Forest tree genomics: 10 achievements from the past 10 years and future prospects

Annals of Forest Science

Volumn 73, Issue 1, 2016, Pages 77-103

  Plomion, Christophe ^a,b   Bastien, Catherine ^c   Bogeat Triboulot, Marie Béatrice ^d,e   Bouffier, Laurent ^a,b   Déjardin, Annabelle ^c   Duplessis, Sébastien ^f   Fady, Bruno ^g   Heuertz, Myriam ^a,b,h   Le Gac, Anne Laure ⁱ   Le Provost, Grégoire ^a,b   Legué, Valérie ^j,k   Lelu Walter, Marie Anne ^c   Leplé, Jean Charles ^c   Maury, Stéphane ⁱ   Morel, Alexandre ^c   Oddou Muratorio, Sylvie ^g   Pilate, Gilles ^c   Sanchez, Léopoldo ^c   Scotti, Ivan ^g   Scotti Saintagne, Caroline ^g   Segura, Vincent ^c   Trontin, Jean François ^l   Vacher, Corinne ^a,b   more..

^a UMR 1202 BIOGECO   (France)

^b UNIVERSITÉ DE BORDEAUX   (France)

^c National Institute for Agricultural Research   (France)

^d LERFoB   (France)

^e UNIVERSITÉ DE LORRAINE   (France)

^f UNIVERSITÉ DE LORRAINE   (France)

^g French National Institute for Agriculture   (France)

^h INIA   (Spain)

ⁱ UNIVERSITÉ D'ORLÉANS   (France)

^j UNIVERSITÉ CLERMONT AUVERGNE   (France)

^k PIAF   (France)

^l FCBA   (France)

more..

Author keywords

Breeding and conservation; Developmental biology; Epigenetics; Forest trees; Genomics; Interactome; Micro evolution

Indexed keywords

ADAPTATION; BIOINFORMATICS; DEVELOPMENTAL BIOLOGY; ENVIRONMENTAL STRESS; EVOLUTIONARY BIOLOGY; FOREST ECOSYSTEM; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC RESOURCE; GENETIC VARIATION; GENOMICS; PLANT BREEDING; TREE;

EID: 84958818989     PISSN: 12864560     EISSN: 1297966X     Source Type: Journal    
DOI: 10.1007/s13595-015-0488-3     Document Type: Review

References (299)

