M. Adli, The CRISPR Tool Kit for Genome Editing and Beyond, Nature Communications, vol.9, issue.1, p.1911, 2018.

E. Afgan, D. Baker, B. Batut, M. Van-den, D. Beek et al., The Galaxy Platform for Accessible, Reproducible and Collaborative Biomedical Analyses, vol.46, pp.537-581, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01360125

,

T. Agarwal, E. Grotewold, A. I. Doseff, and J. Gray, , 2016.

, Syntelogs Exhibit Divergent Regulation of Phenylpropanoid Genes in Maize , Sorghum and Rice

G. Agati, E. Azzarello, S. Pollastri, and M. Tattini, Flavonoids as Antioxidants in Plants: Location and Functional Significance, Plant Science, vol.196, pp.67-76, 2012.

A. Aharoni, S. Dixit, R. Jetter, E. Thoenes, G. Van-arkel et al., The SHINE Clade of AP2 Domain Transcription Factors Activates Wax Biosynthesis, Alters Cuticle Properties, and Confers Drought Tolerance When Overexpressed in Arabidopsis, The Plant Cell, vol.16, issue.9, pp.2463-80, 2004.

R. Ahmed, A. Imtiaz, M. Ding, Y. Xie, and . Kong, Progress in Optimization of Agrobacterium-Mediated Transformation in Sorghum (Sorghum Bicolor), International Journal of Molecular Sciences, vol.19, issue.10, 2018.

M. Aida, H. Ishida, H. Fukaki, M. Fujisawa, and . Tasaka, Genes Involved in Organ Separation in Arabidopsis: An Analysis of the Cup-Shaped Cotyledon Mutant, The Plant Cell, vol.9, issue.6, pp.841-57, 1997.

C. Albenne, H. Canut, G. Boudart, Y. Zhang, R. Hélène-san-clemente et al., Plant Cell Wall Proteomics: Mass Spectrometry Data, 2009.

, Trove for Research on Protein Structure/Function Relationships, Molecular Plant, vol.2, issue.5, pp.977-89

C. Albenne, H. Canut, L. Hoffmann, and E. Jamet, Plant Cell Wall Proteins: A Large Body of Data, but What about Runaways?, Proteomes, vol.2, issue.2, pp.224-266, 2014.

,

P. Albersheim, A. Darvill, K. Roberts, R. Sederoff, and A. Staehelin, Plant Cell Walls, from Chemistry to Biology, Garland Science, pp.227-272, 2011.

A. A. Rahnenfuhrer and J. , topGO: Enrichment Analysis for Gene Ontology, 2019.

A. Almodares and M. R. Hadi, Production of Bioethanol from Sweet Sorghum: A Review, African Journal of Agricultural Research, vol.4, issue.9, pp.772-80, 2009.

. Altpeter, N. M. Fredy, L. E. Springer, A. E. Bartley, T. P. Blechl et al., Advancing Crop Transformation in the Era of Genome Editing, Plant Cell, vol.28, issue.7, pp.1510-1530, 2016.

A. Kaur and S. Kumar-sah, Genetic Transformation of Rice: Problems, Progress and Prospects, Rice Research: Open Access, vol.03, issue.01, pp.1-10, 2014.

P. An, X. Li, Y. Zheng, A. Matsuura, J. Abe et al., Effects of NaCl on Root Growth and Cell Wall Composition of Two Soya Bean Cultivars with Contrasting Salt Tolerance, Journal of Agronomy and Crop Science, vol.200, issue.3, pp.212-230, 2014.

,

S. Anami and E. Njuguna, Higher Plant Transformation: Principles and Molecular Tools, International Journal of Developmental Biology, vol.57, issue.6-8, pp.483-94, 2013.

M. C. Andersen, Synthesis and Application of Plant Cell Wall Oligogalactans, 2014.

S. Andrews, FastQC: A Quality Control Tool for High Throughput Sequence Data, 2010.

C. Armstrong, . Williaml, W. Petersen, . Buchholz, . Benjamina et al., Factors Affecting PEG-Mediated Stable Transformation of Maize Protoplasts, Plant Cell Reports, vol.9, issue.6, 1990.

T. Asai, G. Tena, J. Plotnikova, M. R. Willmann, W. Chiu et al., MAP Kinase Signalling Cascade in Arabidopsis Innate Immunity, Nature, vol.415, issue.6875, pp.977-83, 2002.

,

J. Aufrère, R. Baumont, L. Delaby, J. R. Peccatte, J. Andrieu et al., Prévision de La Digestibilité Des Fourrages Par La Méthode Pepsine-Cellulase. Le Point Sur Les Équations Proposées, Productions Animales, vol.20, issue.2, pp.129-165, 2007.

S. Bae, J. Kweon, H. Kim, and J. Kim, Microhomology-Based Choice of Cas9 Nuclease Target Sites, Nature Methods, vol.11, issue.7, pp.705-711, 2014.

,

S. Balazadeh, H. Siddiqui, A. D. Allu, L. P. Matallana-ramirez, C. Caldana et al., A Gene Regulatory Network Controlled by the NAC Transcription Factor ANAC092/AtNAC2/ORE1 during Salt-Promoted Senescence, The Plant Journal, vol.62, issue.2, pp.250-64, 2010.

R. Barrangou, C. Fremaux, H. Deveau, M. Richards, P. Boyaval et al.,

. Horvath, CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes, Science, vol.315, issue.5819, pp.1709-1721, 2007.

J. Barros, L. Escamilla-trevino, L. Song, X. Rao, J. C. Serrani-yarce et al., 4-Coumarate 3-Hydroxylase in the Lignin Biosynthesis Pathway Is a Cytosolic Ascorbate Peroxidase, Nature Communications, vol.10, issue.1, pp.1-11, 2019.

J. Barros, H. Serk, I. Granlund, and E. Pesquet, The Cell Biology of Lignification in Higher Plants, Annals of Botany, vol.115, issue.7, pp.1053-74, 2015.

,

L. Bashline, L. Lei, S. Li, and Y. Gu, Cell Wall, Cytoskeleton, and Cell Expansion in Higher Plants, Molecular Plant, vol.7, issue.4, pp.586-600, 2014.

,

M. Battraw and T. C. Hall, Stable Transformation of Sorghum Bicolor Protoplasts with Chimeric Neomycin Phosphotransferase II and ?-Glucuronidase Genes, Theoretical and Applied Genetics, vol.82, issue.2, pp.161-68, 1991.

C. H. Beckman, Phenolic-Storing Cells: Keys to Programmed Cell Death and Periderm Formation in Wilt Disease Resistance and in General Defence Responses in Plants, Physiological and Molecular Plant Pathology, vol.57, issue.3, pp.101-111, 2000.

,

S. Belide, T. Vanhercke, J. R. Petrie, and S. Singh, Robust Genetic Transformation of Sorghum (Sorghum Bicolor L.) Using Differentiating Embryogenic Callus Induced from Immature Embryos, Plant Methods, vol.13, issue.1, pp.1-12, 2017.

,

J. L. Bennetzen and M. Chen, Grass Genomic Synteny Illuminates Plant Genome Function and Evolution, Rice, vol.1, issue.2, pp.109-127, 2008.

S. Berthet, N. Demont-caulet, B. Pollet, P. Bidzinski, L. Cézard et al., Disruption of LACCASE4 and 17 Results in Tissue-Specific Alterations to Lignification of Arabidopsis Thaliana Stems, The Plant Cell, vol.23, issue.3, pp.1124-1161, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000145

. Bhargava, S. D. Apurva, . Mansfield, C. Hardy, C. J. Hall et al., MYB75 Functions in Regulation of Secondary Cell Wall Formation in the Arabidopsis Inflorescence Stem, Plant Physiology, vol.154, issue.3, pp.1428-1466, 2010.

R. Bhatia, S. Dalton, L. A. Roberts, O. M. Moron-garcia, R. Iacono et al., Modified Expression of ZmMYB167 in Brachypodium Distachyon and Zea Mays Leads to Increased Cell Wall Lignin and Phenolic Content, Scientific Reports, vol.9, issue.1, p.8800, 2019.

S. S. Bhojwani and M. K. Razdan, Plant Tissue Culture : Plant Tissue Culture, 1996.

N. H. Bhuiyan, G. Selvaraj, Y. Wei, and J. King, Gene Expression Profiling and Silencing Reveal That Monolignol Biosynthesis Plays a Critical Role in Penetration Defence in Wheat against Powdery Mildew Invasion, Journal of Experimental Botany, vol.60, issue.2, pp.509-530, 2009.

,

M. Bibikova, D. Carroll, D. J. Segal, J. K. Trautman, J. Smith et al., Stimulation of Homologous Recombination through Targeted Cleavage by Chimeric Nucleases, Molecular and Cellular Biology, vol.21, issue.1, pp.289-97, 2001.

,

C. Billot, P. Ramu, S. Bouchet, J. Chantereau, M. Deu et al., Massive Sorghum Collection Genotyped with SSR Markers to Enhance Use of Global Genetic Resources, PLoS ONE, vol.8, issue.4, pp.1-16, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01595265

,

A. K. Biswal, Z. Hao, S. Pattathil, X. Yang, K. Winkeler et al., Downregulation of GAUT12 in Populus Deltoides by RNA Silencing Results in Reduced Recalcitrance, Increased Growth and Reduced Xylan and Pectin in a Woody Biofuel Feedstock, Biotechnology for Biofuels, vol.8, issue.1, p.41, 2015.

M. Block, D. D. De, P. Brouwer, and . Tenning, Transformation of Brassica Napus and Brassica Oleracea Using Agrobacterium Tumefaciens and the Expression of the Bar and Neo Genes in the Transgenic Plants, Plant Physiology, vol.91, issue.2, pp.694-701, 1989.

,

M. Block, L. De, M. Herrera-estrella, J. Van-montagu, P. Schelil et al., Regenerated Plants And, vol.3, pp.1681-89, 1984.

J. Boch, H. Scholze, S. Schornack, A. Landgraf, S. Hahn et al., Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors, Science, vol.326, issue.5959, pp.1509-1521, 2009.

W. Boerjan, J. Ralph, and M. Baucher, Lignin Biosynthesis, Annual Review of Plant Biology, vol.54, issue.1, pp.519-565, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02766568

N. D. Bonawitz and C. C. , The Genetics of Lignin Biosynthesis: Connecting Genotype to Phenotype, Annual Review of Genetics, vol.44, issue.1, pp.337-63, 2010.

,

M. Bosch, C. Mayer, A. Cookson, and I. S. Donnison, Identification of Genes Involved in Cell Wall Biogenesis in Grasses by Differential Gene Expression Profiling of Elongating and Non-Elongating Maize Internodes, Journal of Experimental Botany, vol.62, issue.10, pp.3545-61, 2011.

A. Brandt, J. Gräsvik, J. P. Hallett, and T. Welton, Deconstruction of Lignocellulosic Biomass with Ionic Liquids, Green Chemistry, vol.15, issue.3, p.550, 2013.

Z. W. Brenton, E. A. Cooper, T. Mathew, R. E. Myers, N. Boyles et al., A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy The Designation of a Functional Model Grass Species and The, vol.204, pp.21-33, 2016.

C. Brett and K. Waldron, The Cell Wall and Intercellular Transport, Physiology and Biochemistry of Plant Cell Walls, pp.114-150, 1990.

,

D. M. Brown, Z. Zhang, E. Stephens, P. Dupree, and S. R. Turner, Characterization of IRX10 and IRX10-like Reveals an Essential Role in Glucuronoxylan Biosynthesis in Arabidopsis, The Plant Journal, vol.57, issue.4, pp.732-778, 2009.

R. Brown and . Malcolm, The Biosynthesis of Cellulose, Journal of Macromolecular Science, Part A, vol.33, issue.10, pp.1345-73, 1996.

P. S. Burks, C. M. Kaiser, E. M. Hawkins, and P. J. Brown, Genomewide Association for Sugar Yield in Sweet Sorghum, Crop Science, vol.55, issue.5, p.2138, 2015.

,

S. J. Burr and S. C. Fry, Extracellular Cross-Linking of Maize Arabinoxylans by Oxidation of Feruloyl Esters to Form Oligoferuloyl Esters and Ether-like Bonds, The Plant Journal, vol.58, issue.4, pp.554-67, 2009.

K. P. Burris, M. Elizabeth, A. G. Dlugosz, C. Collins, S. C. Stewart et al., Development of a Rapid, Low-Cost Protoplast Transfection System for Switchgrass (Panicum Virgatum L.), Plant Cell Reports, vol.35, issue.3, pp.693-704, 2016.

R. A. Burton, Cellulose Synthase-Like CslF Genes Mediate the Synthesis of Cell Wall (1,3;1,4)--D-Glucans, Science, vol.311, issue.5769, pp.1940-1982, 2006.

R. A. Burton, J. Michael, G. B. Gidley, and . Fincher, Heterogeneity in the Chemistry, Structure and Function of Plant Cell Walls, Nature Chemical Biology, vol.6, issue.10, pp.724-756, 2010.

. Busse-wicher, . Marta, C. F. Thiago, T. Gomes, N. Tryfona et al., The Pattern of, 2014.

, Xylan Acetylation Suggests Xylan May Interact with Cellulose Microfibrils as a Twofold Helical Screw in the Secondary Plant Cell Wall of Arabidopsis Thaliana, The Plant Journal, vol.79, issue.3, pp.492-506

D. R. Buxton and D. D. Redfearn, Plant Limitations to Fiber Digestion and Utilization, The Journal of Nutrition, vol.127, issue.5, pp.814-818, 1997.

K. Caffall, D. Hosmer, and . Mohnen, The Structure, Function, and Biosynthesis of Plant Cell Wall Pectic Polysaccharides, Carbohydrate Research, vol.344, issue.14, pp.1879-1900, 2009.

,

. Cai, C. Bin, J. Hui-li, and . Huang, Systematic Identification of Cell-Wall Related Genes in Populus Based on Analysis of Functional Modules in Co-Expression Network, PLoS ONE, vol.9, issue.4, 2014.

Z. Cai, H. Nakajima, M. Woldu, A. Berglund, M. Bergman et al., In Vitro Corrosion Resistance of Titanium Made Using Different Fabrication Methods, Biomaterials, vol.20, issue.2, pp.183-90, 1999.

D. Cantu, A. R. Vicente, J. M. Labavitch, A. B. Bennett, and A. L. Powell, Strangers in the Matrix: Plant Cell Walls and Pathogen Susceptibility, Trends in Plant Science, vol.13, issue.11, pp.610-627, 2008.

J. Cao, D. Yao, F. Lin, and M. Jiang, PEG-Mediated Transient Gene Expression and Silencing System in Maize Mesophyll Protoplasts: A Valuable Tool for Signal Transduction Study in Maize, Acta Physiologiae Plantarum, vol.36, issue.5, pp.1271-81, 2014.

