메뉴 건너뛰기




Volumn 200, Issue 3, 2013, Pages 727-742

Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions

Author keywords

Network analysis; Phenotype prediction; Populus trichocarpa; Single nucleotide polymorphisms (SNPs); Transcriptomics; Wood chemistry; Wood density; Wood properties

Indexed keywords

BAYESIAN ANALYSIS; DECIDUOUS TREE; GENE EXPRESSION; GENOTYPE; NETWORK ANALYSIS; PHENOTYPE; SELECTION; ULTRASTRUCTURE; WOOD;

EID: 84885421928     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.12419     Document Type: Article
Times cited : (29)

References (59)
  • 2
    • 84870724279 scopus 로고    scopus 로고
    • Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks
    • Bassel GW, Gaudinier A, Brady SM, Hennig L, Rhee SY, De Smet I. 2012. Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 24: 3859-3875.
    • (2012) Plant Cell , vol.24 , pp. 3859-3875
    • Bassel, G.W.1    Gaudinier, A.2    Brady, S.M.3    Hennig, L.4    Rhee, S.Y.5    De Smet, I.6
  • 4
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. 2001. Random forests. Machine Learning 45: 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 7
    • 57749102574 scopus 로고    scopus 로고
    • Perturbed lignification impacts tree growth in hybrid Poplar-A function of sink strength, vascular integrity, and photosynthetic assimilation
    • Coleman HD, Samuels AL, Guy RD, Mansfield SD. 2008. Perturbed lignification impacts tree growth in hybrid Poplar-A function of sink strength, vascular integrity, and photosynthetic assimilation. Plant Physiology 148: 1229-1237.
    • (2008) Plant Physiology , vol.148 , pp. 1229-1237
    • Coleman, H.D.1    Samuels, A.L.2    Guy, R.D.3    Mansfield, S.D.4
  • 9
    • 30644464444 scopus 로고    scopus 로고
    • Gene selection and classification of microarray data using random forest
    • Diaz-Uriarte R, de Andres SA. 2006. Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7: 3.
    • (2006) BMC Bioinformatics , vol.7 , pp. 3
    • Diaz-Uriarte, R.1    de Andres, S.A.2
  • 10
    • 84885425911 scopus 로고    scopus 로고
    • Genetic modification of short rotation poplar biomass feedstock for efficient conversion to ethanol: bioenergy feedstock development program, environmental sciences division
    • Dinus RJ. 2000. Genetic modification of short rotation poplar biomass feedstock for efficient conversion to ethanol: bioenergy feedstock development program, environmental sciences division. Oak Ridge National Laboratory 6: 7.
    • (2000) Oak Ridge National Laboratory , vol.6 , pp. 7
    • Dinus, R.J.1
  • 12
    • 34547788797 scopus 로고    scopus 로고
    • Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks
    • Ferrazzi F, Sebastiani P, Ramoni MF, Bellazzi R. 2007. Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks. BMC Bioinformatics 8: S2.
    • (2007) BMC Bioinformatics , vol.8
    • Ferrazzi, F.1    Sebastiani, P.2    Ramoni, M.F.3    Bellazzi, R.4
  • 20
    • 79551537130 scopus 로고    scopus 로고
    • Association genetics of complex traits in plants
    • Ingvarsson PK, Street NR. 2011. Association genetics of complex traits in plants. New Phytologist 189: 909-922.
    • (2011) New Phytologist , vol.189 , pp. 909-922
    • Ingvarsson, P.K.1    Street, N.R.2
  • 21
    • 0034046157 scopus 로고    scopus 로고
    • Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis
    • Kawaoka A, Kaothien P, Yoshida K, Endo S, Yamada K, Ebinuma H. 2000. Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis. Plant Journal 22: 289-301.
    • (2000) Plant Journal , vol.22 , pp. 289-301
    • Kawaoka, A.1    Kaothien, P.2    Yoshida, K.3    Endo, S.4    Yamada, K.5    Ebinuma, H.6
  • 22
    • 4444335600 scopus 로고    scopus 로고
    • Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus
    • Kirst M, Myburg AA, De Leon JPG, Kirst ME, Scott J, Sederoff R. 2004. Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus. Plant Physiology 135: 2368-2378.