1. Abril N, Gion JM, Kerner R, Müller-Starck G, Cerrillo RMN, Plomion C, Renaut J, Valledor L, Jorrin-Novo JV (2011) Proteomics research on forest trees, the most recalcitrant and orphan plant species. Phytochemistry 72:1219–1242
2. Abu-Abied M, Szwerdszarf D, Morde-Haev I, Levy A, Rogovoy O, Belausov E, Yaniv Y, Uliel S, Katzenellenbogen M, Riov J, Ophir R, Sadot E (2012) Microarray analysis revealed upregulation of nitrate reductase in juvenile cuttings of Eucalyptus grandis, which correlated with increased nitric oxide production and adventitious root formation. Plant J 71:787–799
3. Allendorf FW, Hohenlohe PA, Luikart GH (2010) Genomics and the future of conservation genetics. Nat Rev Genet 11:697–709
4. Allendorf FW, Luikart GH, Aitken SN (2013) Conservation and the genetics of populations, 2nd edn. Wiley-Blackwell, Oxford
5. Allis CD, Jenuwein T, Reinberg D, Caparros M-L (2007) Epigenetics, 1st edn. Cold Spring Harbor Laboratory Press, New York
6. Allona I, Quinn M, Shoop E, Swope K, Cyr SS, Carlis J, Riedl J, Retzel E, Campbell MM, Sederoff R, Whetten RW (1998) Analysis of xylem formation in pine by cDNA sequencing. Proc Natl Acad Sci U S A 95:9693–9698
7. Alves AA, Conçalves Rosado CC, Faria DA, da Silva Guimaraes LM, Lau D, Brommonschenkel SH, Grattapaglia D, Alfenas AC (2012) Genetic mapping provides evidence for the role of additive and non-additive QTLs in the response of inter-specific hybrids of Eucalyptus to Puccinia psidii rust infection. Euphytica 183:27–38
8. Andersson-Gunneras S, Mellerowicz EJ, Love J, Segerman B, Ohmiya Y, Coutinho PM, Nilsson P, Henrissat B, Moritz T, Sundberg B (2006) Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J 45:144–165
9. Audigeos D, Brousseau L, Traissac S, Scotti-Saintagne C, Scotti I (2013) Molecular divergence in tropical tree populations occupying environmental mosaics. J Evol Biol 26:529–544
10. Baba K, Park YW, Kaku T, Kaida R, Takeuchi M, Yoshida M, Hosoo Y, Ojio Y, Okuyama T, Taniguchi T, Ohmiya Y, Kondo T, Shani Z, Shoseyov O, Awano T, Serada S, Norioka N, Norioka S, Hayashi T (2009) Xyloglucan for generating tensile stress to bend tree stem. Mol Plant 2:893–903
11. Baker PA, Fritz SC, Dick CW, Eckert AJ, Horton BK, Manzoni S, Ribas CC, Garzione CN, Battisti DS (2014) The emerging field of geogenomics: constraining geological problems with genetic data. Earth-Sci Rev 135:38–47
12. Bálint M, Tiffin P, Hallström B, O’Hara RB, Olson MS, Fankhauser JD, Piepenbring M, Schmitt I (2013) Host genotype shapes the foliar fungal microbiome of balsam poplar (Populus balsamifera). PLoS ONE 8:e53987
13. Bálint M, Bartha L, O’Hara RB, Olson MS, Otte J, Pfenninger M, Robertson AL, Tiffin P, Schmitt I (2015) Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars. Mol Ecol 24:235–248
14. Bassett CL, Wisniewski ME, Artlip TS, Norelli JL, Renaut J, Farrell RE (2006) Global analysis of genes regulated by low temperature and photoperiod in peach bark. J Am Soc Hortic Sci 131:551–563
15. Beaulieu J, Doerksen T, Clément S, MacKay J, Bousquet J (2014) Accuracy of genomic selection models in a large population of open-pollinated families in white spruce. Heredity 113:343–352
16. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13:969–980
17. Bedon F, Villar E, Vincent D, Dupuy JW, Lomenech AM, Mabialangoma A, Chaumeil P, Barre A, Plomion C, Gion JM (2012) Proteomic plasticity of two Eucalyptus genotypes under contrasted water regimes in the field. Plant Cell Environ 35:790–805
18. Bernhardsson C, Ingvarsson PK (2012) Geographical structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremula L., Salicaceae). Mol Ecol 21:2197–2207
19. Berta M, Giovannelli A, Sebastiani F, Camussi A, Racchi ML (2010) Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit. Plant Biol 12:341–354
20. Berthet S, Thevenin J, Baratiny D, Demont-Caulet N, Debeaujon I, Bidzinski P, Leple JC, Huis R, Hawkins S, Gomez LD, Lapierre C, Jouanin L (2012) Role of plant laccases in lignin polymerization. In: Jouann L, Lapierre C eds. Lignins: biosynthesis, biodegradation and bioengineering, 145–172
21. Bielenberg DG, Wang Y, Li Z, Zhebentyayeva T, Fan S, Reighard GL, Scorza R, Abbott AG (2008) Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation. Tree Genet Genomes 4:495–507
22. Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B, Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, Bohlmann J, Jones SJ (2013) Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics 29:1492–1497
23. Biswal AK, Soeno K, Gandla ML, Immerzeel P, Pattathil S, Lucenius J, Serimaa R, Hahn MG, Moritz T, Jonsson LJ, Israelsson-Nordstrom M, Mellerowicz EJ (2014) Aspen pectate lyase PtxtPL1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield. Biotechnol Biofuels 7:11
24. Bogeat-Triboulot MB, Brosche M, Renaut J, Jouve L, Le Thiec D, Fayyaz P, Vinocur B, Witters E, Laukens K, Teichmann T, Altman A, Hausman JF, Polle A, Kangasjarvi J, Dreyer E (2007) Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions. Plant Physiol 143:876–892
25. Bonawitz ND, Chapple C (2010) The genetics of lignin biosynthesis: connecting genotype to phenotype. Annu Rev Genet 44:337–363
26. Bonhomme L, Monclus R, Vincent D, Carpin S, Claverol S, Lomenech AM, Labas V, Plomion C, Brignolas F, Morabito D (2009) Genetic variation and drought response in two Populus x euramericana genotypes through 2-DE proteomic analysis of leaves from field and glasshouse cultivated plants. Phytochemistry 70:988–1002
27. Borer ET, Kinkel LL, May G, Seabloom EW (2013) The world within: quantifying the determinants and outcomes of a host’s microbiome. Basic Appl Ecol 14:533–539
28. Bossdorf O, Richards CL, Pigliucci M (2008) Epigenetics for ecologists. Ecol Lett 11:106–115
29. Bradshaw HD, Stettler RF (1995) Molecular genetics of growth and development in Populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics 139:963-973
30. Braun P, Carvunis AR, Charloteaux B, Dreze M, Ecker JR, Hill DE, Roth FP, Vidal M, Galli M, Balumuri P, Bautista V, Chesnut JD, Kim RC, Reyes C d l, Gilles P, Kim CJ, Matrubutham U, Mirchandani J, Olivares E, Patnaik S, Quan R, Ramaswamy G, Shinn P, Swamilingiah GM, Wu S, Byrdsong D, Dricot A, Duarte M, Gebreab F, Gutierrez BJ, MacWilliams A, Monachello D, Mukhtar MS, Poulin MM, Reichert P, Romero V, Tam S, Waaijers S, Weiner EM, Cusick ME, Tasan M, Yazaki J, Ahn YY, Barabasi AL, Chen HM, Dangl JL, Fan CY, Gai LT, Ghoshal G, Hao T, Lurin C, Milenkovic T, Moore J, Pevzner SJ, Przulj N, Rabello S, Rietman EA, Rolland T, Santhanam B, Schmitz RJ, Spooner W, Stein J, Vandenhaute J, Ware D, Arabidopsis Interactome Mapping Consortium (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333:601–607
31. Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C (2013) Plant protein interactomes. Annu Rev Plant Biol 64:161–187
32. Bräutigam K, Vining KJ, Lafon-Placette C, Fossdal CG, Mirouze M, Marcos JG, Fluch S, Fraga MF, Guevara MA, Abarca D, Johnsen Ø, Maury S, Strauss SH, Campbell MM, Rohde A, Díaz-Sala C, Cervera MT (2013) Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol Evol 3:399–415
33. Bresson A, Jorge V, Dowkiw A, Guerin V, Bourgait I, Tuskan GA, Schmutz J, Chalhoub B, Bastien C, Faivre-Rampant P (2011) Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar. New Phytol 192:151–163
34. Brinker M, van Zyl L, Liu W, Craig D, Sederoff RR, Clapham DH, von Arnold S (2004) Microarray analyses of gene expression during adventitious root development in Pinus contorta. Plant Physiol 135:1526–1539
35. Brousseau L, Bonal D, Cigna J, Scotti I (2013) Highly local environmental variability promotes intra-population divergence of quantitative traits: an example from tropical rainforest trees. Ann Bot 112:1169–1179
36. Budde KB, Gonzalez-Martinez SC, Hardy OJ, Heuertz M (2013) The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa. Heredity 111:66–76
37. Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456