,

. Capella-gutiérrez, J. M. Salvador, T. Silla-martínez, and . Gabaldón, TrimAl: A Tool for Automated Alignment Trimming in Large-Scale Phylogenetic Analyses, Bioinformatics, vol.25, issue.15, pp.1972-73, 2009.

. Cassan-wang, N. Hua, M. N. Goué, S. Saidi, P. Legay et al., Identification of Novel Transcription Factors Regulating Secondary Cell Wall Formation in Arabidopsis, Frontiers in Plant Science, vol.4, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01565043

A. L. Casto, A. Brian, K. M. Mckinley, J. Yu, W. L. Rooney et al., Sorghum Stem Aerenchyma Formation Is Regulated by SbNAC_D during Internode Development, Plant Direct, vol.2, issue.11, p.85, 2018.

M. Chan, H. Chang, S. Ho, W. Tong, and S. Yu, Agrobacterium-Mediated Production of Transgenic Rice Plants Expressing a Chimeric ?-Amylase Promoter/?-Glucuronidase Gene, Plant Molecular Biology, vol.22, issue.3, pp.491-506, 1993.

,

J. Chantereau and C. Kondombo, Estimation du taux d'allogamie chez les sorghos de la race guinea, Progress food grain research and production in semi-arid Africa, pp.309-313, 1994.

J. Chantereau, J. F. Cruz, A. Ratnadass, and G. Et-trouche, Le sorgho, Versailles-Gembloux, Éditions Quae-Presses agronomiques de Gembloux, « Agricultures tropicales en poche, vol.245, 2013.

S. Char, J. Nian, Q. Wei, X. Mu, Z. J. Li et al., An Agrobacterium -delivered CRISPR /Cas9 System for Targeted Mutagenesis in Sorghum, Plant Biotechnology Journal, pp.1-3, 2019.

H. Chauhan and P. Khurana, Wheat Genetic Transformation Using Mature Embryos as Explants, In Methods in Molecular Biology, pp.153-67, 2017.

S. Chaw, C. Chang, H. Chen, and W. Li, Dating the Monocot?Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes, Journal of Molecular Evolution, vol.58, issue.4, pp.424-465, 2004.

P. Che, A. Anand, E. Wu, J. D. Sander, M. K. Simon et al.,

. Sigmund, Developing a Flexible, High-Efficiency Agrobacterium-Mediated Sorghum Transformation System with Broad Application, Plant Biotechnology Journal, vol.16, issue.7, pp.1388-95, 2018.

J. Chen, Q. Yi, Q. Song, Y. Gu, J. Zhang et al., A Highly Efficient Maize Nucellus Protoplast System for Transient Gene Expression and Studying Programmed Cell Death-Related Processes, Plant Cell Reports, vol.34, issue.7, pp.1239-51, 2015.

K. Chen, Y. Wang, R. Zhang, H. Zhang, and C. Gao, CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture, Annual Review of Plant Biology, vol.70, issue.1, pp.667-97, 2019.

L. Chen, S. Zhang, R. N. Beachy, and C. M. Fauquet, A Protocol for Consistent, Large-Scale Production of Fertile Transgenic Rice Plants, Plant Cell Reports, vol.18, issue.1-2, pp.25-31, 1998.

,

S. Chen, L. Tao, L. Zeng, M. E. Vega-sanchez, K. Umemura et al., A Highly Efficient Transient Protoplast System for Analyzing Defence Gene Expression and Protein-Protein Interactions in Rice, Molecular Plant Pathology, vol.7, issue.5, pp.417-444, 2006.

,

D. Chiniquy, V. Sharma, A. Schultink, E. E. Baidoo, C. Rautengarten et al., XAX1 from Glycosyltransferase Family 61 Mediates Xylosyltransfer to Rice Xylan, Proceedings of the National Academy of Sciences, vol.109, issue.42, pp.17117-17139, 2012.

,

V. Chinnusamy, J. Zhu, and J. Zhu, Cold Stress Regulation of Gene Expression in Plants, Trends in Plant Science, vol.12, issue.10, pp.444-51, 2007.

,

H. T. Cho and H. Kende, Expression of Expansin Genes Is Correlated with Growth in Deepwater Rice, The Plant Cell, vol.9, issue.9, pp.1661-71, 1997.

P. Chomzynski and N. Sacchi, Single-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction, Analytical Biochemistry, vol.162, issue.1, pp.156-59, 1987.

,

A. H. Christensen and P. Quail, Ubiquitin Promoter-Based Vectors for High-Level Expression of Selectable and/or Screenable Marker Genes in Monocotyledonous Plants, Transgenic Research, vol.5, issue.3, pp.213-231, 1996.

P. Christou, Genetic Transformation of Crop Plants Using Microprojectile Bombardment, The Plant Journal, vol.2, issue.3, pp.275-81, 1992.

M. Cleene, J. De, and . Ley, The Host Range of Crown Gall, The Botanical Review, vol.42, issue.4, pp.389-466, 1976.

B. Clerget, . Dingkuhn, . Chantereau, G. Hemberger, M. Louarn et al., Does Panicle Initiation in Tropical Sorghum Depend on Day-to-Day Change in Photoperiod?, Field Crops Research, vol.88, issue.1, pp.21-37, 2004.

S. J. Clough and A. F. Bent, Floral Dip: A Simplified Method for Agrobacterium-Mediated Transformation of Arabidopsis Thaliana, Plant Journal, vol.16, issue.6, pp.735-778, 1998.

,

E. C. Cocking, Protoplasts from Root Hairs of Crop Plants, Nature Biotechnology, vol.3, issue.12, pp.1104-1110, 1985.

K. C. Cone, M. Suzy, F. A. Cocciolone, B. Burr, and . Burr, Maize Anthocyanin Regulatory Gene Pl Is a Duplicate of C1 That Functions in the Plant, The Plant Cell, vol.5, issue.12, p.1795, 1993.

M. P. Corcoran, D. L. Mckay, and J. B. Blumberg, Flavonoid Basics: Chemistry, Sources, Mechanisms of Action, and Safety, Journal of Nutrition in Gerontology and Geriatrics, vol.31, issue.3, pp.176-89, 2012.

M. Cornejo, D. Luth, K. M. Blankenship, O. D. Anderson, and A. E. Blechl, Activity of a Maize Ubiquitin Promoter in Transgenic Rice, Plant Molecular Biology, vol.23, issue.3, pp.567-81, 1993.

D. J. Cosgrove, Assembly and enlargement of the primary cell wall in plants, Annual Review of Cell and Developmental Biology, vol.13, issue.1, pp.171-201, 1997.

,

D. J. Cosgrove, Loosening of Plant Cell Walls by Expansins, Nature, vol.407, issue.6802, pp.321-347, 2000.

D. J. Cosgrove, Plant Cell Wall Extensibility: Connecting Plant Cell Growth with Cell Wall Structure, Mechanics, and the Action of Wall-Modifying Enzymes, Journal of Experimental Botany, vol.67, issue.2, pp.463-76, 2016.

D. J. Cosgrove, Diffuse Growth of Plant Cell Walls, Plant Physiology, vol.176, issue.1, pp.16-27, 2018.

F. Daayf, A. E. Hadrami, A. F. El-bebany, M. A. Henriquez, Z. Yao et al., Phenolic Compounds in Plant Defense and Pathogen Counter-Defense Mechanisms, Recent Advances in Polyphenol Research, pp.191-208, 2012.

S. Dai, P. Zheng, P. Marmey, S. Zhang, W. Tian et al., Comparative Analysis of Transgenic Rice Plants Obtained by Agrobacterium-Mediated Transformation and Particle Bombardment, Molecular Breeding, vol.7, issue.1, pp.25-33, 2001.

S. J. Dalton, Plant Regeneration from Cell Suspension Protoplasts of Festuca Arundinacea Schreb. (Tall Fescue) and Lolium Perenne L. (Perennial Ryegrass), Journal of Plant Physiology, vol.132, issue.2, pp.80156-80157, 1988.

S. Dam, U. Van, A. Võsa, L. Van-der-graaf, J. Franke et al., Gene Co-Expression Analysis for Functional Classification and Gene-Disease Predictions, Briefings in Bioinformatics, vol.19, issue.4, pp.575-92, 2018.

M. R. Davey, J. B. Anthony, K. C. Power, and . Lowe, Plant Protoplasts: Status and Biotechnological Perspectives, Biotechnology Advances, vol.23, issue.2, pp.131-71, 2005.

,

R. M. Davidson, M. Gowda, G. Moghe, H. Lin, B. Vaillancourt et al., Comparative Transcriptomics of Three Poaceae Species Reveals Patterns of Gene Expression Evolution, The Plant Journal, 2012.

,

L. B. Davin and N. G. Lewis, Dirigent Proteins and Dirigent Sites Explain the Mystery of Specificity of Radical Precursor Coupling in Lignan and Lignin Biosynthesis, Plant Physiology, vol.123, issue.2, pp.453-62, 2000.

M. Delalande, J. L. Regnard, E. Costes, M. Reymond, D. Luquet et al., DiaPHEN: Field Platform to Analyze Mechanisms of Drought Tolerance at Field Level, 2015.

D. P. Delmer and Y. Amor, Cellulose Biosynthesis, The Plant Cell, vol.7, issue.7, pp.987-1000, 1995.

D. P. Delmer and C. H. Haigler, The Regulation of Metabolic Flux to Cellulose, a Major Sink for Carbon in Plants, Metabolic Engineering, vol.4, issue.1, pp.22-28, 2002.

,

T. Demura and . Zheng-hua-ye, Regulation of Plant Biomass Production, Current Opinion in Plant Biology, vol.13, issue.3, pp.298-303, 2010.

R. T. Derose, D. Begum, and T. C. Hall, Analysis of Kafirin Promoter Activity in Transgenic Tobacco Seeds, Plant Molecular Biology, vol.32, issue.6, pp.1029-1064, 1996.

,

M. Deu, J. Rattunde, and . Chantereau, A Global View of Genetic Diversity in Cultivated Sorghums Using a Core Collection, Genome, vol.49, issue.2, pp.168-80, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02662565

V. Dharanishanthi and M. Dasgupta, Co-Expression Network of Transcription Factors Reveal Ethylene-Responsive Element-Binding Factor as Key Regulator of Wood Phenotype in Eucalyptus Tereticornis, Biotech, vol.3, issue.7, p.315, 2018.

,

K. S. Dhugga, Guar Seed -Mannan Synthase Is a Member of the Cellulose Synthase Super Gene Family, Science, vol.303, issue.5656, pp.363-66, 2004.

B. S. Dien, G. Sarath, J. F. Pedersen, S. E. Sattler, H. Chen et al., Improved Sugar Conversion and Ethanol Yield for Forage Sorghum (Sorghum Bicolor L. Moench) Lines with Reduced Lignin Contents, Bioenergy Research, vol.2, issue.3, pp.153-64, 2009.

. Ding, M. E. Shi-you, and . Himmel, The Maize Primary Cell Wall Microfibril: A New Model Derived from Direct Visualization, Journal of Agricultural and Food Chemistry, vol.54, issue.3, pp.597-606, 2006.

Z. Ding, S. Weissmann, M. Wang, B. Du, L. Huang et al., Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species, PLoS ONE, vol.10, issue.10, pp.1-19, 2015.

R. A. Dixon and N. L. Paiva, Stress-Induced Phenylpropanoid Metabolism, The Plant Cell, pp.1085-97, 1995.

R. A. Dixon, P. Lahoucine-achnine, C. Kota, M. S. Liu, L. Srinivasa-reddy et al., The Phenylpropanoid Pathway and Plant Defence-a Genomics Perspective, Molecular Plant Pathology, vol.3, issue.5, pp.371-90, 2002.

P. T. Do, H. Lee, M. Mookkan, W. R. Folk, and Z. J. Zhang, Rapid and Efficient Agrobacterium-Mediated Transformation of Sorghum (Sorghum Bicolor) Employing Standard Binary Vectors and Bar Gene as a Selectable Marker, Plant Cell Reports, vol.35, issue.10, pp.2065-76, 2016.

M. S. Doblin, I. Kurek, D. Jacob-wilk, and D. P. Delmer, Cellulose Biosynthesis in Plants: From Genes to Rosettes, Plant and Cell Physiology, vol.43, issue.12, pp.1407-1427, 2002.

M. S. Doblin, A. Filomena, S. M. Pettolino, R. Wilson, R. A. Campbell et al., A Barley Cellulose Synthase-like CSLH Gene Mediates (1,3;1,4)-?-D-Glucan Synthesis in Transgenic Arabidopsis, Proceedings of the National Academy of Sciences of the United States of America, vol.106, issue.14, pp.5996-6001, 2009.

,

M. S. Doblin, F. Pettolino, and A. Bacic, Evans Review: Plant Cell Walls: The Skeleton of the Plant World, Functional Plant Biology, vol.37, issue.5, pp.357-81, 2010.

,

J. G. Doench, N. Fusi, M. Sullender, M. Hegde, E. W. Vaimberg et al., Optimized SgRNA Design to Maximize Activity and Minimize Off-Target Effects of CRISPR-Cas9, Nature Biotechnology, vol.34, issue.2, pp.184-91, 2016.

,

J. -. Dong, M. Zhuo, . Yang, . Shi-rong, N. Jia et al., Transformation of Melon (Cucumis Melo L.) and Expression from the Cauliflower Mosaic Virus, vol.35, 1991.

. Transgenic-melon-plants, Nature Biotechnology, vol.9, issue.9, pp.858-63

H. Du, B. Feng, S. Yang, Y. Huang, and Y. Tang, The R2R3-MYB Transcription Factor Gene Family in Maize, vol.7, pp.1-12, 2012.

,

C. Dubos, J. L. Gourrierec, A. Baudry, G. Huep, E. Lanet et al., MYBL2 Is a New Regulator of Flavonoid Biosynthesis in Arabidopsis Thaliana, The Plant Journal, vol.55, issue.6, pp.940-53, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01203970

C. Dubos, R. Stracke, E. Grotewold, B. Weisshaar, C. Martin et al., MYB Transcription Factors in Arabidopsis, Trends in Plant Science, vol.15, issue.10, pp.573-81, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01203945

,

J. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann et al., Tree Pattern Matching in Phylogenetic Trees: Automatic Search for Orthologs or Paralogs in Homologous Gene Sequence Databases, Bioinformatics, vol.21, issue.11, pp.2596-2603, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00427861

,

D. V. Dugas, M. K. Monaco, A. Olson, S. Robert-r-klein, D. Kumari et al., Functional Annotation of the Transcriptome of Sorghum Bicolor in Response to Osmotic Stress and Abscisic Acid, BMC Genomics, vol.12, issue.1, p.514, 2011.