    • (2004) Plant Physiology , vol.135 , pp. 2368-2378
    • Kirst, M.1    Myburg, A.A.2    De Leon, J.P.G.3    Kirst, M.E.4    Scott, J.5    Sederoff, R.6
  • 23
    • 77957741379 scopus 로고    scopus 로고
    • Tyloses and phenolic deposits in xylem vessels impede water transport in low-lignin transgenic poplars: a study by cryo-fluorescence microscopy
    • Kitin P, Voelker SL, Meinzer FC, Beeckman H, Strauss SH, Lachenbruch B. 2010. Tyloses and phenolic deposits in xylem vessels impede water transport in low-lignin transgenic poplars: a study by cryo-fluorescence microscopy. Plant Physiology 154: 887-898.
    • (2010) Plant Physiology , vol.154 , pp. 887-898
    • Kitin, P.1    Voelker, S.L.2    Meinzer, F.C.3    Beeckman, H.4    Strauss, S.H.5    Lachenbruch, B.6
  • 24
    • 37849044667 scopus 로고    scopus 로고
    • Downregulation of cinnamoyl-coenzyme a reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure
    • Leple J-C, Dauwe R, Morreel K, Storme V, Lapierre C, Pollet B, Naumann A, Kang K-Y, Kim H, Ruel K et al. 2007. Downregulation of cinnamoyl-coenzyme a reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell 19: 3669-3691.
    • (2007) Plant Cell , vol.19 , pp. 3669-3691
    • Leple, J.-C.1    Dauwe, R.2    Morreel, K.3    Storme, V.4    Lapierre, C.5    Pollet, B.6    Naumann, A.7    Kang, K.-Y.8    Kim, H.9    Ruel, K.10
  • 26
    • 80053350637 scopus 로고    scopus 로고
    • Transcriptome profiling of Pinus radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics
    • Li X, Wu HX, Southerton SG. 2011. Transcriptome profiling of Pinus radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics. BMC Genomics 12: 480.
    • (2011) BMC Genomics , vol.12 , pp. 480
    • Li, X.1    Wu, H.X.2    Southerton, S.G.3
  • 27
    • 84865171132 scopus 로고    scopus 로고
    • Identification of putative candidate genes for juvenile wood density in Pinus radiata
    • Li X, Wu HX, Southerton SG. 2012. Identification of putative candidate genes for juvenile wood density in Pinus radiata. Tree Physiology 32: 1046-1057.
    • (2012) Tree Physiology , vol.32 , pp. 1046-1057
    • Li, X.1    Wu, H.X.2    Southerton, S.G.3
  • 28
    • 25444453244 scopus 로고    scopus 로고
    • Screening large-scale association study data: exploiting interactions using random forests
    • Lunetta KL, Hayward LB, Segal J, Van Eerdewegh P. 2004. Screening large-scale association study data: exploiting interactions using random forests. BMC Genetics 5: 32.
    • (2004) BMC Genetics , vol.5 , pp. 32
    • Lunetta, K.L.1    Hayward, L.B.2    Segal, J.3    Van Eerdewegh, P.4
  • 29
    • 35948931439 scopus 로고    scopus 로고
    • An Arabidopsis gene network based on the graphical Gaussian model
    • Ma S, Gong Q, Bohnert HJ. 2007. An Arabidopsis gene network based on the graphical Gaussian model. Genome Research 17: 1614-1625.
    • (2007) Genome Research , vol.17 , pp. 1614-1625
    • Ma, S.1    Gong, Q.2    Bohnert, H.J.3
  • 30
  • 32
    • 78751550555 scopus 로고    scopus 로고
    • Forest tree genomics: growing resources and applications
    • Neale DB, Kremer A. 2011. Forest tree genomics: growing resources and applications. Nature Reviews Genetics 12: 111-122.
    • (2011) Nature Reviews Genetics , vol.12 , pp. 111-122
    • Neale, D.B.1    Kremer, A.2
  • 35
    • 36248982734 scopus 로고    scopus 로고
    • Differential expansion and expression of alpha- and beta-tubulin gene families in Populus
    • Oakley RV, Wang Y-S, Ramakrishna W, Harding SA, Tsai C-J. 2007. Differential expansion and expression of alpha- and beta-tubulin gene families in Populus. Plant Physiology 145: 961-973.
    • (2007) Plant Physiology , vol.145 , pp. 961-973
    • Oakley, R.V.1    Wang, Y.-S.2    Ramakrishna, W.3    Harding, S.A.4    Tsai, C.-J.5
  • 39
    • 83455186445 scopus 로고    scopus 로고
    • Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway
    • Porth I, Hamberger B, White R, Ritland K. 2011. Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway. BMC Genomics 12: 608.