38. 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
39. Busov V, Yordanov YS, Gou J, Meilan R, Ma C, Regan S, Strauss S (2010) Activation tagging is an effective gene tagging system in Populus. Tree Genet Genomes 7:91–101
40. Cairney J, Pullman GS (2007) The cellular and molecular biology of conifer embryogenesis. New Phytol 176:511–536
41. Canales J, Bautista R, Label P, Gómez-Maldonado J, Lesur I, FernÁndez-Pozo N, Rueda-López M, Guerrero-Fernández D, Castro-Rodríguez V, Benzekri H, Cañas RA, Guevara MA, Rodrigues A, Seoane P, Teyssier C, Morel A, Ehrenmann F, Le Provost G, Lalanne C, Noirot C, Klopp C, Reymond I, García-Gutiérrez A, Trontin JF, Lelu-Walter M-A, Miguel C, Cervera MT, Cantón FR, Plomion C, Harvengt L, Avila C, Claros MG, Cánovas FM (2014) De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotech J 12:286–299
42. Carstens BC, Brennan RS, Chua V, Duffie CV, Harvey MG, Koch RA, McMahan CD, Nelson BJ, Newman CE, Satler JD, Seeholzer G, Posbic K, Tank DC, Sullivan J (2013) Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Mol Ecol 22:4014–4028
43. Carstens BC, Richards CL (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution 61:1439–1454
44. Castell WZ, Ernst D (2012) Experimental “omics” data in tree research: facing complexity. Trees Struct Funct 26:1723–1735
45. Chancerel E, Lamy JB, Lesur I, Noirot C, Klopp C, Ehrenmann F, Boury C, Le Provost G, Label P, Lalanne C, Léger V, Salin F, Gion JM, Plomion C (2013) High density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination. BMC Biol 11:50
46. Chao WS, Foley ME, Horvath DP, Anderson JV (2007) Signals regulating dormancy in vegetative buds. Int J Plant Dev Biol 1:49–56
47. Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I (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
48. Cohen D, Bogeat-Triboulot MB, Vialet-Chabrand S, Merret R, Courty PE, Moretti S, Bizet F, Guilliot A, Hummel I (2013) Developmental and environmental regulation of aquaporin gene expression across Populus species: divergence or redundancy? PLoS ONE 8:e55506
49. Coince A, Caël O, Bach C, Lengellé J, Cruaud C, Gavory F, Morin E, Murat C, Marçais B, Buée M (2013) Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest. Fungal Ecol 6:223–235
50. Coince A, Cordier T, Lengellé J, Defossez E, Vacher C, Robin C, Buée M, Marçais B (2014) Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns. PLoS ONE 9:e100668
51. Coleman HD, Canam T, Kang KY, Ellis DD, Mansfield SD (2007) Over-expression of UDP-glucose pyrophosphorylase in hybrid poplar affects carbon allocation. J Exp Bot 58:4257–4268
52. Coleman HD, Yan J, Mansfield SD (2009) Sucrose synthase affects carbon partitioning to increase cellulose production and altered cell wall ultrastructure. Proc Natl Acad Sci U S A 106:13118–13123
53. Cordier T, Robin C, Capdevielle X, Desprez-Loustau M-L, Vacher C (2012a) Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecol 5:509–520
54. Cordier T, Robin C, Capdevielle X, Fabreguettes O, Desprez-Loustau M-L, Vacher C (2012b) The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica) varies significantly along an elevation gradient. New Phytol 196:510–519
55. Cornille A, Giraud T, Bellard C, Tellier A, Le Cam B, Smulders MJM, Kleinschmit J, Roldan-Ruiz I, Gladieux P (2013) Postglacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple. Mol Ecol 22:2249–2263
56. Cortijo S, Wardenaar R, Colome-Tatche M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F (2014) Mapping the epigenetic basis of complex traits. Science 343:1145–1148
57. Couvreur T, Chatrou L, Sosef M, Richardson J (2008) Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees. BMC Biol 6:54
58. Csillery K, Lalagüe H, Vendramin GG, Gonzalez-Martinez SC, Fady B, Oddou-Muratorio S (2014) Detecting local adaptation and epistatic selection in climate related candidate genes at a short spatial scale in European beech (Fagus sylvatica) populations. Mol Ecol 23:4696–4708
59. Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L, Marmeisse R (2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS ONE 7:e28967
60. Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. Murray, London
61. Dauby G, Duminil J, Heuertz M, Koffi GK, Stévart T, Hardy OJ (2014) Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover. Mol Ecol 23:2299–2312
62. De Bodt S, Proost S, Vandepoele K, Rouze P, van de Peer Y (2009) Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10:288
63. de Vega-Bartol JJ, Simões M, Lorenz WW, Rodrigues AS, Alba R, Dean JFD, Miguel C (2013) Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster. BMC Plant Biol 13:123
64. Déjardin A, Leplé J-C, Lesage-Descauses M-C, Costa G, Pilate G (2004) Expressed sequence tags from poplar wood tissues—a comparative analysis from multiple libraries. Plant Biol 6:55–64
65. Déjardin A, Arnaud D, Laurans F, Breton C, Pilate G, Leplé JC (2010) Wood formation in angiosperms. CR Biol 333:325–334
66. Denis M, Bouvet J-M (2013) Efficiency of genomic selection with models including dominance effect in the context of Eucalyptus breeding. Trees Geneti Genomes 9:37–51
67. Dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ, Yang Z (2012) Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc R Soc B 279:3491–3500
68. Dowkiw A, Voisin E, Bastien C (2010) Potential of Eurasian poplar rust to overcome a major quantitative resistance factor. Plant Pathol 59:523–534
69. Drost DR, Benedict CI, Berg A, Novaes E, Novaes CRDB, Yu Q, Dervinis C, Maia JM, Yap J, Miles B, Kirst M (2010) Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus. Proc Natl Acad Sci U S A 107:8492–8497
70. Du J, Mansfield SD, Groover AT (2009) The Populus homeobox gene ARBORKNOX2 regulates cell differentiation during secondary growth. Plant J 60:1000–1014
71. Du J, Miura E, Robischon M, Martinez C, Groover A (2011) The Populus class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems. PLoS ONE 6:e17458
72. Dubos C, Le Provost G, Pot D, Salin F, Lalane C, Madur D, Frigerio JM, Plomion C (2003) Identification and characterization of water-stress-responsive genes in hydroponically grown maritime pine (Pinus pinaster) seedlings. Tree Physiol 23:169–179
73. Duminil J, Kenfack D, Viscosi V, Grumiau L, Hardy OC (2012) Testing species delimitation in sympatric species complexes: the case of an African tropical tree, Carapa spp. (Meliaceae). Mol Phylogenet Evol 62:275–285
74. Duplessis S, Major I, Martin F, Seguin A (2009) Poplar and pathogen interactions: insights from Populus genome-wide analyses of resistance and defense gene families and gene expression profiling. Crit Rev Plant Sci 28:309–334
75. Eckert AJ, Tearse BR, Hall BD (2008) A phylogeographical analysis of the range disjunction for foxtail pine (Pinus balfouriana, Pinaceae): the role of Pleistocene glaciation. Mol Ecol 17:1983–1997
76. Eckert AJ, Bower AD, González-MartÍnez SC, Wegrzyn JL, Coop G, Neale DB (2010) Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Mol Ecol 19:3789–3805
77. El Kassaby Y, Lstiburek M (2009) Breeding without breeding. Genet Res 91:111–120
78. Elhiti M, Stasolla C, Wang A (2013) Molecular regulation of plant somatic embryogenesis. In vitro Cell Dev Pl 49:631–642
79. Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, Brunner AM, Schackwitz W, Gunter L, Chen JG, Tuskan GA, DiFazio SP (2014) Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 46:1089–1096
80. Faino L, Thomma BP (2014) Get your high-quality low-cost genome sequence. Trends Plant Sci 19:288–291
81. Felten J, Kohler A, Morin E, Bhalerao RP, Palme K, Martin F, Ditengou FA, Legué V (2009) The ectomycorrhizal fungus Laccaria bicolor stimulates lateral root formation in poplar and Arabidopsis through auxin transport and signaling. Plant Physiol 151:1991–2005
82. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 107:8689–8694
83. Ford EB (1964) Ecological genetics. Chapman and Hall, London