K. K. Dwivedi, D. Roche, and J. G. Carman, Expression in Arabidopsis of a Nucellus-Specific Promoter from Watermelon (Citrullus Lanatus), Plant Science, vol.179, issue.5, pp.549-52, 2010.

L. Dykes and L. W. Rooney, Sorghum and Millet Phenols and Antioxidants, Journal of Cereal Science, vol.44, issue.3, pp.236-51, 2006.

A. Ebringerová, Structural Diversity and Application Potential of Hemicelluloses, Macromolecular Symposia, vol.232, issue.333, pp.1-12, 2006.

A. Ebringerová, Z. Hromádková, and T. Heinze, In Polysaccharides I, 1-67, 2005.

N. A. Eckardt, Cellulose Synthesis Takes the CesA Train, The Plant Cell, vol.15, issue.8, pp.1685-87, 2003.

L. A. Elkonin, J. V. Italyanskaya, V. M. Panin, and N. Y. Selivanov, Development of Transgenic Sorghum Plants with Improved In Vitro Kafirin Digestibility, In Plant Engineering. InTech, 2017.

R. J. Elshire, C. Jeffrey, Q. Glaubitz, J. A. Sun, K. Poland et al., A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species, PLoS ONE, vol.6, issue.5, p.19379, 2011.

,

J. Enciso, J. Jifon, L. Ribera, S. D. Zapata, and G. K. Ganjegunte, Yield, Water Use Efficiency and Economic Analysis of Energy Sorghum in South Texas, Biomass and Bioenergy, vol.81, pp.339-383, 2015.

H. Endo, M. Yamaguchi, T. Tamura, Y. Nakano, N. Nishikubo et al., Multiple Classes of Transcription Factors Regulate the Expression of VASCULAR-RELATED NAC-DOMAIN7, a Master Switch of Xylem Vessel Differentiation, Plant and Cell Physiology, vol.56, issue.2, pp.242-54, 2015.

R. A. Ermawar, M. Helen, C. S. Collins, N. S. Byrt, M. Betts et al., Distribution, Structure and Biosynthetic Gene Families of (1,3;1,4)-?-Glucan in Sorghum Bicolor, Journal of Integrative Plant Biology, vol.57, issue.4, pp.429-474, 2015.

,

R. A. Ermawar, M. Helen, C. S. Collins, M. Byrt, . Henderson et al., Genetics and Physiology of Cell Wall Polysaccharides in the Model C4 Grass, Setaria Viridis Spp, BMC Plant Biology, vol.15, p.236, 2015.

M. A. Ermeydan, E. Cabane, A. Masic, J. Koetz, and I. Burgert, Flavonoid Insertion into Cell Walls Improves Wood Properties, ACS Applied Materials & Interfaces, vol.4, issue.11, pp.5782-89, 2012.

. Esquerré-tugayé, G. Marie-thérèse, B. Boudart, and . Dumas, Cell Wall Degrading Enzymes, Inhibitory Proteins, and Oligosaccharides Participate in the Molecular Dialogue between Plants and Pathogens, Plant Physiology and Biochemistry, vol.38, issue.1-2, pp.157-63, 2000.

, , pp.161-164

K. Fan, M. Wang, Y. Miao, M. Ni, N. Bibi et al., Molecular Evolution and Expansion Analysis of the NAC Transcription Factor in Zea Mays, 2014.

L. Fan, R. Linker, S. Gepstein, E. Tanimoto, R. Yamamoto et al.,

. Neumann, Progressive Inhibition by Water Deficit of Cell Wall Extensibility and Growth along the Elongation Zone of Maize Roots Is Related to Increased Lignin Metabolism and Progressive Stelar Accumulation of Wall Phenolics, Plant Physiology, vol.140, issue.2, pp.603-615, 2006.

,

Y. Fang, J. You, K. Xie, W. Xie, and L. Xiong, Systematic Sequence Analysis and Identification of Tissue-Specific or Stress-Responsive Genes of NAC Transcription Factor Family in Rice, Molecular Genetics and Genomics, vol.280, issue.6, pp.547-63, 2008.

,

I. Farré and J. Faci, Comparative Response of Maize (Zea Mays L.) and Sorghum (Sorghum Bicolor L. Moench) to Deficit Irrigation in a Mediterranean Environment, Agricultural Water Management, vol.83, issue.1-2, pp.135-178, 2006.

. Festucci-buselli, A. Reginaldo, C. Wagner, C. P. Otoni, and . Joshi, Structure, Organization, and Functions of Cellulose Synthase Complexes in Higher Plants, Brazilian Journal of Plant Physiology, vol.19, issue.1, pp.1-13, 2007.

S. P. Ficklin and F. A. Feltus, Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice, Plant Physiology, vol.156, issue.3, pp.1244-56, 2011.

S. Fornalé, E. Lopez, J. E. Salazar-henao, P. Fernández-nohales, J. Rigau et al., AtMYB7, a New Player in the Regulation of UV-Sunscreens in Arabidopsis Thaliana, Plant and Cell Physiology, vol.55, issue.3, pp.507-523, 2014.

,

S. Fornalé, X. Shi, C. Chai, A. Encina, S. Irar et al., ZmMYB31 Directly Represses Maize Lignin Genes and Redirects the Phenylpropanoid Metabolic Flux, The Plant Journal, vol.64, issue.4, pp.633-677, 2010.

,

S. Fornalé, F. Sonbol, T. Maes, M. Capellades, P. Puigdomènech et al., Down-Regulation of the Maize and Arabidopsis Thaliana Caffeic Acid O-Methyl-Transferase Genes by Two New Maize R2R3-MYB Transcription Factors, Plant Molecular Biology, vol.62, issue.6, pp.809-832, 2006.

R. T. Fraley, S. G. Rogers, R. B. Horsch, P. R. Sanders, J. S. Flick et al., Expression of Bacterial Genes in Plant Cells, Proceedings of the National Academy of Sciences, vol.80, issue.15, pp.4803-4810, 1983.

C. M. Fraser and C. Chapple, The Phenylpropanoid Pathway in Arabidopsis, The Arabidopsis Book, vol.9, p.152, 2011.

C. H. Frère, J. Peter, E. K. Prentis, A. M. Gilding, A. Mudge et al., Lack of Low Frequency Variants Masks Patterns of Non-Neutral Evolution Following Domestication, Amdam. PLoS ONE, vol.6, issue.8, p.23041, 2011.

,

M. E. Fromm, F. Morrish, C. Armstrong, R. Williams, J. Thomas et al., Inheritance and Expression of Chimeric Genes in the Progeny of, 1990.

. Transgenic-maize-plants, Nature Biotechnology, vol.8, issue.9, pp.833-872

M. E. Fromm, P. Loverine, V. Taylor, and . Walbot, Stable Transformation of Maize after Gene Transfer by Electroporation, Nature, vol.319, issue.6056, pp.791-93, 1986.

,

S. C. Fry, Oxidative Scission of Plant Cell Wall Polysaccharides by Ascorbate-Induced Hydroxyl Radicals, Biochemical Journal, vol.332, issue.2, pp.507-522, 1998.

Y. Fujikawa, T. Nakanishi, H. Kawakami, K. Yamasaki, H. Masa et al., Split Luciferase Complementation Assay to Detect Regulated Protein-Protein Interactions in Rice Protoplasts in a Large-Scale Format, Rice, vol.7, issue.1, p.11, 2014.

M. Fujita, Y. Fujita, K. Maruyama, M. Seki, K. Hiratsu et al., A Dehydration-Induced NAC Protein, RD26, Is Involved in a Novel ABA-Dependent Stress-Signaling Pathway, The Plant Journal, vol.39, issue.6, pp.863-76, 2004.

S. Fujiwara and N. Mitsuda, ANAC075,a Putative Regulator of VASCULAR-RELATED NAC-DOMAIN7,Is a Repressor of Flowering, Plant Biotechnology, vol.33, issue.4, pp.255-65, 2016.

,

T. Fukao, K. Xu, P. C. Ronald, and J. Bailey-serres, A Variable Cluster of Ethylene Response Factor-Like Genes Regulates Metabolic and Developmental Acclimation Responses to Submergence in Rice, The Plant Cell, vol.18, issue.8, pp.2021-2055, 2006.

,

P. Furtwengler and L. Avérous, From D-Sorbitol to Five-Membered Bis(Cyclo-Carbonate) as a Platform Molecule for the Synthesis of Different Original Biobased Chemicals and Polymers, Scientific Reports, vol.8, issue.1, p.9134, 2018.

L. Gallego-giraldo, G. Shadle, H. Shen, J. Barros-rios, S. F. Corrales et al., Combining Enhanced Biomass Density with Reduced Lignin Level for Improved Forage Quality, Plant Biotechnology Journal, vol.14, issue.3, pp.895-904, 2016.

E. R. Gamazon, E. Heather, K. P. Wheeler, . Shah, V. Sahar et al.,

R. J. Michaels, A. E. Carroll, and . Eyler, A Gene-Based Association Method for Mapping Traits Using Reference Transcriptome Data, Nature Genetics, vol.47, issue.9, pp.1091-98, 2015.

,

Z. Gao, X. Xie, Y. Ling, S. Muthukrishnan, and G. H. Liang, Agrobacterium Tumefaciens-Mediated Sorghum Transformation Using a Mannose Selection System, Plant Biotechnology Journal, vol.3, issue.6, pp.591-99, 2005.

J. C. Gardner, J. W. Maranville, and E. T. Paparozzi, Nitrogen Use Efficiency among Diverse Sorghum Cultivars, Crop Science, vol.34, issue.3, p.728, 1994.

,

P. Garofalo and M. Rinaldi, Water-Use Efficiency of Irrigated Biomass Sorghum in a Mediterranean Environment, Spanish Journal of Agricultural Research, vol.11, issue.4, p.1153, 2013.

O. Garsmeur, G. Droc, R. Antonise, J. Grimwood, B. Potier et al., A Mosaic Monoploid Reference Sequence for the Highly Complex Genome of Sugarcane, Nature Communications, vol.9, issue.1, p.2638, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02628799

C. S. Gasser and R. T. Fraley, Genetically Engineering Plants for Crop Improvement, Science, vol.244, issue.4910, pp.1293-99, 1989.

C. Gatz, Chemically Inducible Promoters in Transgenic Plants, Current Opinion in Biotechnology, vol.7, issue.2, pp.168-72, 1996.

M. Gelli, Y. Duo, A. Konda, C. Zhang, D. Holding et al., Identification of Differentially Expressed Genes between Sorghum Genotypes with Contrasting Nitrogen Stress Tolerance by Genome-Wide Transcriptional Profiling, BMC Genomics, vol.15, issue.1, p.179, 2014.

S. B. Gelvin, Plant Transformation: The Biology behind the 'Gene-Jockeying' Tool, Society, vol.67, issue.1, pp.16-37, 2003.

S. Gille and M. Pauly, O-Acetylation of Plant Cell Wall Polysaccharides, Frontiers in Plant Science, vol.3, pp.1-7, 2012.

V. Girijashankar, H. C. Sharma, K. K. Sharma, V. Swathisree, L. Prasad et al., Development of Transgenic Sorghum for Insect Resistance against the Spotted Stem Borer (Chilo Partellus), Plant Cell Reports, vol.24, issue.9, pp.513-535, 2005.

,

V. Girijashankar and V. Swathisree, Genetic Transformation of Sorghum Bicolor, Physiology and Molecular Biology of Plants, vol.15, issue.4, pp.287-302, 2009.

M. Goicoechea, E. Lacombe, S. Legay, S. Mihaljevic, P. Rech et al., EgMYB2, a New Transcriptional Activator from Eucalyptus Xylem, Regulates Secondary Cell Wall Formation and Lignin Biosynthesis, Plant Journal, vol.43, issue.4, pp.553-67, 2005.
URL : https://hal.archives-ouvertes.fr/cirad-00846177

M. V. Golovkin, M. Ábrahám, S. Mórocz, and S. Bottka, Production of Transgenic Maize Plants by Direct DNA Uptake into Embryogenic Protoplasts, Plant Science, vol.90, issue.1, pp.41-52, 1993.

Q. Guan, X. Yue, H. Zeng, and J. Zhu, The Protein Phosphatase RCF2 and Its Interacting Partner NAC019 Are Critical for Heat Stress-Responsive Gene Regulation and Thermotolerance in Arabidopsis, The Plant Cell, vol.26, issue.1, pp.438-53, 2014.

,

S. Guindon, J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-328, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

,

C. Gupta and A. Pereira, Recent Advances in Gene Function Prediction Using Context-Specific Coexpression Networks in Plants, F1000Research, vol.8, pp.1-10, 2019.

S. Gurel, E. Gurel, R. Kaur, J. Wong, L. Meng et al., Efficient, Reproducible Agrobacterium-Mediated Transformation of Sorghum Using Heat Treatment of Immature Embryos, Plant Cell Reports, vol.28, issue.3, pp.429-473, 2009.

,

S. Gurel, E. Gurel, T. I. Miller, and P. G. Lemaux, Agrobacterium-Mediated Transformation of Sorghum Bicolor Using Immature Embryos, pp.109-131, 2012.

,

. Gutjahr, M. Sylvain, M. Vaksmann, K. Dingkuhn, G. Thera et al., Grain, Sugar and Biomass Accumulation in Tropical Sorghums. I. Trade-Offs and Effects of Phenological Plasticity, Functional Plant Biology, vol.40, issue.4, pp.342-54, 2013.

N. Haga, K. Kato, M. Murase, S. Araki, M. Kubo et al., R1R2R3-Myb Proteins Positively Regulate Cytokinesis through Activation of KNOLLE Transcription in, 2007.

A. Thaliana, Development, vol.134, issue.6, pp.1101-1111

. Hagio, A. D. Takashi, E. D. Blowers, and . Earle, Stable Transformation of Sorghum Cell Cultures after Bombardment with DNA-Coated Microprojectiles, Plant Cell Reports, vol.10, issue.5, pp.260-64, 1991.

C. H. Haigler, V. M. Babb, S. Hwang, V. Vadim, and . Salnikov, Regulation of Cellulose Biosynthesis in Developing Xylem, pp.80050-80052, 2001.

A. Hallam, I. C. Anderson, and D. R. Buxton, Comparative Economic Analysis of Perennial, Annual, and Intercrops for Biomass Production, Biomass and Bioenergy, vol.21, issue.6, pp.407-431, 2001.

, , pp.51-55

H. Hamada, Q. Linghu, Y. Nagira, R. Miki, N. Taoka et al., An in Planta Biolistic Method for Stable Wheat Transformation, Scientific Reports, vol.7, issue.1, pp.2-9, 2017.

