does gene variation differ from trait variation in trees? BMC Proceedings 5(Suppl 7): I1.
  • Kubo M, Udagawa M, Nishikubo N, Horiguchi G, Yamaguchi M, Ito J, Mimura T, Fukuda H, Demura T. 2005. Transcription switches for protoxylem and metaxylem vessel formation. Genes & Development 19: 18551860.
  • Kumar R, Mago G, Balan V, Wyman CE. 2009. Physical and chemical characterizations of corn stover and poplar solids resulting from leading pretreatment technologies. Bioresource Technology 100: 39483962.
  • Kumar M, Thammannagowda S, Bulone V, Chiang V, Han K-H, Joshi CP, Mansfield SD, Mellerowicz E, Sundberg B, Teeri T et al. 2009. An update on the nomenclature for the cellulose synthase genes in Populus. Trends in Plant Science 14: 248254.
  • Lafarguette F, Leple JC, Dejardin A, Laurans F, Costa G, Lesage-Descauses MC, Pilate G. 2004. Poplar genes encoding fasciclin-like arabinogalactan proteins are highly expressed in tension wood. New Phytologist 164: 107121.
  • Loiselle BA, Sork VL, Nason J, Graham C. 1995. Spatial genetic-structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). American Journal of Botany 82: 14201425.
  • Ma S, Gong Q, Bohnert HJ. 2007. An Arabidopsis gene network based on the graphical Gaussian model. Genome Research 17: 16141625.
  • Macciotta NPP, Gaspa G, Steri R, Pieramati C, Carnier P, Dimauro C. 2009. Pre-selection of most significant SNPS for the estimation of genomic breeding values. BMC Proceedings 3(Suppl 1): S14.
  • Mackay TFC, Stone EA, Ayroles JF. 2009. The genetics of quantitative traits: challenges and prospects. Nature Reviews Genetics 10: 565577.
  • MacMillan CP, Mansfield SD, Stachurski ZH, Evans R, Southerton SG. 2010. Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus. Plant Journal 62: 689703.
  • Mansfield SD, Kang K-Y, Chapple C. 2012. Designed for deconstruction – poplar trees altered in cell wall lignification improve the efficacy of bioethanol production. New Phytologist 194: 91101.
  • Mansfield SD, Mooney C, Saddler JN. 1999. Substrate and enzyme characteristics that limit cellulose hydrolysis. Biotechnology Progress 15: 804816.
  • Mosier N, Wyman C, Dale B, Elander R, Lee YY, Holtzapple M, Ladisch M. 2005. Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresource Technology 96: 673686.
  • Nakatsubo T, Mizutani M, Suzuki S, Hattori T, Umezawa T. 2008. Characterization of Arabidopsis thaliana pinoresinol reductase, a new type of enzyme involved in lignan biosynthesis. Journal of Biological Chemistry 283: 1555015557.
  • Novaes E, Osorio L, Drost DR, Miles BL, Boaventura-Novaes CRD, Benedict C, Dervinis C, Yu Q, Sykes R, Davis M et al. 2009. Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen concentrations. New Phytologist 182: 878890.
  • Novembre J, Stephens M. 2008. Interpreting principal component analysis of spatial population genetic variation. Nature Genetics 40: 646649.
  • Olson MS, Robertson AL, Takebayashi N, Silim S, Schroeder WR, Tiffin P. 2010. Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera). New Phytologist 186: 526536.
  • Pant SD, Schenkel FS, Verschoor CP, You Q, Kelton DF, Moore SS, Karrow NA. 2010. A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in holstein cattle. Genomics 95: 176182.
  • Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. Plos Genetics 2: 20742093.
  • Peloso GM, Lunetta KL. 2011. Chioce of population structure informative principal componentsfor adjustment in case–control study. BMC Genetics 12: 64.
  • Peres-Neto PR, Legendre P, Dray S, Borcard D. 2006. Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology 87: 26142625.
  • Persson S, Wei HR, Milne J, Page GP, Somerville CR. 2005. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proceedings of the National Academy of Sciences, USA 102: 86338638.
  • Pinheiro J, Bates D. 2000. Mixed-effects models in S and S-PLUS. New York, USA: Springer.
  • Porth I, Klápště J, Skyba O, Lai BS, Geraldes A, Muchero W, Tuskan GA, Douglas CJ, El-Kassaby YA, Mansfield SD. 2013. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations. New Phytologist 197: 777790.
  • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38: 904909.
  • Price AL, Zaitlen NA, Reich D, Patterson N. 2010. New approaches to population stratification in genome-wide association studies. Nature Reviews Genetics 11: 459463.
  • Rafalski JA. 2010. Association genetics in crop improvement. Current Opinion in Plant Biology 13: 174180.