84. François O, Durand E (2010) Spatially explicit Bayesian clustering models in population genetics. Mol Ecol Res 10:773–784
85. Freeman JS, Potts BM, Vaillancourt RE (2008) Few Mendelian genes underlie the quantitative response of a forest tree, Eucalyptus globulus, to a natural fungal epidemic. Genetics 178:563–571
86. Gao JIE, Wang B, Mao J-F et al (2012) Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan plateau. Mol Ecol 21:4811–4827
87. Gao M, Huang Q, Chu Y, Ding C, Zhang B, Su X (2014) Analysis of the leaf methylomes of parents and their hybrids provides new insight into hybrid vigor in Populus deltoides. BMC Genet 15:S8
88. Geisler-Lee J, O’Toole N, Ammar R, Provart NJ, Millar AH, Geisler M (2007) A predicted interactome for Arabidopsis. Plant Physiol 145:317–329
89. Gentil MV, Maury S (2007) Characterization of epigenetic biomarkers using new molecular approaches. In: Varshney R, Tuberosa R (eds) Springer, pp 351–370
90. Gion JM, Lalanne C, Le Provost G, Ferry-Dumazet H, Paiva J, Frigerio JM, Chaumeil P, Barré A, de Daruvar A, Brach J, Claverol S, Bonneu M, Plomion C (2005) The proteome of maritime pine wood forming tissue. Proteomics 5:3731–3751
91. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100
92. González-Martínez SC, Krutovsky KV, Neale DB (2006) Forest-tree population genomics and adaptive evolution. New Phytol 170:227–238
93. Gorzsás A, Stenlund H, Persson P, Trygg J, Sundberg B (2011) Cell-specific chemotyping and multivariate imaging by combined FT-IR microspectroscopy and orthogonal projections to latent structures (OPLS) analysis reveals the chemical landscape of secondary xylem. Plant J 66:903–914
94. Gourcilleau D, Bogeat-Triboulot M-B, Thiec D, Lafon-Placette C, Delaunay A, El-Soud WA, Brignolas F, Maury S (2010) DNA methylation and histone acetylation: genotypic variations in hybrid poplars, impact of water deficit and relationships with productivity. Ann Forest Sci 67:208
95. Grattapaglia D, Resende MDV (2011) Genomic selection in forest tree breeding. Tree Genet Genomes 7:241–255
96. Gray-Mitsumune M, Blomquist K, McQueen-Mason S, Teeri TT, Sundberg B, Mellerowicz EJ (2008) Ectopic expression of a wood-abundant expansin PttEXPA1 promotes cell expansion in primary and secondary tissues in aspen. Plant Biotechnol J 6:62–72
97. Grivet D, Sebastiani F, Alía R, Bataillon T, Torre S, Zabal-Aguirre M, Vendramin GG, González-Martínez SC (2011) Molecular footprints of local adaptation in two Mediterranean conifers. Mol Bio Evol 28:101–116
98. Guichoux E, Garnier-Géré P, Lagache L, Lang T, Boury C, Petit RJ (2013) Outlier loci highlight the direction of introgression in oaks. Mol Ecol 22:450–462
99. Guttman DS, Mc Hardy AC, Schulze-Lefert P (2014) Microbial genome-enabled insights into plant-microorganism interactions. Nat Rev Genet 15:797–813
100. Hacquard S, Schadt CW (2015) Towards a holistic understanding of the beneficial interactions across the Populus microbiome. New Phytol 205:1424–1430
101. Hakman I, Fowke LC, von Arnold S, Eriksson T (1985) The development of somatic embryogenesis in tissue cultures initiated from immature embryos of Picea abies (Norway spruce). Plant Sci 38:53–59
102. 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
103. Harfouche A, Meilan R, Altman A (2014) Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement. Tree Physiol (in press)
104. Hasbún R, Valledor L, Rodríguez JL, Santamaria E, Rıos D, Sanchez M, Canal MJ, Rodrıguez R (2008) HPCE quantification of 5-methyl-2′-deoxycytidine in genomic DNA: methodological optimization for chestnut and other woody species. Plant Physiol Biochem 46:815–822
105. He J, Li H, Luo J, Ma C, Li S, Qu L, Gai Y, Jiang X, Janz D, Polle A, Tyree M, Luo ZB (2013) A transcriptomic network underlies microstructural and physiological responses to cadmium in Populus x canescens. Plant Physiol 162:424–439
106. Hedenström M, Wiklund-Lindström S, Öman T, Lu F, Gerber L, Schatz P, Sundberg B, Ralph J (2009) Identification of lignin and polysaccharide modifications in populus wood by chemometric analysis of 2D NMR spectra from dissolved cell walls. Mol Plant 2:933–942
107. Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Bio Evol 27:570–580
108. Hernandez-Serrano A, Verdu M, Gonzalez-Martinez SC, Pausas JG (2013) Fire structures pine serotiny at different scales. Am J Bot 100:2349–2356
109. Heuertz M, De Paoli E, Källman T, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174:2095–2105
110. Heuertz M, Duminil J, Dauby G, Savolainen V, Hardy OJ (2014) Comparative phylogeography in rainforest trees from lower Guinea, Africa. PLoS ONE 9:e84307
111. Hibbett DS, Ohman A, Kirk PM (2009) Fungal ecology catches fire. New Phytol 184:279–282
112. Hoenicka H, Lautner S, Klingberg A, Koch G, El-Sherif F, Lehnhardt D, Zhang B, Burgert I, Odermatt J, Melzer S, Fromm J, Fladung M (2012) Influence of over-expression of the FLOWERING PROMOTING FACTOR 1 gene (FPF1) from Arabidopsis on wood formation in hybrid poplar (Populus tremula L. x P. tremuloides Michx.). Planta 235:359–373
113. Hood L, Heath JR, Phelps ME, Lin BY (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306:640–643
114. Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Nordborg M, Subramanian S, Vetter MM, Vilhja BJ, Gordon JI, Bergelson J (2014) Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat Commun 5:5320
115. Horvath DP, Anderson JV, Chao WS, Foley ME (2003) Knowing when to grow: signals regulating bud dormancy. Trends Plant Sci 8:534–540
116. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
117. IRGSP (2005) The map-based sequence of the rice genome. Nature 436:793–800
118. 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
119. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467
120. Janz D, Behnke K, Schnitzler JP, Kanawati B, Schmitt-Kopplin P, Polle A (2010) Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms. BMC Plant Biol 10:150
121. Janz D, Lautner S, Wildhagen H, Behnke K, Schnitzler JP, Rennenberg H, Fromm J, Polle A (2012) Salt stress induces the formation of a novel type of ‘pressure wood’ in two Populus species. New Phytol 194:129–141
122. Jaramillo-Correa JP, Grivet D, Terrab A et al (2010) The Strait of Gibraltar as a major biogeographic barrier in Mediterranean conifers: a comparative phylogeographic survey. Mol Ecol 19:5452–5468
123. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–100
124. Jones DG, Dangl JL (2006) The plant immune system. Nature 444:323–329
125. Jones AF, Cerón-Souza I, Hardesty BD, Dick CW (2013) Genetic evidence of Quaternary demographic changes in four rain forest tree species sampled across the Isthmus of Panama. J Biogeogr 40:720–731
126. Joost S, Bonin A, Bruford MW, Després L, Conord C, Erhardt G, Taberlet P (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol Ecol 16:3955–3969
127. Jorge V, Dowkiw A, Faivre-Rampant P, Bastien C (2005) Genetic architecture of qualitative and quantitative Melampsora larici-populina leaf rust resistance in hybrid poplar: genetic mapping and QTL detection. New Phytol 167:113–127
128. Jump AS, Hunt JM, Martínez-Izquierdo JA, Peñuelas J (2006) Natural selection and climate change: temperature-linked spatial and temporal trends in gene frequency in Fagus sylvatica. Mol Ecol 15:3469–3480
129. Jumpponen A, Jones KL (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184:438–448
130. Jumpponen A, Jones KL (2010) Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytol 186:496–513
131. Junghans DT, Alfenas AC, Brommonschenkel SH, Oda S, Mello EJ, Grattapaglia D (2004) Resistance to rust Puccinia psidii winter in Eucalyptus: mode of inheritance and mapping of a major gene with RAPD markers. Theor Appl Genet 108:175–18
132. Källman T, De Mita S, Larsson H, Gyllenstrand N, Heuertz M, Parducci L, Suyama Y, Lagercrantz U, Lascoux M (2014) Patterns of nucleotide diversity at photoperiod related genes in Norway spruce [Picea abies (L.) Karst.]. PloS ONE 9:e95306