R. Hamid, S. Javed, M. Ahmad, and M. Ahmad,

J. Khan and . Musarrat, Chitinases: An Update, Journal of Pharmacy and Bioallied Sciences, vol.5, issue.1, p.21, 2013.

P. P. Handakumbura and S. P. Hazen, Transcriptional Regulation of Grass Secondary Cell Wall Biosynthesis: Playing Catch-Up with Arabidopsis Thaliana, Frontiers in Plant Science, vol.3, 2012.

P. P. Handakumbura, D. A. Matos, K. S. Osmont, J. Michael, K. Harrington et al., Perturbation of Brachypodium Distachyon CELLULOSE SYNTHASE A4 or 7 Results in Abnormal Cell Walls, BMC Plant Biology, vol.13, issue.1, p.131, 2013.

G. Hansen, Evidence for Agrobacterium-Induced Apoptosis in Maize Cells, Molecular Plant-Microbe Interactions, vol.13, issue.6, pp.649-57, 2000.

,

W. Hansen, Recent Advances in the Transformation of Plants, Trends in Plant Science, vol.4, issue.6, pp.226-257, 1999.

P. J. Harris and J. A. Trethewey, The Distribution of Ester-Linked Ferulic Acid in the Cell Walls of Angiosperms, Phytochemistry Reviews, vol.9, issue.1, pp.19-33, 2010.

,

R. Harris, M. Wright, M. Byrne, J. Varnum, B. Brightwell et al., Callus Formation and Plantlet Regeneration from Protoplasts Derived from Suspension Cultures of Wheat (Triticum Aestivum L.), Plant Cell Reports, vol.7, issue.5, pp.337-377, 1988.

,

D. Harshavardhan, T. Shyamala, R. , K. Ulaganathan, and N. Seetharama, An Improved Protocol for Regeneration of Sorghum Bicolor from Isolated Shoot Apices, Plant Biotechnology, vol.19, issue.3, pp.163-71, 2002.

. He, R. Xin-jian, W. Mu, Z. Cao, J. Zhang et al., AtNAC2, a Transcription Factor Downstream of Ethylene and Auxin Signaling Pathways, Is Involved in Salt Stress Response and Lateral Root Development, The Plant Journal, vol.44, issue.6, pp.903-919, 2005.

L. Hennet, A. Berger, N. Trabanco, E. Ricciuti, J. Dufayard et al., Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-Expression Gene Network and Comparative Genomics Analyses, Frontiers in Plant Science, vol.11, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02542105

,

. Hernández-blanco, D. X. Camilo, J. Feng, A. Hu, -. Sánchez et al., Impairment of Cellulose Synthases Required for Arabidopsis Secondary Cell Wall Formation Enhances Disease Resistance, Plant Cell, vol.19, issue.3, pp.890-903, 2007.

K. Hibara, S. Takada, and M. Tasaka, CUC1 Gene Activates the Expression of SAM-Related Genes to Induce Adventitious Shoot Formation, The Plant Journal, vol.36, issue.5, pp.687-96, 2003.

K. Hibara, M. Ichiro, S. Karim, K. I. Takada, M. Taoka et al., Arabidopsis CUP-SHAPED, vol.3, 2006.

, Regulates Postembryonic Shoot Meristem and Organ Boundary Formation, Plant Cell, vol.18, issue.11, pp.2946-57

Y. Hiei and T. Komari, Agrobacterium-Mediated Transformation of Rice Using Immature Embryos or Calli Induced from Mature Seed, Nature Protocols, vol.3, issue.5, pp.824-858, 2008.

,

Y. Hiei, S. Ohta, T. Komari, and T. Kumashiro, Efficient Transformation of Rice (Oryza Sativa L.) Mediated by Agrobacterium and Sequence Analysis of the Boundaries of the T-DNA, The Plant Journal, vol.6, issue.2, pp.271-82, 1994.

Y. Higashi and K. Saito, Network Analysis for Gene Discovery in Plant-Specialized Metabolism, Plant, Cell and Environment, vol.36, issue.9, pp.1597-1606, 2013.

,

K. Hirano, K. Aya, Y. Morinaka, S. Nagamatsu, Y. Sato et al., Survey of Genes Involved in Rice Secondary Cell Wall Formation Through a Co-Expression Network, Plant and Cell Physiology, vol.54, issue.11, pp.1803-1824, 2013.

K. Hirano, M. Kondo, K. Aya, A. Miyao, Y. Sato et al., Identification of Transcription Factors Involved in Rice Secondary Cell Wall Formation, Plant and Cell Physiology, vol.54, issue.11, pp.1791-1802, 2013.

R. A. Hoorn and . Van-der, Plant Proteases: From Phenotypes to Molecular Mechanisms, Annual Review of Plant Biology, vol.59, issue.1, pp.191-223, 2008.

,

R. B. Horsch, T. Robert, . Fraley, G. Stephen, P. R. Rogers et al., Inheritance of Functional Foreign Genes in Plants Published by, Advancement of Science Stable URL, vol.223, issue.4635, pp.496-98, 2016.

A. Howe, S. Sato, I. Dweikat, M. Fromm, and T. Clemente, Rapid and Reproducible Agrobacterium-Mediated Transformation of Sorghum, Plant Cell Reports, vol.25, issue.8, pp.784-91, 2006.

P. D. Hsu, A. David, J. A. Scott, A. Weinstein, S. Ran et al., DNA Targeting Specificity of RNA-Guided, p.9, 2013.

. Nucleases, Nature Biotechnology, vol.31, issue.9, pp.827-859

R. Hu, G. Qi, Y. Kong, D. Kong, Q. Gao et al., Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus Trichocarpa, BMC Plant Biology, vol.10, issue.1, p.145, 2010.

R. Hu, Y. Xu, C. Yu, K. He, Q. Tang et al., Transcriptome Analysis of Genes Involved in Secondary Cell Wall Biosynthesis in Developing Internodes of Miscanthus Lutarioriparius, Scientific Reports, vol.7, issue.1, pp.1-16, 2017.

J. Huang, S. Vendramin, L. Shi, and K. M. Mcginnis, Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data, Plant Physiology, vol.175, issue.1, pp.568-83, 2017.

T. E. Hughes, J. A. Langdale, and S. Kelly, The Impact of Widespread Regulatory Neofunctionalization on Homeolog Gene Evolution Following Whole-Genome Duplication in Maize, Genome Research, vol.24, issue.8, pp.1348-55, 2014.

,

S. G. Hussey, N. Mohammed, C. A. Saïdi, A. A. Hefer, J. Myburg et al., Structural, Evolutionary and Functional Analysis of the NAC Domain Protein Family in Eucalyptus, New Phytologist, vol.206, issue.4, pp.1337-50, 2015.

,

S. G. Hussey, E. Mizrachi, V. Antanas, G. Spokevicius, D. K. Bossinger et al., 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, vol.11, issue.1, p.173, 2011.

K. Iiyama, T. Lam, and B. A. Stone, Phenolic acid bridges between polysacharides and lignin in wheat internodes, Phytochemistry, vol.29, pp.733-737, 1990.

Y. Ishida, H. Saito, S. Ohta, Y. Hiei, T. Komari et al., High Efficiency Transformation of Maize (Zea Mays L.) Mediated by Agrobacterium Tumefaciens, Nature Biotechnology, vol.14, issue.6, pp.745-50, 1996.

T. Ishii, Structure and Functions of Feruloylated Polysaccharides, Plant Science, vol.127, issue.2, pp.130-131, 1997.

A. Ismagul, N. Yang, E. Maltseva, G. Iskakova, I. Mazonka et al., A Biolistic Method for High-Throughput Production of Transgenic Wheat Plants with Single Gene Insertions, BMC Plant Biology, vol.18, issue.1, pp.1-8, 2018.

M. Ito, Conservation and Diversification of Three-Repeat Myb Transcription Factors in Plants, Journal of Plant Research, vol.118, issue.1, pp.61-69, 2005.

M. Jain, A. Nijhawan, R. Arora, P. Agarwal, S. Ray et al., F-Box Proteins in Rice. Genome-Wide Analysis, Classification, Temporal and Spatial Gene Expression during Panicle and Seed Development, and Regulation by Light and Abiotic Stress, Plant Physiology, vol.143, issue.4, pp.1467-83, 2007.

S. Jambagi, R. Bhat, S. Bhat, and M. Kuruvinashetti, Agrobacterium -Mediated Transformation Studies in Sorghum Using an Improved Gfp Reporter Gene, SAT EJournal, vol.8, pp.1-5, 2010.

K. M. Janas, M. Cvikrová, A. Pa??giewicz, and J. Eder, Alterations in Phenylpropanoid Content in Soybean Roots during Low Temperature Acclimation, Plant Physiology and Biochemistry, vol.38, issue.7-8, pp.778-784, 2000.

T. Janda, G. Szalai, K. Rios-gonzalez, O. Veisz, and E. Páldi, Comparative Study of Frost Tolerance and Antioxidant Activity in Cereals, Plant Science, vol.164, issue.2, pp.301-307, 2003.

M. Jarvis, Cellulose Stacks Up, Nature, vol.426, issue.6967, pp.611-623, 2003.

,

M. Jasin and R. Rothstein, Repair of Strand Breaks by Homologous Recombination, Cold Spring Harbor Perspectives in Biology, vol.5, issue.11, pp.12740-012740, 2013.

,

M. Jawaid, M. T. Paridah, and N. Saba, Lignocellulosic Fibre and Biomass-Based Composite Materials: Processing, Properties and Applications, 2017.

J. Jensen, N. R. Krüger, C. G. Johnson, and . Wilkerson, Arabidopsis Thaliana IRX10 and Two Related Proteins from Psyllium and Physcomitrella Patens Are Xylan Xylosyltransferases, The Plant Journal, vol.80, issue.2, pp.207-222, 2014.

J. M. Jeoung, S. Krishnaveni, S. Muthukrishnan, H. N. Trick, and G. H. Liang, Optimization of Sorghum Transformation Parameters Using Genes for Green Fluorescent Protein and Beta-Glucuronidase as Visual Markers, Hereditas, vol.137, issue.1, pp.20-28, 2002.

G. Jiang, Molecular Marker-Assisted Breeding: A Plant Breeder's Review, Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools, pp.431-72, 2015.

. Jiao, J. J. Yinping, R. Burke, G. Chopra, J. Burow et al., A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses, The Plant Cell, 2016.

H. Jin, Transcriptional Repression by AtMYB4 Controls Production of UV-Protecting Sunscreens in Arabidopsis, The EMBO Journal, vol.19, issue.22, pp.6150-61, 2000.

,

J. Jin, F. Tian, C. De, Y. Q. Yang, L. Meng et al., PlantTFDB 4.0: Toward a Central Hub for Transcription Factors and Regulatory Interactions in Plants, Nucleic Acids Research, vol.45, issue.D1, pp.1040-1085, 2017.

M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J. A. Doudna et al., A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity, Science, vol.337, issue.6096, pp.816-837, 2012.

M. Joersbo, L. Donaldson, J. Kreiberg, J. Steen-guldager-petersen, . Brunstedt et al., Analysis of Mannose Selection Used for Transformation of Sugar Beet, Molecular Breeding, vol.4, issue.2, pp.111-128, 1998.

G. Jogeswar, D. Ranadheer, V. Anjaiah, and P. B. Kavi-kishor, High Frequency Somatic Embryogenesis and Regeneration in Different Genotypes of Sorghum Bicolor (L.) Moench from, 2007.

. Immature-inflorescence-explants, In Vitro Cellular & Developmental Biology -Plant, vol.43, issue.2, pp.159-66

K. Jørgensen, A. Vinther-rasmussen, M. Morant, A. Holm-nielsen, N. Bjarnholt et al., Metabolon Formation and Metabolic Channeling in the Biosynthesis of Plant Natural Products, Current Opinion in Plant Biology, vol.8, issue.3, pp.280-91, 2005.

C. P. Joshi, T. Shivegowda-thammannagowda, J. Fujino, U. Gou, C. H. Avci et al., Perturbation of Wood Cellulose Synthesis Causes Pleiotropic Effects in Transgenic Aspen, Molecular Plant, vol.4, issue.2, pp.331-376, 2011.

,

Y. Kadier, Y. Yi-zu, G. Qing-min-dai, . Song, Q. Shi-wen-lin et al., Genome-Wide Identification, Classification and Expression Analysis of NAC Family of Genes in Sorghum, Plant Growth Regulation, vol.83, issue.2, pp.301-313, 2017.

H. F. Kaeppler and J. F. Pedersen, Media Effects on Phenotype of Callus Cultures Initiated from Photoperiod-Insensitive, Elite Inbred Sorghum Lines, Maydica, vol.41, issue.2, pp.83-89, 1996.

J. Kapila, R. De-rycke, M. Van-montagu, and G. Angenon, An Agrobacterium-Mediated Transient Gene Expression System for Intact Leaves, Plant Science, vol.122, issue.1, pp.101-109, 1997.

, , pp.4541-4545

A. Katiyar, S. Smita, K. Sangram, R. Lenka, V. Rajwanshi et al., Genome-Wide Classification and Expression Analysis of MYB Transcription Factor Families in Rice and Arabidopsis, BMC Genomics, vol.13, issue.1, 2012.

K. Katoh, J. Rozewicki, D. Kazunori, and . Yamada, MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization, Briefings in Bioinformatics, pp.1-7, 2017.

W. E. Kayal, Expression Profile of CBF-like Transcriptional Factor Genes from Eucalyptus in Response to Cold, Journal of Experimental Botany, vol.57, issue.10, pp.2455-69, 2006.

,

T. H. Kebrom, B. Mckinley, and J. E. Mullet, Dynamics of Gene Expression during Development and Expansion of Vegetative Stem Internodes of Bioenergy Sorghum, Biotechnology for Biofuels, vol.10, issue.1, pp.1-16, 2017.

H. Kende, E. Van-der-knaap, and H. Cho, Deepwater Rice: A Model Plant to Study Stem Elongation, Plant Physiology, vol.118, issue.4, pp.1105-1115, 1998.

,

R. A. Kerstetter, R. A. Krista-bollman, K. Taylor, R. Bomblies, and . Scott-poethig, KANADI Regulates Organ Polarity in Arabidopsis, Nature, vol.411, issue.6838, pp.706-715, 2001.

,

G. Keshavareddy, A. R. Kumar, and V. S. Ramu, Methods of Plant Transformation-A Review, International Journal of Current Microbiology and Applied Sciences, vol.7, issue.07, pp.2656-68, 2018.