    • (2011) BMC Genomics , vol.12 , pp. 608
    • Porth, I.1    Hamberger, B.2    White, R.3    Ritland, K.4
  • 42
    • 84866045433 scopus 로고    scopus 로고
    • Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce
    • Porth I, White R, Jaquish B, Alfaro R, Ritland C, Ritland K. 2012. Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce. PLoS ONE 7: e44397.
    • (2012) PLoS ONE , vol.7
    • Porth, I.1    White, R.2    Jaquish, B.3    Alfaro, R.4    Ritland, C.5    Ritland, K.6
  • 45
    • 4544352472 scopus 로고    scopus 로고
    • A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity
    • Schrader J, Nilsson J, Mellerowicz E, Berglund A, Nilsson P, Hertzberg M, Sandberg G. 2004. A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. Plant Cell 16: 2278-2292.
    • (2004) Plant Cell , vol.16 , pp. 2278-2292
    • Schrader, J.1    Nilsson, J.2    Mellerowicz, E.3    Berglund, A.4    Nilsson, P.5    Hertzberg, M.6    Sandberg, G.7
  • 48
    • 72449203628 scopus 로고    scopus 로고
    • Identification of a cis-acting regulatory polymorphism in a Eucalypt COBRA-like gene affecting cellulose content
    • 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: 1153-1164.
    • (2009) Genetics , vol.183 , pp. 1153-1164
    • Thumma, B.R.1    Matheson, B.A.2    Zhang, D.3    Meeske, C.4    Meder, R.5    Downes, G.M.6    Southerton, S.G.7
  • 54
    • 79952531450 scopus 로고    scopus 로고
    • Transgenic poplars with reduced lignin show impaired xylem conductivity, growth efficiency and survival
    • Voelker SL, Lachenbruch B, Meinzer FC, Kitin P, Strauss SH. 2011. Transgenic poplars with reduced lignin show impaired xylem conductivity, growth efficiency and survival. Plant, Cell & Environment 34: 655-668.
    • (2011) Plant, Cell & Environment , vol.34 , pp. 655-668
    • Voelker, S.L.1    Lachenbruch, B.2    Meinzer, F.C.3    Kitin, P.4    Strauss, S.H.5
  • 55
    • 84859148157 scopus 로고    scopus 로고
    • On-off switches for secondary cell wall biosynthesis
    • Wang H-Z, Dixon RA. 2012. On-off switches for secondary cell wall biosynthesis. Molecular Plant 5: 297-303.
    • (2012) Molecular Plant , vol.5 , pp. 297-303
    • Wang, H.-Z.1    Dixon, R.A.2
  • 56
    • 77957107435 scopus 로고    scopus 로고
    • Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem
    • 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: 515-532.
    • (2010) New Phytologist , vol.188 , pp. 515-532
    • Wegrzyn, J.L.1    Eckert, A.J.2    Choi, M.3    Lee, J.M.4    Stanton, B.J.5    Sykes, R.6    Davis, M.F.7    Tsai, C.-J.8    Neale, D.B.9
  • 57
    • 84865139666 scopus 로고    scopus 로고
    • Synbreed: a framework for the analysis of genomic prediction data using R
    • Wimmer V, Albrecht T, Auinger HJ, Schön CC. 2012. Synbreed: a framework for the analysis of genomic prediction data using R. Bioinformatics 28: 2086-2087.
    • (2012) Bioinformatics , vol.28 , pp. 2086-2087
    • Wimmer, V.1    Albrecht, T.2    Auinger, H.J.3    Schön, C.C.4
  • 58
    • 64849086371 scopus 로고    scopus 로고
    • Ecotypic mode of regional differentiation caused by restricted gene migration: a case in black cottonwood (Populus trichocarpa) along the Pacific Northwest coast
    • 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 39: 519-526.
    • (2009) Canadian Journal of Forest Research , vol.39 , pp. 519-526
    • Xie, C.-Y.1    Ying, C.C.2    Yanchuk, A.D.3    Holowachuk, D.L.4
  • 59
    • 26944468704 scopus 로고    scopus 로고
    • The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl
    • Zhao CS, Craig JC, Petzold HE, Dickerman AW, Beers EP. 2005. The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl. Plant Physiology 138: 803-818.
    • (2005) Plant Physiology , vol.138 , pp. 803-818
    • Zhao, C.S.1    Craig, J.C.2    Petzold, H.E.3    Dickerman, A.W.4    Beers, E.P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.