133. Keir KR, Bemmels JB, Aitken SN (2011) Low genetic diversity, moderate local adaptation, and phylogeographic insights in Cornus nuttallii (Cornaceae). Am J Bot 98:1327–1336
134. Kell DB, Brown M, Davey HM, Dunn WB, Spasic I, Oliver SG (2005) Metabolic footprinting and systems biology: the medium is the message. Nat Rev Microbiol 3:557–565
135. Keller SR, Olson MS, Silim S, Schroeder W, Tiffin P (2010) Genomic diversity, population structure, and migration following rapid range expansion in the balsam poplar, Populus balsamifera. Mol Ecol 19:1212–1226
136. Kembel SW, Mueller RC (2014) Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities. Botany 92:303–311
137. Kembel SW, Connor TKO, Arnold HK, Hubbell SP, Wright SJ (2014) Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc Natl Acad Sci 111:13715–13720
138. Kinloch BB Jr, Sniezko RA, Dupper GE (2004) Virulence gene distribution and dynamics of the white pine blister rust pathogen in Western North America. Phytopathology 94:751–758
139. Kirst M, Basten CJ, Myburg AA, Zeng Z-B, Sederoff RR (2005) Genetic architecture of transcript-level variation in differentiating xylem of a Eucalyptus hybrid. Genetics 169:2295–2303
140. Klimaszewska K, Overton C, Stewart D, Rutledge RG (2011) Initiation of somatic embryos and regeneration of plants from primordial shoots of 10-year-old somatic white spruce and expression profiles of 11 genes followed during the tissue culture process. Planta 233:635–647
141. Klimaszewska K, Hargreaves C, Lelu-Walter M-A, Trontin J-F (2015). Advances in conifer somatic embryogenesis since year 2000. In: In vitro plant embryogenesis in higher plants, Germanà MA, Lambardi M (eds), Methods in molecular biology, Springer-Humana Press (in press)
142. Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6:1378–1390
143. Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, Duchaussoy F, Meyers BC, Boerjan W, Martin F (2008) Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Mol Biol 66:619–636
144. Koskela J, Lefèvre F, Schüler S, Kraigher H, Olrik DC, Hubert J, Longauer R, Bozzano M, Yrjänä L, Alizoti P, Rotach P, Vietto L, Bordács S, Myking T, Eysteinsson T, Souvannavong O, Fady B, De Cuyper B, Heinze B, von Wühlisch G, Ducousso A, Ditlevsen B (2013) Translating conservation genetics into management: pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity. Biol Conserv 157:39–49
145. Kress WJ, Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci U S A 105:2761–2762
146. Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J (2009) Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol 149:461–473
147. La Mantia J, Klápště J, El-Kassaby YA, Azam S, Guy RD, Douglas CJ, Mansfield SD, Hamelin R (2013) Association analysis identifies Melampsora x Columbiana poplar leaf rust resistance SNPs. PLoS ONE 8:e78423
148. Lafon-Placette C, Faivre-Rampant P, Delaunay A, Street N, Brignolas F, Maury S (2013) Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state. New Phytol 197:416–430
149. Lalagüe H, Csilléry K, Oddou-Muratorio S, Safrana J, de Quattro C, Fady B, González-Martínez SC, Vendramin GG (2014) Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France. Tree Genet Genomes 10:15–26
150. Lang GA, EarlyJD MGC, Darnell RL (1987) Endo-, para- and eco-dormancy: physiological, terminology and classification for dormancy research. HortSci 22:371–377
151. Lascoux M, Petit RJ (2010) The ‘New Wave’ in plant demographic inference: more loci and more individuals. Mol Ecol 19:1075–1078
152. Lefevre F, Koskela J, Hubert J, Kraigher H, Longauer R, Olrik DC, Schueler S, Bozzano M, Alizoti P, Bakys R, Baldwin C, Ballian D, Black-Samuelsson S, Bednarova D, Bordacs S, Collin E, De Cuyper B, De Vries SMG, Eysteinsson T, Frydl J, Haverkamp M, Ivankovic M, Konrad H, Koziol C, Maaten T, Paino EN, Ozturk H, Pandeva ID, Parnuta G, Pilipovic A, Postolache D, Ryan C, Steffenrem A, Varela MC, Vessella F, Volosyanchuk RT, Westergren M, Wolter F, Yrjana L, Zarina I (2013) Dynamic conservation of forest genetic resources in 33 European countries. Conserv Biol 27:373–384
153. Leff JW, Del Tredici P, Friedman WE, Fierer N (2015) Spatial structuring of bacterial communities within individual Ginkgo biloba trees. Environ Microbiol. doi:10.1111/1462-2920.12695
154. Legué V, Rigal A, Bhalerao RP (2014) Adventitious root formation in tree species: involvement of transcription factors. Physiol Plant 151:192–198
155. Lelu-Walter MA, Thompson D, Harvengt L, Sanchez L, Toribio M, Pâques LE (2013) Somatic embryogenesis in forestry with a focus on Europe: state-of-the-art, benefits, challenges and future direction. Tree Genet Genomes 9:883–899
156. Lesica P, Allendorf FW (1995) When are peripheral populations valuable for conservation? Conserv Biol 9:753–760
157. Li E, Bhargava A, Qiang W, Friedmann MC, Forneris N, Savidge RA, Johnson LA, Mansfield SD, Ellis BE, Douglas CJ (2012) The class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus. New Phytol 194:102–115
158. Li W, Lin YC, Li Q, Shi R, Lin CY, Chen H, Chuang L, Qu GZ, Sederoff RR, Chiang VL (2014a) A robust chromatin immunoprecipitation protocol for studying transcription factor–DNA interactions and histone modifications in wood-forming tissue. Nat Methods 9:2180–2193
159. Li WF, Zhang SG, Han SY, Wu T, Zhang JH, Qi LW (2014b) The post-transcriptional regulation of LaSCL6 by miR171 during maintenance of embryogenic potential in Larix kaempferi (Lamb.) Carr. Tree Genet Genomes 10:223–229
160. Liang D, Zhang Z, Wu H, Huang C, Shuai P, Ye C-Y, Tang S, Wang Y, Yang L, Wang J, Yin W, Xia W (2014) Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress. BMC Genet 15:S9
161. Lin MZ, Zhou X, Shen XL, Mao CZ, Chen X (2011) The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. Plant Cell 23:911–922
162. Lin YC, Li W, Sun YH, Kumari S, Wei HR, Li QZ, Tunlaya-Anukit S, Sederoff RR, Chiang VL (2013) SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell 25:4324–4341
163. Lippert D, Zhuang J, Ralph S, Ellis DE, Gilbert M, Olafson R, Ritland K, Ellis B, Douglas CJ, Bohlmann J (2005) Proteome analysis of early somatic embryogenesis in Picea glauca. Proteomics 5:461–473
164. Liu JJ, Sturrock RN, Benton R (2013) Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola. BMC Genomics 14:884
165. Liu LJ, Filkov V, Groover A (2014) Modeling transcriptional networks regulating secondary growth and wood formation in forest trees. Physiol Plant 151:156–163
166. Lorenz WW, Ayyampalayam S, Boedeaux JM, Howe GT, Jermstad KD, Neale DB, Rogers DL, Dean JFD (2012) Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species. Tree Genet Genomes 8:1477–1485
167. Lu S, Sun Y-H, Shi R, Clark C, Li CVL (2005) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17:2186–2203
168. Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, Liu B, Qiu Q, Wang Z, Zhang J, Wang K, Jiang D, Gou C, Yu L, Zhan D, Zhou R, Luo W, Ma H, Yang Y, Pan S, Fang D, Luo Y, Wang X, Wang G, Wang J, Wang Q, Lu X, Chen Z, Liu J, Lu Y, Yin Y, Yang H, Abbott RJ, Wu Y, Wan D, Li J, Yin T, Lascoux M, DiFazio SP, Tuskan GA, Wang J, Liu J (2013) Genomic insights into salt adaptation in a desert poplar. Nat Commun 4:2797
169. Maher B (2008) The case of the missing heritability. Nature 456:18–21
170. Malé P-JG, Bardon L, Besnard G, Coissac E, Delsuc F, Engel J, Lhuillier E, Scotti-Saintagne C, Tinaut A, Chave J (2014) Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Mol Ecol Res 14:966–975
171. Mankessi F, Saya AR, Favreau B, Doulbeau S, Conejero G, Lartaud M, Verdeil J-L, Monteuuis O (2011) Variations of DNA methylation in Eucalyptus urophylla × Eucalyptus grandis shoot tips and apical meristems of different physiological ages. Physiol Plant 143:178–187