F. Kieffer, The Fungal Elicitor Cryptogein Induces Cell Wall Modifications on Tobacco Cell Suspension, Journal of Experimental Botany, vol.51, issue.352, pp.1799-1811, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02686942

,

J. R. Kikkert, G. S. Ali, P. G. Wallace, B. Reisch, and G. M. Reustle, Expression Of A Fungal Chitinase In Vitis Vinifera L. 'Merlot' And 'Chardonnay' Plants Produced By Biolistic Transformation, Acta Horticulturae, issue.528, pp.299-306, 2000.

,

D. Kim, B. Langmead, and S. L. Salzberg, HISAT: A Fast Spliced Aligner with Low Memory Requirements, Nature Methods, vol.12, p.357, 2015.

,

H. Kim, D. Koo, E. Luquet, M. Van-oosterom, G. Dingkuhn et al., Regulation of Tillering in Sorghum: Genotypic Effects, Annals of Botany, vol.106, issue.1, pp.69-78, 2010.

,

M. Kim and D. F. Day, Composition of Sugar Cane, Energy Cane, and Sweet Sorghum Suitable for Ethanol Production at Louisiana Sugar Mills, Journal of Industrial Microbiology and Biotechnology, vol.38, issue.7, pp.803-810, 2011.

W. Kim, J. Chan, J. H. Kim, J. Ko, K. Kim et al., Transcription Factor MYB46 Is an Obligate Component of the Transcriptional Regulatory Complex for Functional Expression of Secondary Wall-Associated Cellulose Synthases in Arabidopsis Thaliana, Journal of Plant Physiology, vol.170, issue.15, pp.1374-78, 2013.

,

Y. Kim, S. Kim, J. Park, H. Park, M. Lim et al., A Membrane-Bound NAC Transcription Factor Regulates Cell Division in Arabidopsis, The Plant Cell, vol.18, issue.11, pp.3132-3176, 2006.

,

A. Kitajima, S. Asatsuma, H. Okada, Y. Hamada, K. Kaneko et al., The Rice ?-Amylase Glycoprotein Is Targeted from the Golgi Apparatus through the Secretory Pathway to the Plastids, The Plant Cell, vol.21, issue.9, pp.2844-58, 2009.

,

J. H. Ko, H. W. Jeon, W. C. Kim, J. Y. Kim, and K. H. Han, The MYB46/MYB83-Mediated Transcriptional Regulatory Programme Is a Gatekeeper of Secondary Wall Biosynthesis, Annals of Botany, vol.114, issue.6, pp.1099-1107, 2014.

J. -. Ko, W. Heung, K. Kim, and . Han, Ectopic Expression of MYB46 Identifies Transcriptional Regulatory Genes Involved in Secondary Wall Biosynthesis in Arabidopsis, The Plant Journal, vol.60, issue.4, pp.72-74, 2009.

,

G. Krouk, J. Lingeman, A. M. Colon, G. Coruzzi, and D. Shasha, Gene Regulatory Networks in Plants: Learning Causality from Time and Perturbation, Genome Biology, vol.14, issue.6, p.123, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00920683

W. Kruijer, M. P. Boer, M. Malosetti, P. J. Flood, B. Engel et al., Marker-Based Estimation of Heritability in Immortal Populations, Genetics, vol.199, issue.2, pp.379-98, 2015.

M. Kubo, Transcription Switches for Protoxylem and Metaxylem Vessel Formation, Genes & Development, vol.19, issue.16, pp.1855-60, 2005.

. Kumar, L. M. Vinod, K. S. Campbell, and . Rathore, Rapid Recovery-and Characterization of Transformants Following Agrobacterium-Mediated T-DNA Transfer to Sorghum, Plant Cell, Tissue and Organ Culture, vol.104, issue.2, pp.137-183, 2011.

,

T. Kuriyama, S. Shimada, and M. Matsui, Improvement of Agrobacterium-Mediated Transformation for Tannin-Producing Sorghum, Plant Biotechnology, vol.36, issue.1, pp.43-48, 2019.

,

J. Kyozuka, Y. Hayashi, and K. Shimamoto, High Frequency Plant Regeneration from Rice Protoplasts by Novel Nurse Culture Methods, MGG Molecular & General Genetics, vol.206, issue.3, pp.408-421, 1987.

P. Lam, Y. Ying, Y. Tobimatsu, S. Takeda, M. Suzuki et al., Disrupting Flavone Synthase II Alters Lignin and Improves Biomass Digestibility, Plant Physiology, vol.174, issue.2, pp.972-85, 2017.

S. Lam, C. L. Kwan, S. Siu, S. Hillmer, G. Jang et al.,

R. and L. Jiang, Rice SCAMP1 Defines Clathrin-Coated, Trans -Golgi-Located Tubular-Vesicular Structures as an Early Endosome in Tobacco BY-2 Cells, The Plant Cell, vol.19, issue.1, pp.296-319, 2007.

P. Langfelder and S. Horvath, WGCNA: An R Package for Weighted Correlation Network Analysis, BMC Bioinformatics, vol.9, 2008.

P. Langfelder and S. Horvath, Fast R Functions for Robust Correlations and Hierarchical Clustering, Journal of Statistical Software, vol.46, issue.11, 2012.

,

S. Lee, P. Seo, H. Lee, and C. Park, A NAC Transcription Factor NTL4 Promotes Reactive Oxygen Species Production during Drought-Induced Leaf Senescence in Arabidopsis, The Plant Journal, vol.70, issue.5, pp.831-875, 2012.

J. Leene, J. Van, . Blomme, R. Shubhada, B. Kulkarni et al., Functional Characterization of the Arabidopsis Transcription Factor BZIP29 Reveals Its Role in Leaf and Root Development, Journal of Experimental Botany, vol.67, pp.5825-5865, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01602885

. Legay, P. Sylvain, A. S. Sivadon, N. Blervacq, A. Pavy et al., EgMYB1, an R2R3 MYB Transcription Factor from Eucalyptus Negatively Regulates Secondary Cell Wall Formation in Arabidopsis and Poplar, New Phytologist, vol.188, issue.3, pp.774-86, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01565046

M. Leucci, M. S. Rosaria, G. Lenucci, G. Piro, and . Dalessandro, Water Stress and Cell Wall Polysaccharides in the Apical Root Zone of Wheat Cultivars Varying in Drought Tolerance, Journal of Plant Physiology, vol.165, issue.11, pp.1168-80, 2008.

,

A. Li, S. Jia, A. Yobi, Z. Ge, S. J. Sato et al., Editing of an Alpha-Kafirin Gene Family Increases, Digestibility and Protein Quality in Sorghum, Plant Physiology, vol.177, issue.4, pp.1425-1463, 2018.

E. Li, A. Bhargava, W. Qiang, M. C. Friedmann, N. Forneris et al.,

L. A. Savidge, S. D. Johnson, B. E. Mansfield, C. J. Ellis, and . Douglas, The Class II KNOX Gene KNAT7 Negatively Regulates Secondary Wall Formation in Arabidopsis and Is Functionally Conserved in Populus, New Phytologist, vol.194, issue.1, pp.102-117, 2012.

,

Q. Li, Y. Lin, Y. Sun, J. Song, H. Chen et al., Splice Variant of the SND1 Transcription Factor Is a Dominant Negative of SND1 Members and Their Regulation in Populus Trichocarpa, Proceedings of the National Academy of Sciences, vol.109, issue.36, pp.14699-704, 2012.

X. Li, C. Guo, S. Ahmad, Q. Wang, J. Yu et al., Systematic Analysis of MYB Family Genes in Potato and Their Multiple Roles in Development and Stress Responses, Planta, vol.249, issue.5, pp.1487-1501, 2019.

Y. Liu and C. Douglas, A Role for OVATE FAMILY PROTEIN1 (OFP1) and OFP4 in a BLH6-KNAT7 Multi-Protein Complex Regulating Secondary Cell Wall Formation in Arabidopsis Thaliana, Plant Signaling & Behavior, vol.10, issue.7, p.1033126, 2015.

,

Y. Liu, S. You, M. Taylor-teeples, W. L. Li, M. Schuetz et al.,

C. J. Brady and . Douglas, BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 Interact and Regulate Secondary Cell Wall Formation via Repression of REVOLUTA, The Plant Cell Online, vol.26, issue.12, pp.4843-61, 2014.

,

C. Loix, M. Huybrechts, J. Vangronsveld, and M. Gielen, Reciprocal Interactions between Cadmium-Induced Cell Wall Responses and Oxidative Stress in Plants, Frontiers in Plant Science, vol.8, 2017.

,

A. Lourenço and H. Pereira, Compositional Variability of Lignin in Biomass, In Lignin -Trends and Applications. InTech, 2018.

S. X. Lu, M. Stephen, C. Knowles, M. S. Andronis, E. M. Ong et al., CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL Function Synergistically in the Circadian Clock of Arabidopsis, Plant Physiology, vol.150, issue.2, pp.834-877, 2009.

,

M. Martin, Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads, EMBnet J, vol.17, issue.1, pp.10-12, 2011.

X. Ma, Q. Zhang, Q. Zhu, W. Liu, Y. Chen et al., A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants, Molecular Plant, vol.8, issue.8, pp.1274-84, 2015.

,

X. Ma, H. Zhao, W. Xu, Q. You, H. Yan et al., Co-Expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development, Frontiers in Genetics, vol.9, pp.1-15, 2018.

,

C. Maas, C. Reichel, J. Schell, and H. H. Steinbi?, Preparation and Transformation of Monocot Protoplasts, Methods in Cell Biology, vol.50, pp.61045-61051, 1995.

K. Ma?kowska, A. Jarosz, and E. Grzebelus, Plant Regeneration from Leaf-Derived Protoplasts within the Daucus Genus: Effect of Different Conditions in Alginate Embedding and Phytosulfokine Application, Plant Cell, Tissue and Organ Culture, vol.117, issue.2, pp.241-52, 2014.

J. M. Maia, L. Eduardo, . Voigt, L. Sérgio, A. Ferreira-silva et al., Differences in Cowpea Root Growth Triggered by Salinity and Dehydration Are Associated with Oxidative Modulation Involving Types I and III Peroxidases and Apoplastic Ascorbate, Journal of Plant Growth Regulation, vol.32, issue.2, pp.376-87, 2013.

,

S. Maleki, K. Sadat, K. Mohammadi, and J. Shu, Characterization of Cellulose Synthesis in Plant Cells, Scientific World Journal, 2016.

D. G. Mann, Z. R. King, W. Liu, L. Blake, R. J. Joyce et al., Switchgrass (Panicum Virgatum L.) Polyubiquitin, 2011.

, PvUbi1 and PvUbi2) Promoters for Use in Plant Transformation, BMC Biotechnology, vol.11, issue.1, p.74

V. Manova and D. Gruszka, DNA Damage and Repair in Plants -from Models to Crops, Frontiers in Plant Science, vol.6, 2015.

K. Marinova, L. Pourcel, B. Weder, M. Schwarz, D. Barron et al., The Arabidopsis MATE Transporter TT12 Acts as a Vacuolar Flavonoid/H + -Antiporter Active in Proanthocyanidin-Accumulating Cells of the Seed Coat, vol.19, pp.2023-2061, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02667126

M. Masani, G. A. Abdul, G. Noll, R. Parveez, D. Sambanthamurthi et al., Efficient Transformation of Oil Palm Protoplasts by PEG-Mediated Transfection and DNA Microinjection, PLoS ONE, vol.9, issue.5, p.96831, 2014.

K. Matsui, Y. Umemura, and M. Ohme-takagi, AtMYBL2, a Protein with a Single MYB Domain, Acts as a Negative Regulator of Anthocyanin Biosynthesis in Arabidopsis, The Plant Journal, vol.55, issue.6, pp.954-67, 2008.

G. G. Mcbee and F. R. Miller, Carbohydrates in Sorghum Culms as Influenced by Cultivars, Spacing, and Maturity over a Diurnal Period 1, Crop Science, vol.22, issue.2, pp.381-85, 1982.

,

R. L. Mccarthy, R. Zhong, S. Fowler, D. Lyskowski, H. Piyasena et al., The Poplar MYB Transcription Factors, PtrMYB3 and PtrMYB20, Are Involved in the Regulation of Secondary Wall Biosynthesis, Plant and Cell Physiology, vol.51, issue.6, pp.1084-90, 2010.

R. L. Mccarthy, R. Zhong, and Z. Ye, MYB83 Is a Direct Target of SND1 and Acts Redundantly with MYB46 in the Regulation of Secondary Cell Wall Biosynthesis in, 2009.

. Arabidopsis, Plant and Cell Physiology, vol.50, issue.11, pp.1950-64

R. F. Mccormick, K. Sandra, A. Truong, J. Sreedasyam, S. Jenkins et al., The Sorghum Bicolor Reference Genome: Improved Assembly, Gene Annotations, a Transcriptome Atlas, and Signatures of Genome Organization, Plant Journal, vol.93, issue.2, pp.338-54, 2018.

H. E. Mcfarlane, A. Döring, and S. Persson, The Cell Biology of Cellulose Synthesis, Annual Review of Plant Biology, vol.65, issue.1, pp.69-94, 2014.

B. Mckinley, W. Rooney, C. Wilkerson, and J. Mullet, Dynamics of Biomass Partitioning, Stem Gene Expression, Cell Wall Biosynthesis, and Sucrose Accumulation during Development of Sorghum Bicolor, The Plant Journal, pp.1-19, 2016.

M. J. Meents, Y. Watanabe, and A. Samuels, The Cell Biology of Secondary Cell Wall Biosynthesis, Annals of Botany, vol.121, issue.6, pp.1107-1132, 2018.

,

E. J. Mellerowicz, M. Baucher, B. Sundberg, and W. Boerjan, Unravelling Cell Wall Formation in the Woody Dicot Stem, Plant Molecular Biology, vol.47, issue.1-2, pp.239-74, 2001.

,

J. Miao, D. Guo, J. Zhang, Q. Huang, G. Qin et al., Targeted Mutagenesis in Rice Using CRISPR-Cas System, Cell Research, vol.23, issue.10, pp.1233-1269, 2013.

E. Miedes, R. Vanholme, W. Boerjan, and A. Molina, The Role of the Secondary Cell Wall in Plant Resistance to Pathogens, Frontiers in Plant Science, vol.5, pp.1-13, 2014.

J. Mierziak, K. Kostyn, and A. Kulma, Flavonoids as Important Molecules of Plant Interactions with the Environment, Molecules, vol.19, issue.10, pp.16240-65, 2014.

,

B. Miki and S. Mchugh, Selectable Marker Genes in Transgenic Plants: Applications, Alternatives and Biosafety, Journal of Biotechnology, vol.107, issue.3, pp.193-232, 2004.

,

F. R. Miller, , vol.24, p.1224, 1984.

G. Miller, N. Suzuki, S. Ciftci-yilmaz, and R. Mittler, Reactive Oxygen Species Homeostasis and Signalling during Drought and Salinity Stresses, Plant, Cell & Environment, vol.33, issue.4, pp.453-67, 2010.