  • Rajangam AS, Kumar M, Aspeborg H, Guerriero G, Arvestad L, Pansri P, Brown CJL, Hober S, Blomqvist K, Divne C et al. 2008. MAP20, a microtubule-associated protein in the secondary cell walls of hybrid aspen, is a target of the cellulose synthesis inhibitor 2,6-dichlorobenzonitrile. Plant Physiology 148: 12831294.
  • Ralph SG, Chun HJE, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJM et al. 2008. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics 9: 57.
  • Ruprecht C, Mutwil M, Saxe F, Eder M, Nikoloski Z, Persson S. 2011. Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Frontiers in Plant Science 2: 23.
  • Sannigrahi P, Ragauskas AJ, Tuskan GA. 2010. Poplar as a feedstock for biofuels: a review of compositional characteristics. Biofuels Bioproducts & Biorefining-Biofpr 4: 209226.
  • Setakis E, Stirnadel H, Balding D. 2006. Logistic regression protects against population structure in genetic association studies. Genome Research 16: 290296.
  • Shen H, He X, Poovaiah CR, Wuddineh WA, Ma J, Mann DGJ, Wang H, Jackson L, Tang Y, Stewart CN Jr et al. 2012. Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks. New Phytologist 193: 121136.
  • Shin JH, Blay S, McNeney B, Graham J. 2006. LDheatmap: an R runction for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. Journal of Statistical Software 16: Code Snippet 3.
  • Shriner D. 2011. Investigating population stratification and admixture using eigenanalysis of dense genotypes. Heredity 107: 413420.
  • Sillanpaa MJ. 2011. Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses. Heredity 106: 511519.
  • Slatkin M, Muirhead CA. 1999. Overdominant alleles in a population of variable size. Genetics 152: 775781.
  • Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA et al. 2012. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist 196: 713725.
  • Stanton B, Neale D, Li S. 2010. Populus breeding: from the classical to the genomic approach. In: Jansson S, Rishikesh B, Groover A, eds. Genetics and genomics of  Populus. New York, USA: Springer, 309348.
  • Steinwand BJ, Kieber JJ. 2010. The role of receptor-like kinases in regulating cell wall function. Plant Physiology 153: 479484.
  • Stewart JJ, Kadla JF, Mansfield SD. 2006. The influence of lignin chemistry and ultrastructure on the pulping efficiency of clonal aspen (Populus tremuloides Michx.). Holzforschung 60: 111122.
  • Studer MH, DeMartini JD, Davis MF, Sykes RW, Davison B, Keller M, Tuskan GA, Wyman CE. 2011. Lignin content in natural Populus variants affects sugar release. Proceedings of the National Academy of Sciences, USA 108: 63006305.
  • Taylor NG, Howells RM, Huttly AK, Vickers K, Turner SR. 2003. Interactions among three distinct CesA proteins essential for cellulose synthesis. Proceedings of the National Academy of Sciences, USA 100: 14501455.
  • Team RDC. 2011. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
  • Teyssèdre S, Dupuis MC, Guérin G, Schibler L, Denoix JM, Elsen JM, Ricard A. 2012. Genome-wide association studies for osteochondrosis in French Trotter horses. Journal of Animal Science 90: 4553.
  • Thomas A, Abel HJ, Di Y, Faye LL, Jin J, Liu J, Wu Z, Paterson AD. 2011. Effect of linkage disequilibrium on the identification of functional variants. Genetic Epidemiology 35(Suppl 1): S115S119.
  • Thumma BR, Matheson BA, Zhang D, Meeske C, Meder R, Downes GM, Southerton SG. 2009. Identification of a cis-acting regulatory polymorphism in a Eucalypt COBRA-like gene affecting cellulose content. Genetics 183: 11531164.
  • 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 Genetics & Genomes 6: 305317.
  • 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: 15961604.
  • 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 Phytologist 188: 515532.
  • Xie C-Y, Ying CC, Yanchuk AD, Holowachuk DL. 2009. Ecotypic mode of regional differentiation caused by restricted gene migration: a case in black cottonwood (Populus trichocarpa) along the Pacific Northwest coast. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere 39: 519526.
  • Xu S. 2003. The theoretical basis of the Beavis effect. Genetics 165: 22592268.
  • Yuan JS, Tiller KH, Al-Ahmad H, Stewart NR, Stewart CN Jr. 2008. Plants to power: bioenergy to fuel the future. Trends in Plant Science 13: 421429.
  • Zhong R, Lee C, Zhou J, McCarthy RL, Ye Z-H. 2008. A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant Cell 20: 27632782.
  • Zhong RQ, Pena MJ, Zhou GK, Nairn CJ, Wood-Jones A, Richardson EA, Morrison WH, Darvill AG, York WS, Ye ZH. 2005. Arabidopsis fragile fiber8, which encodes a putative glucuronyltransferase, is essential for normal secondary wall synthesis. Plant Cell 17: 33903408.
  • Zhu C, Yu J. 2009. Nonmetric multidimensional scaling corrects for population structure in association mapping with different sample types. Genetics 182: 875888.