172. Margulis L (1991) Symbiogenesis and symbionticism. In: Margulis L, Fester R (eds) Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. MIT Press, Cambridge, pp 1–14
173. Marjoram P, Zubair A, Nuzhdin SV (2014) Post-GWAS: where next? More samples, more SNPs or more biology? Heredity 112:79–88
174. McCormack JE, Hird SM, Zellmer AJ, Carstens BC, Brumfield RT (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 66:526–538
175. McPherson H, van der Merwe M, Delaney S, Edwards MA, Henry RJ, McIntosh E, Rymer PD, Milner ML, Siow J, Rossetto M (2013) Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol 13:8
176. Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, DeMeyer T (2014) Next-generation technologies and data analytical approaches for epigenomics: next-generation technologies for epigenomics. Environ Mol Mutagen 55:155–170
177. Menzel A, Fabian P (1999) Growing season extended in Europe. Nature 397:659
178. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
179. Micheneau C, Dauby G, Bourland N, Doucet JL, Hardy OJ (2011) Development and characterization of microsatellite loci in Pericopsis elata (Fabaceae) using a cost-efficient approach. Am J Bot 98:e268–e270
180. Moller I, Sørensen I, Bernal AJ, Blaukopf C, Lee K, Øbro J, Pettolino F, Roberts A, Mikkelsen JD, Knox JP, Bacic A, Willats WGT (2007) High-throughput mapping of cell-wall polymers within and between plants using novel microarrays. Plant J 50:1118–1128
181. Monteuuis O, Baurens FC, Goh DKS, Uimado MQ, Oulbeau SD, Verdeil JL (2009) DNA methylation in Acacia mangium in vitro and ex-vitro buds, in relation to their within-shoot position, age and leaf morphology of the shoots. Silvae Genet 58:287–292
182. Morel A, Teyssier C, Trontin JF, Pešek B, Eliášová K, Beaufour M, Morabito D, Boizot N, Le Metté C, Belal-Bessai L, Reymond I, Harvengt L, Cadene M, Corbineau F, Vágner M, Label P, Lelu-Walter MA (2014a) Early molecular events involved in Pinus pinaster Ait. somatic embryo development under reduced water availability: transcriptomic and proteomic analysis. Physiol Plant 152:184–201
183. Morel A, Trontin JF, Corbineau F, Lomenech A-M, Beaufour M, Reymond I, Le Metté C, Ader K, Harvengt L, Cadene M, Label P, Teyssier C, Lelu-Walter M-A (2014b) Cotyledonary somatic embryos of Pinus pinaster Ait. most closely resemble fresh, maturing cotyledonary zygotic embryos: biological, carbohydrate and proteomic analyses. Planta (in press)
184. Moritz C (1994) Defining ‘evolutionarily significant units’ for conservation. Trends Ecol Evol 9:373–375
185. Morjan CL, Rieseberg LH (2004) How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles. Mol Ecol 13:1341–1356
186. Morreel K, Dima O, Kim H, Lu F, Niculaes C, Vanholme R, Dauwe R, Goeminne G, Inzé D, Messens E, Ralph J, Boerjan W (2010) Mass spectrometry-based sequencing of lignin oligomers. Plant Physiol 153:1464–1478
187. Morris AB, Ickert-Bond SM, Brunson DB, Soltis DE, Soltis PS (2008) Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae). Mol Ecol 17:3889–3900
188. Muchero W, Labbé J, Ranjan P, DiFazio S, Tuskan GA (2014) Genome resequencing in Populus: revealing large-scale genome variation and implications on specialized-trait genomics. In: Challenges and Opportunities for the World’s Forests in the 21st Century. Springer, pp 587–595
189. Muranty H, Jorge V, Bastien C, Lepoittevin C, Bouffier L, Sanchez L (2014) Potential for marker-assisted selection for forest tree breeding: lessons from 20 years of MAS in crops. Tree Genet Genomes (in press)
190. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J (2014) The genome of Eucalyptus grandis. Nature 510:356–362
191. Naor A, Flaishman M, Stern R, Moshe A, Erez A (2003) Temperature effect on dormancy completion of vegetative buds in apple. J Am Soc Hortic Sci 128:636–641
192. Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nature Rev Genet 12:111–121
193. Neale D, Langley C, Salzberg S, Wegrzyn J (2013) Open access to tree genomes: the path to a better forest. Genome Biol 14:120
194. Neale D, Wegrzyn J, Stevens K, Zimin A, Puiu D, Crepeau M, Cardeno C, Koriabine M, Holtz-Morris A, Liechty J, Martinez-Garcia P, Vasquez-Gross H, Lin B, Zieve J, Dougherty W, Fuentes-Soriano S, Wu L-S, Gilbert D, Marcais G, Roberts M, Holt C, Yandell M, Davis J, Smith K, Dean J, Lorenz W, Whetten R, Sederoff R, Wheeler N, McGuire P, Main D, Loopstra C, Mockaitis K, deJong P, Yorke J, Salzberg S, Langley C (2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 15:R59
195. Neiman M, Olson MS, Tiffin P (2009) Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates. New Phytol 183:740–750
196. 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 4:29–37
197. Newcombe G, Bradshaw HD Jr, Chastagner GA, Stettler RF (1996) A major gene for resistance to Melampsora medusa f.sp. deltoidae in a hybrid poplar pedigree. Phytopathology 86:87–94
198. Nicotra AB, Atkin OK, Bonser SP, Davidson AM, Finnegan EJ, Mathesius U, Poot P, Purugganan MD, Richards CL, Valladares F, Van Kleunen M (2010) Plant phenotypic plasticity in a changing climate. Trends Plant Sci 15:684–692
199. Nielsen R, Beaumont MA (2009) Statistical inferences in phylogeography. Mol Ecol 18:1034–1047
200. Nimchuk Z, Eulgem T, Holt BF, Dangl JL (2003) Recognition and response in the plant immune system. Annu Rev Genet 37:579–609
201. Nishikubo N, Takahashi J, Roos AA, Derba-Maceluch M, Piens K, Brumer H, Teeri TT, Stalbrand H, Mellerowicz EJ (2011) Xyloglucan endo-transglycosylase-mediated xyloglucan rearrangements in developing wood of hybrid aspen. Plant Physiol 155: 399–413
202. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Gil RG, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–584
203. Ohtani M, Nishikubo N, Xu B, Yamaguchi M, Mitsuda N, Goue N, Shi F, Ohme-Takagi M, Demura T (2011) A NAC domain protein family contributing to the regulation of wood formation in poplar. Plant J 67:499–512
204. Öpik M, Metsis M, Daniell TJ, Zobel M, Moora M (2009) Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreo-nemoral forest. New Phytol 184:424–437
205. Paiva J, Garcés M, Alves A, Garnier-Géré P, Rodrigues J-C, Lalanne C, Porcon S, Le Provost G, da Silva D, Perez BJ, Frigerio JM, Claverol S, Barré A, Fevereiro P, Plomion C (2008a) Molecular and phenotypic profiling from the base to the crown in maritime pine wood forming tissue. New Phytol 178:283–301
206. Paiva J, Garnier-Géré PH, Rodrigues JC, Alves A, Santos S, Graça J, Le Provost G, Chaumeil P, da Silva-Perez D, Bosc A, Fevereiro P, Plomion C (2008b) Plasticity of maritime pine (Pinus pinaster Ait) wood forming tissues during a growing season. New Phytol 179:1080–1094
207. Palsbøll PJ, Bérubé M, Allendorf FW (2007) Identification of management units using population genetic data. Trends Ecol Evol 22:11–16
208. Pandey V, Haikio E, Lehesranta S, Koistinen K, Karenlampi S, Oksanen E (2013) Proteomic analysis of two hybrid aspen clones subjected to long-term chronic ozone exposure in open field. Curr Proteomics 10:67–74
209. Pâques (2013) Forest tree breeding in Europe (2013) Edited by L. Pâques. Springer, 527 p
210. Park YW, Ki B, Furuta Y, Iida I, Sameshima K, Arai M, Hayashi T (2004) Enhancement of growth and cellulose accumulation by overexpression of xyloglucanase in poplar. FEBS Lett 564:183–187
211. Paux E, Carocha V, Marques C, Mendes de Sousa A, Borralho N, Sivadon P, Grima-Pettenati J (2005) Transcript profiling of Eucalyptus xylem genes during tension wood formation. New Phytol 167:89–100
212. Petit RJ, Hampe A (2006) Some evolutionary consequences of being a tree. Annu Rev Ecol Evol Syst 37:187–214
213. Petit RJ, Aguinagalde I, de Beaulieu J-L, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Müller-Starck G, Demesure-Musch B, Palmé A, Martín JP, Rendell S, Vendramin GG (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300:1563–1565
214. Plomion C, Pionneau C, Brach J, Costa P, Baillères H (2000) Compression wood-responsive proteins in developing xylem of maritime pine (Pinus pinaster Ait). Plant Physiol 123:959–969