R. A. Mitchell, P. Dupree, and P. R. Shewry, A Novel Bioinformatics Approach Identifies Candidate Genes for the Synthesis and Feruloylation of Arabinoxylan, Plant Physiology, vol.144, issue.1, pp.43-53, 2007.

N. Mitsuda, A. Iwase, H. Yamamoto, M. Yoshida, M. Seki et al., NAC Transcription Factors, NST1 and NST3, Are Key Regulators of the Formation of Secondary Walls in Woody Tissues of Arabidopsis, The Plant Cell Online, vol.19, issue.1, pp.270-80, 2007.

N. Mitsuda, M. Seki, K. Shinozaki, and M. Ohme-takagi, The NAC Transcription Factors NST1 and NST2 of Arabidopsis Regulate Secondary Wall Thickenings and Are Required for Anther Dehiscence, The Plant Cell, vol.17, pp.2993-3006, 2005.

,

A. Mliki, R. Jardak, G. M. Reustle, and A. Ghorbel, Isolation and Culture of Leaf Protoplasts from Tunisian Grapes, Journal International Des Sciences de La Vigne et Du Vin, vol.37, issue.3, pp.145-53, 2003.

D. Mohnen, Pectin Structure and Biosynthesis, Current Opinion in Plant Biology, vol.11, issue.3, pp.266-77, 2008.

A. Mohr and S. Raman, Lessons from First Generation Biofuels and Implications for the Sustainability Appraisal of Second Generation Biofuels, Energy Policy, vol.63, pp.114-136, 2013.

M. Mølhøj, S. Pagant, and H. Höfte, Towards Understanding the Role of Membrane-Bound Endo-?-1,4-Glucanases in Cellulose Biosynthesis, Plant and Cell Physiology, vol.43, issue.12, pp.1399-1406, 2002.

H. B. Molinari, K. Till, J. Pellny, P. R. Freeman, . Shewry et al., Grass Cell Wall Feruloylation: Distribution of Bound Ferulate and Candidate Gene Expression in Brachypodium Distachyon, Frontiers in Plant Science, vol.4, 2013.

,

R. L. Monk, F. R. Miller, and G. G. Mcbee, Sorghum Improvement for Energy Production, Biomass, vol.6, issue.1-2, pp.90017-90026, 1984.

M. Mookkan, K. Nelson-vasilchik, J. Hague, J. Zhanyuan, A. P. Zhang et al., Selectable Marker Independent Transformation of Recalcitrant Maize Inbred B73 and Sorghum P898012 Mediated by Morphogenic Regulators BABY BOOM and WUSCHEL2, Plant Cell Reports, vol.36, issue.9, pp.1477-91, 2017.

M. J. Moscou and A. J. Bogdanove, A Simple Cipher Governs DNA Recognition by TAL Effectors, Science, vol.326, issue.5959, pp.1501-1501, 2009.

J. Moura, C. A. Silva, J. Valencise-bonine, . De-oliveira-fernandes, M. C. Viana et al., Abiotic and Biotic Stresses and Changes in the Lignin Content and Composition in Plants, Journal of Integrative Plant Biology, vol.52, issue.4, pp.360-76, 2010.

G. Mu, N. Chang, K. Xiang, and Y. Sheng, Genetic Transformation of Maize Female Inflorescence Following Floral Dip Method Mediated by Agrobacterium, Biotechnology(Faisalabad), vol.11, issue.3, pp.178-83, 2012.

,

Y. Murakami, The Differentiation of Contact Cells and Isolation Cells in the Xylem Ray Parenchyma of Populus Maximowiczii, Annals of Botany, vol.84, issue.4, pp.429-464, 1999.

,

T. Murashige and F. Skoog, A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures, Physiologia Plantarum, vol.15, issue.3, pp.473-97, 1962.

,

S. C. Murray, L. William, S. E. Rooney, A. Mitchell, P. E. Sharma et al.,

S. Mullet and . Kresovich, Genetic Improvement of Sorghum as a Biofuel Feedstock: II. QTL for Stem and Leaf Structural Carbohydrates, Crop Science, vol.48, issue.6, pp.2180-93, 2008.

,

S. C. Murray, A. Sharma, W. L. Rooney, P. E. Klein, J. E. Mullet et al.,

S. Mitchell and . Kresovich, Genetic Improvement of Sorghum as a Biofuel Feedstock: I. QTL for Stem Sugar and Grain Nonstructural Carbohydrates, Crop Science, vol.48, issue.6, pp.2165-79, 2008.

M. Muthamilarasan, R. Khandelwal, C. Bhan-yadav, V. Suresh-bonthala, Y. Khan et al., Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C 4 Model Plant Foxtail Millet ( Setaria Italica L, p.9, 2014.

,

Y. Nakano, M. Yamaguchi, and H. Endo, NAC-MYB-Based Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Land Plants, Frontiers in Plant Science, vol.6, pp.1-18, 2015.

K. Nakashima, K. Yamaguchi-shinozaki, and K. Shinozaki, The Transcriptional Regulatory Network in the Drought Response and Its Crosstalk in Abiotic Stress Responses Including Drought, Cold, and Heat, Frontiers in Plant Science, vol.5, 2014.

,

M. A. Naoumkina, Q. Zhao, L. Gallego-giraldo, X. Dai, P. X. Zhao et al., Genome-Wide Analysis of Phenylpropanoid Defence Pathways, Molecular Plant Pathology, 2010.

M. Nasidi, R. Agu, Y. Deeni, and G. Walker, Improved Production of Ethanol Using Bagasse from Different Sorghum Cultivars, Biomass and Bioenergy, vol.72, pp.288-99, 2015.

I. Negrutiu, R. Shillito, I. Potrykus, G. Biasini, and F. Sala, Hybrid Genes in the Analysis of Transformation Conditions, Plant Molecular Biology, vol.8, issue.5, pp.363-73, 1987.

,

A. M. Nersissian and E. L. Shipp, Blue Copper-Binding Domains, pp.60056-60063, 2002.

R. H. Newman, S. J. Hill, and P. J. Harris, Wide-Angle X-Ray Scattering and Solid-State Nuclear Magnetic Resonance Data Combined to Test Models for Cellulose Microfibrils in Mung Bean Cell Walls, Plant Physiology, vol.163, issue.4, pp.1558-67, 2013.

L. J. Newman, E. Daniel, L. Perazza, M. M. Juda, and . Campbell, Involvement of the R2R3-MYB, AtMYB61, in the Ectopic Lignification and Dark-Photomorphogenic Components of the Det3 Mutant Phenotype, The Plant Journal, vol.37, issue.2, pp.239-50, 2004.

,

T. Nguyen, T. T. Van, M. Thu, G. Claeys, and . Angenon, Agrobacterium -Mediated Transformation of Sorghum ( Sorghum Bicolor (L.) Moench) Using an Improved in Vitro Regeneration System, Plant Cell, Tissue and Organ Culture, vol.91, issue.2, pp.155-64, 2007.

,

H. Nguyen-kim, Recherche de la fonction de protéines riches en hydroxyproline dans les parois végétales, Laboratoire de Recherche en Siences Végétales (LRSV), 2015.

. Ups/cnrs,

D. S. Nicholl, An Introduction to Genetic Engineering, 2002.

J. Nieuwland, R. Feron, A. H. Bastiaan, A. Huisman, C. W. Fasolino et al., Lipid Transfer Proteins Enhance Cell Wall Extension in Tobacco, The Plant Cell, vol.17, issue.7, pp.2009-2028, 2005.

. Nieves-cordones, A. Manuel, L. Chavanieu, C. Jeanguenin, W. Alcon et al., Distinct Amino Acids in the C-Linker Domain of the Arabidopsis K + Channel KAT2, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00962147

, Determine Its Subcellular Localization and Activity at the Plasma Membrane, Plant Physiology, vol.164, issue.3, pp.1415-1444

K. Nishitani and D. J. Nevins, Enzymic Analysis of Feruloylated Arabinoxylans (Feraxan) Derived from Zea Mays Cell Walls, Plant Physiology, vol.91, issue.1, pp.242-290, 1989.

,

B. Nixon, K. Tracy, A. Mansouri, J. Singh, J. K. Du et al., Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex, Scientific Reports, vol.6, issue.1, p.28696, 2016.

C. A. Norwood and R. S. Currie, Dryland Corn vs. Grain Sorghum in Western Kansas, Jpa, vol.10, issue.1, p.152, 1997.

M. Nuruzzaman, R. Manimekalai, A. M. Sharoni, K. Satoh, H. Kondoh et al., Genome-Wide Analysis of NAC Transcription Factor Family in Rice, Gene, vol.465, issue.1-2, pp.30-44, 2010.

,

. Nuruzzaman, A. M. Mohammed, S. Sharoni, and . Kikuchi, Roles of NAC Transcription Factors in the Regulation of Biotic and Abiotic Stress Responses in Plants, Frontiers in Microbiology, vol.4, pp.1-16, 2013.

M. O'neill, P. Albersheim, and A. Darvill, The Pectic Polysaccharides of Primary Cell Walls, pp.415-456, 1990.

M. Ochoa-villarreal and E. Aispuro-hernndez, Plant Cell Wall Polymers: Function, Structure and Biological Activity of Their Derivatives, Irasema Vargas-Arispuro, and Miguel Ngel, 2012.

J. T. Odell, F. Nagy, and N. Chua, Identification of DNA Sequences Required for Activity of the Cauliflower Mosaic Virus 35S Promoter, Nature, vol.313, issue.6005, pp.810-822, 1985.

,

K. Ohashi-ito, Y. Oda, and H. Fukuda, Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 Directly Regulates the Genes That Govern Programmed Cell Death and Secondary Wall Formation during Xylem Differentiation, The Plant Cell, vol.22, issue.10, pp.3461-73, 2010.

,

M. Ohtani, N. Nishikubo, B. Xu, M. Yamaguchi, N. Mitsuda et al., A NAC Domain Protein Family Contributing to the Regulation of Wood Formation in Poplar, The Plant Journal, vol.67, issue.3, pp.499-512, 2011.

M. C. Oldham, S. Horvath, and D. H. Geschwind, Conservation and Evolution of Gene Coexpression Networks in Human and Chimpanzee Brains, Proceedings of the National Academy of Sciences of the United States of America, vol.103, issue.47, pp.17973-78, 2006.

,

H. Ooka, H. Ooka, K. Satoh, K. Satoh, K. Doi et al., Comprehensive Analysis of NAC Family Genes In, Analysis, vol.247, pp.239-286, 2003.

T. M. Ou-lee, R. Turgeon, and R. Wu, Expression of a Foreign Gene Linked to Either a Plant-Virus or a Drosophila Promoter, after Electroporation of Protoplasts of Rice, Wheat, and Sorghum, Proceedings of the National Academy of Sciences of the United States of America, vol.83, issue.18, pp.6815-6834, 1986.

S. Pagant, A. Bichet, K. Sugimoto, O. Lerouxel, T. Desprez et al., Kobito1 Encodes a Novel Plasma Membrane Protein Necessary for Normal Synthesis of Cellulose during Cell Expansion in Arabidopsis, Plant Cell, vol.14, issue.9, pp.2001-2014, 2002.

M. T. Page, A. J. Martin, E. Parry, and . Carmo-silva, A High-throughput Transient Expression System for Rice, Plant, Cell & Environment, 2019.

N. A. Palmer, E. Scott, A. J. Sattler, D. Saathoff, J. F. Funnell et al., Genetic Background Impacts Soluble and Cell Wall-Bound Aromatics in Brown Midrib Mutants of Sorghum, Planta, vol.229, issue.1, pp.115-142, 2008.

A. N. Panche, A. D. Diwan, and S. R. Chandra, Flavonoids: An Overview, Journal of Nutritional Science, vol.5, p.47, 2016.

J. Paszkowski, R. D. Shillito, M. Saul, V. Mandak, T. Hohn et al., Direct Gene Transfer to Plants, vol.3, issue.12, pp.2717-2739, 1984.

A. H. Paterson, J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood et al., The Sorghum Bicolor Genome and the Diversification of Grasses, Nature, vol.457, issue.7229, pp.551-56, 2009.

P. Pawar, S. Mohan-anupama, M. Koutaniemi, E. J. Tenkanen, and . Mellerowicz, Acetylation of Woody Lignocellulose: Significance and Regulation, Frontiers in Plant Science, vol.4, 2013.

A. Peaucelle, S. Braybrook, and H. Höfte, Cell Wall Mechanics and Growth Control in Plants: The Role of Pectins Revisited, Frontiers in Plant Science, vol.3, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01203961

O. Pechanova, C. Hsu, J. P. Adams, T. Pechan, L. Vandervelde et al., Apoplast Proteome Reveals That Extracellular Matrix Contributes to Multistress Response in Poplar, BMC Genomics, vol.11, issue.1, p.674, 2010.

J. F. Pedersen, J. J. Toy, D. L. Funnell, S. E. Sattler, A. L. Oliver et al., Registration of BN611, AN612, BN612, and RN613 Sorghum Genetic Stocks with, p.12, 2008.

, Journal of Plant Registrations, vol.2, issue.3, p.258

,

B. W. Penning, T. Charles, R. Hunter, A. L. Tayengwa, . Eveland et al.,

A. T. Dugard, W. Olek, and . Vermerris, Genetic Resources for Maize Cell Wall Biology, Plant Physiology, vol.151, issue.4, pp.1703-1731, 2009.

A. Pereira-santana, L. David-alcaraz, E. Castaño, L. Sanchez-calderon, F. Sanchez-teyer et al., Comparative Genomics of NAC Transcriptional Factors in Angiosperms: Implications for the Adaptation and Diversification of Flowering Plants, PLoS ONE, vol.10, issue.11, 2015.

L. Perrier, Analyse et modélisation de la variabilité phénotypique du sorgho biomasse (Sorghum bicolor) pour l'exploration d'idéotypes dans un contecte de diversification des usages, Unité de Recherche AGAP, 2017.

L. Perrier, L. Rouan, S. Jaffuel, A. Clément-vidal, S. Roques et al., Plasticity of Sorghum Stem Biomass Accumulation in Response to Water Deficit: A Multiscale Analysis from Internode Tissue to Plant Level, Frontiers in Plant Science, vol.8, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606927

R. M. Perrin, Xyloglucan Fucosyltransferase, an Enzyme Involved in Plant Cell Wall Biosynthesis, Science, vol.284, issue.5422, pp.1976-79, 1999.

S. Persson, A. Paredez, A. Carroll, H. Palsdottir, M. Doblin et al., Genetic Evidence for Three Unique Components in Primary Cell-Wall Cellulose Synthase Complexes in, 2007.

. Arabidopsis, Proceedings of the National Academy of Sciences of the United States of America, vol.104, pp.15566-71

S. Persson, H. Wei, J. Milne, G. P. Page, and C. R. Somerville, Identification of Genes Required for Cellulose Synthesis by Regression Analysis of Public Microarray Data Sets, Proceedings of the National Academy of Sciences of the United States of America, vol.102, issue.24, pp.8633-8671, 2005.

M. Pertea, D. Kim, G. M. Pertea, J. T. Leek, and S. L. Salzberg, Transcript-Level Expression Analysis of RNA-Seq Experiments with HISAT, StringTie and Ballgown, Nature Protocols, vol.11, p.1650, 2016.

M. Pesch and M. Hülskamp, One, Two, Three?models for Trichome Patterning in Arabidopsis?, Current Opinion in Plant Biology, vol.12, issue.5, pp.587-92, 2009.

,

. Petti, A. E. Carloalberto, M. Harman-ware, R. Tateno, A. Kushwaha et al., Sorghum Mutant RG Displays Antithetic Leaf Shoot Lignin Accumulation Resulting in Improved Stem Saccharification Properties, Biotechnology for Biofuels, vol.6, issue.1, 2013.

C. Petti, K. Hirano, J. Stork, and S. Debolt, Mapping of a Cellulose-Deficient Mutant Named Dwarf1-1 in Sorghum Bicolor to the Green Revolution Gene Gibberellin20-Oxidase Reveals a Positive Regulatory Association between Gibberellin and Cellulose Biosynthesis, Plant Physiology, vol.169, issue.1, pp.705-721, 2015.

,

C. Plomion, A. Leprovost, and . Stokes, Wood Formation in Trees, Plant Physiology, vol.127, issue.4, pp.1513-1536, 2001.
URL : https://hal.archives-ouvertes.fr/hal-01204210

J. Poehlman and . Milton, Breeding Sorghum and Millet, Breeding Field Crops, pp.508-55, 1987.

. Potrykus, M. W. Ingo, J. Saul, J. Petruska, R. D. Paszkowski et al., Direct Gene Transfer to Cells of a Graminaceous Monocot, MGG Molecular & General Genetics, vol.199, issue.2, pp.183-88, 1985.

J. Preston, J. Wheeler, J. Heazlewood, S. F. Li, and R. W. Parish, AtMYB32 Is Required for Normal Pollen Development in Arabidopsis Thaliana, The Plant Journal, vol.40, issue.6, pp.979-95, 2004.

S. Proost, A. Krawczyk, and M. Mutwil, LSTrAP: Efficiently Combining RNA Sequencing Data into Co-Expression Networks, BMC Bioinformatics, vol.18, issue.1, pp.1-9, 2017.

,

J. L. Propheter, S. A. Staggenborg, X. Wu, and D. Wang, Performance of Annual and Perennial Biofuel Crops: Yield during the First Two Years, Agronomy Journal, vol.102, issue.2, p.806, 2010.

J. L. Pruneda-paz, G. Breton, D. H. Nagel, S. E. Kang, K. Bonaldi et al.,

S. Doherty, M. Ravelo, J. R. Galli, S. A. Ecker, and . Kay, A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors, Cell Reports, vol.8, issue.2, pp.622-654, 2014.

R. N. Pu and . Goodman, Induction of Necrogenesis by Agrobacterium Tumefaciens on Grape Explants, Physiological and Molecular Plant Pathology, vol.41, issue.4, pp.241-54, 1992.

,

S. Puranik, P. Pankaj-sahu, S. Nath-mandal, V. Suresh, B. Swarup-kumar-parida et al., Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria Italica L.), PLoS ONE, vol.8, issue.5, 2013.

S. Puranik, P. P. Sahu, P. S. Srivastava, and M. Prasad, NAC Proteins: Regulation and Role in Stress Tolerance, Trends in Plant Science, vol.17, issue.6, pp.369-81, 2012.

,

P. Rabinowicz, E. Braun, A. Wolfe, B. Bowen, and E. Grotewold, Maize R2R3 Myb Genes: Sequence Analysis Reveals Amplification in the Higher Plants, Genetics, vol.153, issue.1, pp.427-471, 1999.

J. Raes, A. Rohde, J. Holst-christensen, Y. Van-de-peer, and W. Boerjan, Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis, Plant Physiology, vol.133, issue.3, pp.1051-71, 2003.

A. Raghuwanshi and R. G. Birch, Genetic Transformation of Sweet Sorghum, Plant Cell Reports, vol.29, issue.9, pp.997-1005, 2010.

K. M. Rai, W. Sandi, . Thu, K. Vimal, C. J. Balasubramanian et al., Identification, Characterization, and Expression Analysis of Cell Wall Related Genes in Sorghum Bicolor (L.) Moench, a Food, Fodder, and Biofuel Crop, Frontiers in Plant Science, vol.7, pp.1-19, 2016.

C. B. Rajashekar and M. J. Burke, Freezing Characteristics of Rigid Plant Tissues (Development of Cell Tension during Extracellular Freezing), Plant Physiology, vol.111, issue.2, pp.597-603, 1996.

C. B. Rajashekar and A. Lafta, Cell-Wall Changes and Cell Tension in Response to Cold Acclimation and Exogenous Abscisic Acid in Leaves and Cell Cultures, Plant Physiology, vol.111, issue.2, pp.605-617, 1996.

M. Rakoczy-trojanowska, Alternative Methods of Plant Transformation: A Short Review, Cellular & Molecular Biology Letters, vol.7, issue.3, pp.849-58, 2002.

J. Ralph, K. Lundquist, G. Brunow, F. Lu, H. Kim et al.,

. Marita, Lignins: Natural Polymers from Oxidative Coupling of 4-Hydroxyphenyl-Propanoids, Phytochemistry Reviews, vol.3, issue.1-2, pp.29-60, 2004.

,

A. Ranjan, N. Pandey, D. Lakhwani, N. Kumar-dubey, V. Uday et al., Comparative Transcriptomic Analysis of Roots of Contrasting Gossypium Herbaceum Genotypes Revealing Adaptation to Drought, BMC Genomics, vol.13, issue.1, p.680, 2012.

X. Rao, X. Chen, H. Shen, Q. Ma, G. Li et al., Gene Regulatory Networks for Lignin Biosynthesis in Switchgrass (Panicum Virgatum), Plant Biotechnology Journal, vol.17, issue.3, pp.580-93, 2019.

X. Rao and R. A. Dixon, Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses, Frontiers in Plant Science, vol.9, pp.1-11, 2018.

,

X. Rao, H. Shen, S. Pattathil, M. G. Hahn, I. Gelineo-albersheim et al., Dynamic Changes in Transcriptome and Cell Wall Composition Underlying Brassinosteroid-Mediated Lignification of Switchgrass Suspension Cells, Biotechnology for Biofuels, vol.10, issue.1, p.266, 2017.

K. Ratanasut, W. Rod-in, and K. Sujipuli, In Planta Agrobacterium -Mediated Transformation of Rice, Rice Science, vol.24, issue.3, pp.181-86, 2017.

,

S. M. Read and A. Bacic, PLANT BIOLOGY: Prime Time for Cellulose, Science, vol.295, issue.5552, pp.59-60, 2002.

E. A. Rennie and H. V. Scheller, Xylan Biosynthesis, Current Opinion in Biotechnology, vol.26, pp.100-107, 2014.

A. Repellin, M. Båga, P. Prem, R. N. Jauhar, and . Chibbar, Genetic Enrichment of Cereal Crops via Alien Gene Transfer: New Challenges, Plant Cell, Tissue and Organ Culture, vol.64, issue.2-3, pp.159-83, 2001.

W. R. Richie and G. Mcbee, Structural Components in Sorghum Stem Biomass, Bioresource Technology, vol.38, issue.1, pp.90216-90223, 1991.

B. L. Ridley, A. Malcolm, D. O'neill, and . Mohnen, Pectins: Structure, Biosynthesis, and Oligogalacturonide-Related Signaling, Phytochemistry, vol.57, issue.6, pp.929-67, 2001.

, , pp.113-116

M. E. Ritchie, B. Phipson, D. Wu, Y. Hu, C. W. Law et al., Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies, Nucleic Acids Research, vol.43, issue.7, 2015.

S. Robert, A. Bichet, O. Grandjean, D. Kierzkowski, B. Satiat-jeunemaître et al., An Arabidopsis Endo-1,4-?-d-Glucanase Involved in Cellulose Synthesis Undergoes Regulated Intracellular Cycling, The Plant Cell, vol.17, issue.12, pp.3378-89, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00119358

,

M. D. Robinson, D. J. Mccarthy, and G. K. Smyth, EdgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data, Bioinformatics, vol.26, issue.1, pp.139-179, 2010.

A. C. Rocateli, R. L. Raper, K. S. Balkcom, F. J. Arriaga, and D. I. Bransby, Biomass Sorghum Production and Components under Different Irrigation/Tillage Systems for the Southeastern U.S, Industrial Crops and Products, vol.36, issue.1, pp.589-98, 2012.

,

J. M. Romano, C. Dubos, M. B. Prouse, O. Wilkins, H. Hong et al., At MYB61, an R2R3-MYB Transcription Factor, Functions as a Pleiotropic Regulator via a Small Gene Network, New Phytologist, vol.195, issue.4, pp.774-86, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01190729

,

W. L. Rooney, J. Blumenthal, B. Bean, and J. E. Mullet, Designing Sorghum as a Dedicated Bioenergy Feedstock, Biofuels, Bioproducts and Biorefining, vol.1, issue.2, pp.147-57, 2007.

,

J. K. Rose, J. Braam, S. C. Fry, and K. Nishitani, The XTH Family of Enzymes Involved in Xyloglucan Endotransglucosylation and Endohydrolysis: Current Perspectives and a New Unifying Nomenclature, Plant and Cell Physiology, vol.43, issue.12, pp.1421-1456, 2002.

D. T. Rosenow, J. E. Quisenberry, C. W. Wendt, and L. E. Clark, Drought Tolerant Sorghum and Cotton Germplasm, Agricultural Water Management, vol.7, issue.1-3, pp.207-229, 1983.

, , pp.90084-90091

J. A. Rosinski and W. R. Atchley, Molecular Evolution of the Myb Family of Transcription Factors: Evidence for Polyphyletic Origin, Journal of Molecular Evolution, vol.46, issue.1, pp.74-83, 1998.

V. Rubio, F. Linhares, R. Solano, A. C. Martín, J. Iglesias et al., A Conserved MYB Transcription Factor Involved in Phosphate Starvation Signaling Both in Vascular Plants and in Unicellular Algae, Genes and Development, vol.15, issue.16, pp.2122-2155, 2001.

K. Ruel, Y. Nishiyama, and J. Joseleau, Crystalline and Amorphous Cellulose in the Secondary Walls of Arabidopsis, Plant Science, pp.48-61, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00720296

,

C. Ruprecht, M. Mutwil, F. Saxe, M. Eder, Z. Nikoloski et al., Large-Scale Co-Expression Approach to Dissect Secondary Cell Wall Formation Across Plant Species, Frontiers in Plant Science, vol.2, 2011.

A. Saballos, Development and Utilization of Sorghum as a Bioenergy Crop, Genetic Improvement of Bioenergy Crops, pp.211-259, 2008.

,

A. Saballos, G. Ejeta, E. Sanchez, C. Kang, and W. Vermerris, A Genomewide Analysis of the Cinnamyl Alcohol Dehydrogenase Family in Sorghum [ Sorghum Bicolor (L.) Moench] Identifies SbCAD2 as the Brown Midrib6 Gene, Genetics, vol.181, issue.2, pp.783-95, 2009.

A. Saballos, S. E. Sattler, E. Sanchez, T. P. Foster, Z. Xin et al., Brown Midrib2 (Bmr2) Encodes the Major 4-Coumarate: Coenzyme A Ligase Involved in Lignin Biosynthesis in Sorghum (Sorghum Bicolor (L.) Moench), Plant Journal, vol.70, issue.5, pp.818-848, 2012.

R. W. Sablowski and E. M. Meyerowitz, A Homolog of NO APICAL MERISTEM Is an Immediate Target of the Floral Homeotic Genes APETALA3/PISTILLATA, Cell, vol.92, issue.1, pp.93-103, 1998.

. Sáez-plaza, M. Purificación, S. Navas, T. Wybraniec, A. Micha?owski et al., An Overview of the Kjeldahl Method of Nitrogen Determination, 2013.

, Working Scale, Instrumental Finish, and Quality Control, Critical Reviews in Analytical Chemistry, vol.43, issue.4, pp.224-72

B. C. Saha, Hemicellulose Bioconversion, Journal of Industrial Microbiology and Biotechnology, vol.30, issue.5, pp.279-91, 2003.

G. Saha and J. In, Characterization and Expression Profiling of MYB Transcription Factors against Stresses and during Male Organ Development in Chinese Cabbage, 2016.

. Pekinensis, Plant Physiology and Biochemistry, vol.104, pp.200-215

,

R. V. Sairam, N. Seetharama, P. S. Devi, A. Verma, U. R. Murthy et al., Culture and Regeneration of Mesophyll-Derived Protoplasts of Sorghum, 1999.

. Moench, Plant Cell Reports, vol.18, issue.12, pp.972-77

L. Samuels, L. Kunst, and R. Jetter, Sealing Plant Surfaces: Cuticular Wax Formation by Epidermal Cells, Annual Review of Plant Biology, vol.59, issue.1, pp.683-707, 2008.

,

R. Sanagala, A. Kumar-moola, and R. Diana, A Review on Advanced Methods in Plant Gene Targeting, Journal of Genetic Engineering and Biotechnology, vol.15, issue.2, pp.317-338, 2017.

C. Sánchez-rodríguez, S. Bauer, K. Hématy, F. Saxe, A. B. Ibáñez et al., CHITINASE-LIKE1/POM-POM1 and Its Homolog CTL2 Are Glucan-Interacting Proteins Important for Cellulose Biosynthesis in Arabidopsis, The Plant Cell, vol.24, issue.2, pp.589-607, 2012.

J. C. Sanford, M. Theodore, E. D. Klein, N. Wolf, and . Allen, Delivery Of Substances Into Cells And Tissues Using A Particle Bombardment Process, Particulate Science and Technology, vol.5, issue.1, pp.27-37, 1987.

S. Sanjari, R. Shirzadian-khorramabad, Z. Sadat-shobbar, and M. Shahbazi, Systematic Analysis of NAC Transcription Factors' Gene Family and Identification of Post-Flowering Drought Stress Responsive Members in Sorghum, Plant Cell Reports, vol.38, issue.3, pp.361-76, 2019.