215. Plomion C, Le Provost G, Stokes A (2001) Wood formation in trees. Plant Physiol 127:1513–1523
216. Polle A, Altman A, Jiang XN (2006) Towards genetic engineering for drought tolerance in trees. Tree transgenesis: recent developments. Springer-Verlag Berlin, Berlin, pp 275–297
217. Preston JC, Sandve SR (2013) Adaptation to seasonality and winter freeze. Front Plant Sci 4:1–18
218. Pullman GS, Johnson S, Peter G, Cairney J, Xu N (2003) Improving Loblolly pine somatic embryo maturation: comparison of somatic and zygotic embryo morphology, germination, and gene expression. Plant Cell Rep 21:747–758
219. Puzey JR, Karger A, Axtell M, Kramer EM (2012) Deep annotation of Populus trichocarpa microRNAs from diverse tissue sets. PLoS ONE 7:e33034
220. Qiu D, Wilson IW, Gan S, Washusen R, Moran GF, Southerton SG (2008) Gene expression in Eucalyptus branch wood with marked variation in cellulose microfibril orientation and lacking G-layers. New Phytol 179:94–103
221. Raherison E, Rigault P, Caron S, Poulin PL, Boyle B, Verta JP, Giguère I, Bomal C, Bohlmann J, MacKay J (2012) Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics 13:434
222. Ramírez-Carvajal GA, Morse AM, Dervinis C, Davis JM (2008) Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development. New Phytol 177:77–89
223. Ramírez-Carvajal GA, Morse AM, Dervinis C, Davis JM (2009) The cytokinin type-B response regulator PtRR13 is a negative regulator of adventitious root development in Populus. Plant Physiol 150:759–771
224. Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12:2885–2893
225. 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
226. 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
227. Rhode A, Ruttink T, Hostyn V, Sterck L, Van Driessche K, Boerjan W (2007) Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar. J Exp Bot 58:4047–4060
228. Riesberg EE, Hildebrandt U, Riederer M, Hentschel U (2013) Distinct phyllosphere bacterial communities on Arabidopsis wax mutant leaves. PLoS ONE 8:e78613
229. Rigal A, Yordanov YS, Perrone I, Karlberg A, Tisserant E, Bellini C, Busov VB, Martin F, Kohler A, Bhalerao R, Legué V (2012) The AINTEGUMENTA LIKE1 homeotic transcription factor PtAIL1 controls the formation of adventitious root primordia in poplar. Plant Physiol 160:1996–2006
230. Rinaldi C, Kohler A, Frey P, Duchaussoy F, Ningre N, Couloux A, Wincker P, Le Thiec D, Fluch S, Martin F, Duplessis S (2007) Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol 144:347–366
231. Robinson AR, Dauwe R, Ukrainetz NK, Cullis IF, White R, Mansfield SD (2009) Predicting the regenerative capacity of conifer somatic embryogenic cultures by metabolomics. Plant Biotech J 7:952–963
232. Rodgers-Melnick E, Culp M, DiFazio SP (2013) Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS. BMC Genomics 14:608
233. Rodriguez JL, Pascual J, Viejo M, Valledor, L, Meijón M, Hasbún R, Yrei NY, Santamaría ME, Pérez M, Fraga MF, Berdasco M, Fernández RR, Cañal MJ (2012) Basic procedures for epigenetic analysis in plant cell and tissue culture. Methods Mol Biol 877:325–341
234. Rosvall O (2011) Review of the Swedish tree breeding programme: http://www.skogforsk.se/PageFiles/57629/Tree%20breeding.pdf
235. Rutledge RG, Stewart D, Caron S, Overton C, Boyle B, MacKay J, Klimaszewska K (2013) Potential link between biotic defense activation and recalcitrance to induction of somatic embryogenesis in shoot primordia from adult trees of white spruce (Picea glauca). BMC Plant Biol 13:116
236. Ruttinkt AM, Morreel K, Storme V, Rombauts S, Fromm J, Bhalerao RP, Boerjan W, Rhode A (2007) A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell 19:2370–2390
237. Saghatelian A, Cravatt BF (2005) Global strategies to integrate the proteome and metabolome. Curr Opin Chem Biol 9:62–68
238. Samils B, Ronnberg-Wastljung AC, Stenlid J (2011) QTL mapping of resistance to leaf rust in Salix. Tree Genet Genomes 7:1219–1235
239. Sanchez C, Vielba JM, Ferro E, Covelo G, Sole A, Abarca D, de Mier BS, Diaz-Sala C (2007) Two SCARECROW-LIKE genes are induced in response to exogenous auxin in rooting-competent cuttings of distantly related forest species. Tree Physiol 27:1459–1470
240. Schoville SD, Bonin A, François O, Lobreaux S, Melodelima C, Manel S (2012) Adaptive genetic variation on the landscape: methods and cases. Annu Rev Ecol Evol S 43:23–43
241. Scotti-Saintagne C, Dick CW, Caron H, Vendramin GG, Guichoux E, Buonamici A, Duret C, Sire P, Valencia R, Lemes MR, Gribel R, Scotti I (2013a) Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa, Meliaceae). J Biogeogr 40:676–692
242. Scotti-Saintagne C, Dick CW, Caron H, Vendramin GG, Troispoux V, Sire P, Casalis M, Buonamici A, Valencia R, Lemes MR, Gribel R, Scotti I (2013b) Amazon diversification and cross-Andean dispersal of the widespread Neotropical tree species Jacaranda copaia (Bignoniaceae). J Biogeogr 40:707–719
243. Sebastiana M, Vieira B, Lino-Neto T, Monteiro F, Figueiredo A, Sousa L, Pais MS, Tavares R, Paulo OS (2014) Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling. PLoS ONE 9:e98376
244. Secchi F, Gilbert ME, Zwieniecki MA (2011) Transcriptome response to embolism formation in stems of Populus trichocarpa provides insight into signaling and the biology of refilling. Plant Physiol 157:1419–1429
245. Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 196:713–725
246. Sork VL, Aitken SN, Dyer RJ, Eckert AJ, Legendre P, Neale DB (2013) Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate. Tree Genet Genomes 9:901–911
247. Spiess N, Oufir M, Matusikova I, Stierschneider M, Kopecky D, Homolka A, Burg K, Fluch S, Hausman JF, Wilhelm E (2012) Ecophysiological and transcriptomic responses of oak (Quercus robur) to long-term drought exposure and rewatering. Environ Exp Bot 77:117–126
248. Stasolla C, van Zyl L, Egertsdotter U, Craig D, Liu W, Sederoff RR (2003) The effects of polyethylene glycol on gene expression of developing white spruce somatic embryos. Plant Physiol 131:49–60
249. Stasolla C, Bozhkov PV, Chu TM, Van Zyl L, Egertsdotter U, Suarez MF, Craig D, Wolfinger RD, Von Arnold S, Sederoff RR (2004) Variation in transcript abundance during somatic embryogenesis in gymnosperms. Tree Physiol 24:1073–1085
250. Sterky F, Regan S, Karlsson J, Hertzberg M, Rohde A, Holmberg A, Amini B, Bhalerao R, Larsson M, Villaroel R, van Montagu M, Sandberg G, Olsson O, Teeri T, Boerjan W, Gustafsson P, Uhlen M, Sundberg B, Lundeberg J (1998) Gene discovery in the wood-forming tissues of poplar: analysis of 5,692 expressed sequence tags. Proc Natl Acad Sci USA 95:13330–13335
251. Stölting KN, Nipper R, Lindtke D, Caseys C, Waeber S, Castiglione S, Lexer C (2013) Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Mol Ecol 22:842–855
252. Stone GN, Nee S, Felsenstein J (2011) Controlling for non-independence in comparative analysis of patterns across populations within species. Phil T R Soc B 366:1410–1424
253. Street NR, Tallis MJ, Tucker J, Brosche M, Kangasjarvi J, Broadmeadow M, Taylor G (2011) The physiological, transcriptional and genetic responses of an ozone- sensitive and an ozone tolerant poplar and selected extremes of their F-2 progeny. Environ Pollut 159:45–54
254. Sturrock RN, Frankel SJ, Brown AV, Hennon PE, Kliejunas JT, Lewis KJ, Worrall JJ, Woods AJ (2011) Climate change and forest diseases. Plant Pathol 60:133–149
255. Teyssier C, Grondin C, Bonhomme L, Lomenech AM, Vallance M, Morabito D, Label P, Lelu-Walter MA (2011) Increased gelling agent concentration promotes somatic embryo maturation in hybrid larch (Larix x eurolepsis): a 2-DE proteomic analysis. Physiol Plant 141:152–165
256. Teyssier C, Maury S, Beaufour M, Grondin C, Delaunay A, Le Metté C, Ader K, Cadene M, Label P, Lelu-Walter M-A (2014) In search of markers for somatic embryo maturation in hybrid larch (Larix x eurolepis): global DNA methylation and proteomic analyses. Physiol Plant 150:271–291
257. Trontin J-F, Klimaszewska K, Morel A, Hargreaves C, Lelu-Walter M-A (2015). Molecular aspects of conifer zygotic and somatic embryo development: a review of genome-wide approaches and recent insights. In: In vitro plant embryogenesis in higher plants, Germanà MA, Lambardi M (eds), Methods in molecular biology, Springer-Humana Press (in press)
258. Turchetto-Zolet AC, Pinheiro F, Salgueiro F, Palma-Silva C (2013) Phylogeographical patterns shed light on evolutionary process in South America. Mol Ecol 22:1193–1213
259. Turner TR, James EK, Poole PS (2013) The plant microbiome. Genome Biol 14:209
260. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. and Gray). Science 313:1596–1604
261. Ueno S, KloppC LJC, Derory J, Noirot C, Leger V, Prince E, Kremer A, Plomion C, Le Provost G (2013) Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing. BMC Genomics 14:236–250
262. Uroz S, Buée M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288
263. van Acker R, Leplé JC, Aerts D, Storme V, Goeminne G, Ivens B, Piens K, Van Montagu M, Santoro N, Foster C, Ralph J, Soetaert W, Pilate G, Boerjan W (2014) Improved saccharification and ethanol yield from field-grown transgenic poplar deficient in cinnamoyl-CoA reductase. Proc Natl Acad Sci U S A 111:845–850
264. van der Merwe M, McPherson H, Siow J, Rossetto M (2014) Next-Gen phylogeography of rainforest trees: exploring landscape-level cpDNA variation from whole-genome sequencing. Mol Ecol Res 14:199–208
265. van Holme R, Morreel K, Darrah C, Oyarce P, Grabber JH, Ralph J, Boerjan W (2012a) Metabolic engineering of novel lignin in biomass crops. New Phytol 196:978–1000
266. van Holme R, Storme V, van Holme B, Sundin L, Christensen JH, Goeminne G, Halpin C, Rohde A, Morreel K, Boerjan W (2012b) A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis. Plant Cell 24:3506–3529
267. van Holme B, Cesarino I, Goeminne G, Kim H, Marroni F, van Acker R, van Holme R, Morreel K, Ivens B, Pinosio S, Morgante M, Ralph J, Bastien C, Boerjan W (2013) Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. New Phytol 198:765–776
268. Vanderschuren H, Lentz E, Zainuddin I, Gruissem W (2013) Proteomics of model and crop plant species: status, current limitations and strategic advances for crop improvement. J Proteomics 93:5–19
269. Veluthakkal R, Dasgupta MG (2010) Pathogenesis-related genes and proteins in forest tree species. Trees 24:993–1006
270. Vestman D, Larsson E, Uddenberg D, Cairney J, Clapham D, Sundberg E, von Arnold S (2011) Important processes during differentiation and early development of somatic embryos of Norway spruce as revealed by changes in global gene expression. Tree Genet Genomes 7:347–362
271. Villalobos DP, Díaz-Moreno SM, Said ES, Cañas RA, Osuna D, van Kerckhoven SHE, Bautista R, Claros MG, Cánovas FM, Cantón MR (2012) Reprogramming of gene expression during compression wood formation in pine: coordinated modulation of S-adenosylmethionine, lignin and lignan related genes. BMC Plant Biol 12:100
272. Villar E, Klopp C, Noirot C, Novaes E, Kirst M, Plomion C, Gion JM (2011) RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus. BMC Genomics 12:538
273. Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH (2012) Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics 13:27
274. Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH (2013) Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biol 13:92
275. Wachowiak W, Salmela MJ, Ennos RA, Iason G, Cavers S (2011) High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland. Heredity 106:775–787
276. Wang JP, Naik PP, Chen HC, Shi R, Lin CY, Liu J, Shuford CM, Li QZ, Sun YH, Tunlaya-Anukit S, Williams CM, Muddiman DC, Ducoste JJ, Sederoff RR, Chiang VL (2014a) Complete proteomic-based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic flux and lignin in Populus trichocarpa. Plant Cell 26:894–914
277. Wang S, Li E, Porth I, Chen J-G, Mansfield SD, Douglas CJ (2014b) Regulation of secondary cell wall biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in Arabidopsis. Sci Rep 4:05054
278. Warren C, Aranda I, Cano FJ (2012) Metabolomics demonstrates divergent responses of two Eucalyptus species to water stress. Metabolomics 8:186–200
279. 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
280. Wolfender JL, Rudaz S, Choi YH, Kim HK (2013) Plant metabolomics: from holistic data to relevant biomarkers. Curr Med Chem 20:1056–1090
281. Xi Z, Ruhfel BR, Schaefer H, Amorim AM, Sugumaran M, Wurdack KJ, Endress PK, Matthews ML, Stevens PF, Mathews S, Davis CC (2012) Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proc Natl Acad Sci U S A 109:17519–17524
282. Xiao X, Yang F, Zhang S, Korpelainen H, Li C (2009) Physiological and proteomic responses of two contrasting Populus cathayana populations to drought stress. Physiol Plant 136:150–168
283. Yakovlev IA, Fossdal CG, Johnsen O, Junttila O, Skroppa T (2006) Analysis of gene expression during bud burst initiation in Norway spruce via ESTs from subtracted cDNA libraries. Tree Genet Genomes 2:39–52
284. Yakovlev IA, Lee Y, Rotter B, Olsen JE, Skrøppa T, Johnsen Ø, Fossdal CG (2014) Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis. Tree Genet Genomes 10:355–366
285. Yamane H, Kashiwa Y, Ooka T, Tao R, Yonemori K (2008) Suppression subtractive hybridization and differential screening reveals endodormancy-associated expression of an SVP/AGL24-type MADS-box gene in lateral vegetative buds of Japanese apricot. J Am Soc Hortic Sci 133:708–716
286. Yang X, Ye C-Y, Bisaria A, Tuskan GA, Kalluri UC (2011) Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics. Plant Sci 181:675–687
287. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92
288. Yu H, Soler M, Mila I, San Clemente H, Savelli B, Dunand C, Jorge APP, Myburg A, Bouzayen M, Grima-Pettenati J, Cassan-Wang H (2014) Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF) gene family in Eucalyptus grandis. PLoS ONE 9:e108906
289. 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 8:1307–1318
290. Zapata-Valenzuela J, Whetten RW, Neale DB, McKeand SE, Isik F (2013) Genomic estimated breeding values using genomic relationship matrices in a cloned population of loblolly pine. Genes Genomes Genet 3:909–916
291. Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol 153:1479–1491
292. Zhang J, Zhang S, Han S, Wu T, Li X, Li W, Qi L (2012a) Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis. Planta 236:647–657
293. Zhang Y, Zhang S, Han S, Li X, Qi L (2012b) Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). Plant Cell Rep 31:1637–1657
294. Zhao Q, Nakashima J, Chen F, Yin Y, Fu C, Yun J, Shao H, Wang X, Wang ZY, Dixon RA (2013a) Laccase is necessary and nonredundant with peroxidase for lignin polymerization during vascular development in Arabidopsis. Plant Cell 25:3976–3987
295. Zhao YJ, Song DL, Sun JY, Li LG (2013b) Populus endo-beta-mannanase PtrMAN6 plays a role in coordinating cell wall remodeling with suppression of secondary wall thickening through generation of oligosaccharide signals. Plant J 74:473–485
296. Zhong R, McCarthy RL, Lee C, Ye ZH (2011) Dissection of the transcriptional program regulating secondary wall biosynthesis during wood formation in poplar. Plant Physiol 157:1452–1468
297. Zhu Y, Song D, Sun J, Wang X, Li L (2013a) PtrHB7, a class III HD-Zip gene, plays a critical role in regulation of vascular cambium differentiation in Populus. Mol Plant 6:1331–1343
298. Zhu R, Shevchenko O, Ma C, Maury S, Freitag M, Strauss SH (2013b) Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology. Planta 237:1483–1493
299. Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marcais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH (2014) Sequencing and assembly of the 22-gb loblolly pine genome. Genetics 196:875–890