R. R. Sant, . Prasad, F. Gautier, S. Homa, S. Pointet et al., A Large Set of 26 New Reference Transcriptomes Dedicated to Comparative Population Genomics in Crops and Wild Relatives, Center for Tropical Crops and Biocommodities, vol.17, pp.565-80, 2011.

T. Sasaki and I. Project, The Map-Based Sequence of the Rice Genome, Nature, vol.436, issue.7052, pp.793-800, 2005.

R. Sasidharan, A. Laurentius, R. Voesenek, and . Pierik, Cell Wall Modifying Proteins Mediate Plant Acclimatization to Biotic and Abiotic Stresses, Critical Reviews in Plant Sciences, vol.30, issue.6, pp.548-62, 2011.

K. Sato, R. Suzuki, N. Nishikubo, S. Takenouchi, S. Ito et al., Isolation of a Novel Cell Wall Architecture Mutant of Rice with Defective Arabidopsis COBL4 Ortholog BC1 Required for Regulated Deposition of Secondary Cell Wall Components, Planta, vol.232, issue.1, pp.257-70, 2010.

S. Sato, T. Clemente, and I. Dweikat, Identification of an Elite Sorghum Genotype with High In Vitro Performance Capacity, In Vitro Cellular & Developmental Biology -Plant, vol.40, issue.1, pp.57-60, 2004.

S. E. Sattler and D. L. Funnell-harris, Modifying Lignin to Improve Bioenergy Feedstocks: Strengthening the Barrier against Pathogens? ?, Frontiers in Plant Science, vol.4, 2013.

S. E. Sattler, A. Saballos, Z. Xin, D. L. Funnell-harris, W. Vermerris et al., Characterization of Novel Sorghum Brown Midrib Mutants from an EMS-Mutagenized Population, pp.2115-2139, 2014.

,

I. M. Saxena, R. M. And, and . Brown, Cellulose Biosynthesis: Current Views and Evolving Concepts, Annals of Botany, vol.96, issue.1, pp.9-21, 2005.

P. Schaeffer and R. D. Hotchkiss, Fusion of Bacterial Protoplasts, Methods in Cell Biology, vol.20, pp.149-58, 1978.

H. Scheller, P. Vibe, and . Ulvskov, Hemicelluloses, Annual Review of Plant Biology, vol.61, issue.1, pp.263-89, 2010.

G. Schindelman, COBRA Encodes a Putative GPI-Anchored Protein, Which Is Polarly Localized and Necessary for Oriented Cell Expansion in Arabidopsis, Genes & Development, vol.15, issue.9, pp.1115-1142, 2001.

H. A. Schmidt, K. Strimmer, M. Vingron, and A. Haeseler, TREE-PUZZLE: Maximum Likelihood Phylogenetic Analysis Using Quartets and Parallel Computing, Bioinformatics, vol.18, issue.3, pp.502-506, 2002.

A. J. Schmitz, K. Begcy, G. Sarath, and H. Walia, Rice Ovate Family Protein 2 ( OFP2 ) Alters Hormonal Homeostasis and Vasculature Development, Plant Science, vol.241, pp.177-88, 2015.

P. S. Schnable, D. Ware, R. S. Fulton, J. C. Stein, F. Wei et al., The B73 Maize Genome: Complexity, Diversity, and Dynamics, vol.326, pp.1112-1127, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00751527

,

P. Schopfer, Biomechanics of Plant Growth, American Journal of Botany, vol.93, issue.10, pp.1415-1440, 2006.

E. D. Scully, T. Gries, G. Sarath, N. A. Palmer, L. Baird et al., Overexpression of SbMyb60 Impacts Phenylpropanoid Biosynthesis and Alters Secondary Cell Wall Composition in Sorghum Bicolor, Plant Journal, vol.85, issue.3, pp.378-95, 2016.

E. D. Scully, T. Gries, D. L. Funnell-harris, Z. Xin, F. A. Kovacs et al., Characterization of Novel Brown Midrib 6 Mutations Affecting Lignin Biosynthesis in Sorghum, Journal of Integrative Plant Biology, vol.58, issue.2, pp.136-185, 2016.

E. D. Scully, T. Gries, N. A. Palmer, G. Sarath, D. L. Funnell-harris et al., Overexpression of SbMyb60 in Sorghum Bicolor Impacts Both Primary and Secondary Metabolism, New Phytologist, vol.63, 2017.

G. J. Seifert and C. Blaukopf, Irritable Walls: The Plant Extracellular Matrix and Signaling, Plant Physiology, vol.153, issue.2, pp.467-78, 2010.

G. J. Seifert and K. Roberts, The Biology of Arabinogalactan Proteins, Annual Review of Plant Biology, vol.58, issue.1, pp.137-61, 2007.

,

N. Shakoor, R. Nair, O. Crasta, G. Morris, A. Feltus et al., A Sorghum Bicolor Expression Atlas Reveals Dynamic Genotype-Specific Expression Profiles for Vegetative Tissues of Grain, Sweet and Bioenergy Sorghums, BMC Plant Biology, vol.14, issue.1, p.35, 2014.

J. Sheen, Signal Transduction in Maize and Arabidopsis Mesophyll Protoplasts, Plant Physiology, vol.127, issue.4, pp.1466-75, 2001.

H. Shen, X. He, C. R. Poovaiah, W. A. Wuddineh, J. Ma et al., Functional Characterization of the Switchgrass (Panicum Virgatum) R2R3-MYB Transcription Factor PvMYB4 for Improvement of Lignocellulosic Feedstocks, New Phytologist, vol.193, issue.1, pp.121-157, 2012.

H. Shen, Y. Yin, F. Chen, Y. Xu, and R. A. Dixon, A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production, BioEnergy Research, vol.2, issue.4, pp.217-249, 2009.

S. Shimada, Y. Makita, T. Kuriyama-kondou, M. Kawashima, Y. Mochizuki et al., Functional and Expression Analyses of Transcripts Based on Full-Length CDNAs of Sorghum Bicolor, DNA Research, vol.22, issue.6, pp.485-93, 2015.

K. Shimamoto, R. Terada, T. Izawa, and H. Fujimoto, Fertile Transgenic Rice Plants Regenerated from Transformed Protoplasts, Nature, vol.338, issue.6212, pp.274-76, 1989.

,

K. Shiriga, R. Sharma, K. Kumar, S. Kumar-yadav, F. Hossain et al., Genome-Wide Identification and Expression Pattern of Drought-Responsive Members of the NAC Family in Maize, Meta Gene, vol.2, issue.1, pp.407-424, 2014.

,

A. L. Shiringani and W. Friedt, QTL for Fibre-Related Traits in Grain × Sweet Sorghum as a Tool for the Enhancement of Sorghum as a Biomass Crop, Theoretical and Applied Genetics, vol.123, issue.6, pp.999-1011, 2011.

S. Shiu and A. B. Bleecker, Receptor-like Kinases from Arabidopsis Form a Monophyletic Gene Family Related to Animal Receptor Kinases, Proceedings of the National Academy of Sciences, vol.98, pp.10763-68, 2001.

A. Shrawat, H. Kumar, and . Lörz, Agrobacterium-Mediated Transformation of Cereals: A Promising Approach Crossing Barriers, Plant Biotechnology Journal, vol.4, issue.6, pp.575-603, 2006.

,

R. Sibout, S. Proost, N. Bjoern-oest-hansen, F. M. Vaid, S. Giorgi et al., Expression Atlas and Comparative Coexpression Network Analyses Reveal Important Genes Involved in the Formation of Lignified Cell Wall in Brachypodium Distachyon, New Phytologist, vol.215, issue.3, pp.1009-1034, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01606765

,

L. S. Silva, J. Da, J. R. Taylor, and . Taylor, Transgenic Sorghum with Altered Kafirin Synthesis: Kafirin Solubility, Polymerization, and Protein Digestion, Journal of Agricultural and Food Chemistry, vol.59, issue.17, pp.9265-70, 2011.

M. Simon, M. M. Lee, Y. Lin, L. Gish, and J. Schiefelbein, Distinct and Overlapping Roles of Single-Repeat MYB Genes in Root Epidermal Patterning, Developmental Biology, vol.311, issue.2, pp.566-78, 2007.

R. Sinclair, M. Ruiz-rosquete, and G. Drakakaki, Post-Golgi Trafficking and Transport of Cell Wall Components, Frontiers in Plant Science, vol.871, pp.1-11, 2018.

,

S. Sircar, N. Parekh, and G. Sablok, Protocol for Coexpression Network Construction and Stress-Responsive Expression Analysis in Brachypodium, In Methods in Molecular Biology, vol.1667, pp.203-224, 2018.

,

B. Skadhauge, K. K. Thomsen, and D. Wettstein, The Role of the Barley Testa Layer and Its Flavonoid Content in Resistance to Fusarium Infections, Hereditas, vol.126, issue.2, pp.147-60, 1997.

A. Skirycz and D. Inzé, More from Less: Plant Growth under Limited Water, Current Opinion in Biotechnology, vol.21, issue.2, pp.197-203, 2010.

,

A. Slater, N. Scott, and M. Fowler, Plant Biotechnology: The Genetic Manipulation of Plants, Annals of Botany, vol.94, issue.4, pp.646-646, 2003.

T. L. Slewinski, Non-Structural Carbohydrate Partitioning in Grass Stems: A Target to Increase Yield Stability, Stress Tolerance, and Biofuel Production, Journal of Experimental Botany, vol.63, issue.13, pp.4647-70, 2012.

M. Smallwood, D. J. Bowles-;-d, P. J. Bowles, D. A. Lillford, I. A. Rees et al., Plants in a Cold Climate, Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, vol.357, pp.831-878, 1423.

,

S. Smita, A. Katiyar, V. Chinnusamy, M. Dev, K. C. Pandey et al., Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice, Frontiers in Plant Science, vol.6, 2015.

,

G. A. Smith, M. O. Bagby, R. T. Lewellan, D. L. Doney, P. H. Moore et al., Evaluation of Sweet Sorghum for Fermentable Sugar Production Potential1, Crop Science, vol.27, issue.4, p.788, 1987.

,

R. A. Smith, M. Schuetz, S. D. Karlen, D. Bird, N. Tokunaga et al., Defining the Diverse Cell Populations Contributing to Lignification in Arabidopsis Stems, Plant Physiology, vol.174, issue.2, pp.1028-1064, 2017.

R. H. Smith and E. E. Hood, Agrobacterium Tumefaciens Transformation of Monocotyledons, Crop Science, vol.35, issue.2, p.301, 1995.

,

P. J. Soest, J. B. Van, B. A. Robertson, and . Lewis, Methods for Dietary Fiber, Neutral Detergent Fiber, and Nonstarch Polysaccharides in Relation to Animal Nutrition, Journal of Dairy Science, vol.74, issue.10, pp.78551-78553, 1991.

D. Solecka, A. Boudet, and A. Kacperska, Phenylpropanoid and Anthocyanin Changes in Low-Temperature Treated Winter Oilseed Rape Leaves, Plant Physiology and Biochemistry, vol.37, issue.6, pp.491-96, 1999.

D. Solecka, J. ?ebrowski, and A. Kacperska, Are Pectins Involved in Cold Acclimation and De-Acclimation of Winter Oil-Seed Rape Plants?, Annals of Botany, vol.101, issue.4, pp.521-551, 2008.

M. Soler, E. Leal-oliveira, V. Camargo, H. Carocha, H. Cassan-wang et al.,

J. Grima-pettenati, The Eucalyptus Grandis R2R3-MYB Transcription Factor Family: Evidence for Woody Growth-Related Evolution and Function, New Phytologist, vol.206, issue.4, pp.1364-77, 2015.

F. Sonbol, S. Fornalé, M. Capellades, A. Encina, S. Touriño et al., The Maize ZmMYB42 Represses the Phenylpropanoid Pathway and Affects the Cell Wall Structure, Composition and Degradability, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00396628

A. Thaliana, Plant Molecular Biology, vol.70, issue.3, pp.283-96

P. Sood, A. Bhattacharya, and A. Sood, Problems and Possibilities of Monocot Transformation, Biologia Plantarum, vol.55, issue.1, pp.1-15, 2011.

E. Souer, A. Van-houwelingen, D. Kloos, J. Mol, and R. Koes, The No Apical Meristem Gene of Petunia Is Required for Pattern Formation in Embryos and Flowers and Is Expressed at Meristem and Primordia Boundaries, Cell, vol.85, issue.2, pp.159-70, 1996.

, , pp.81093-81097

W. R. Souza, P. K. De, J. Martins, . Freeman, K. Till et al., Suppression of a Single BAHD Gene in Setaria Viridis Causes Large, Stable Decreases in Cell Wall Feruloylation and Increases Biomass Digestibility, New Phytologist, vol.218, issue.1, pp.81-93, 2018.

M. Stefanowska, Low Temperature Affects Pattern of Leaf Growth and Structure of Cell Walls in Winter Oilseed Rape (Brassica Napus L., Var. Oleifera L.), Annals of Botany, vol.84, issue.3, pp.313-332, 1999.

S. J. Streatfield, M. E. Magallanes-lundback, K. K. Beifuss, A. Christopher, R. L. Brooks et al., Analysis of the Maize Polyubiquitin-1 Promoter Heat Shock Elements and Generation of Promoter Variants with Modified Expression Characteristics, Transgenic Research, vol.13, issue.4, pp.299-312, 2004.

V. Sutter, R. Vanderhaeghen, S. Tilleman, F. Lammertyn, I. Vanhoutte et al., Exploration of Jasmonate Signalling via Automated and Standardized Transient Expression Assays in Tobacco Cells, The Plant Journal, vol.44, issue.6, pp.1065-76, 2005.

Z. Swigonova, Close Split of Sorghum and Maize Genome Progenitors, Genome Research, vol.14, issue.10a, pp.1916-1939, 2004.

P. M. Szyjanowicz, I. Mckinnon, N. G. Taylor, J. Gardiner, M. C. Jarvis et al., The Irregular Xylem 2 Mutant Is an Allele of Korrigan That Affects the Secondary Cell Wall of Arabidopsis Thaliana, The Plant Journal, vol.37, issue.5, pp.730-770, 2004.

,

Y. Tadesse, L. Sági, R. Swennen, and M. Jacobs, Optimisation of Transformation Conditions and Production of Transgenic Sorghum (Sorghum Bicolor) via, 2003.

M. Bombardment, Plant Cell, Tissue and Organ Culture, vol.75, issue.1, pp.1-18

,

Y. Tai, C. Liu, S. Yu, H. Yang, J. Sun et al., Gene Co-Expression Network Analysis Reveals Coordinated Regulation of Three Characteristic Secondary Biosynthetic Pathways in Tea Plant (Camellia Sinensis), BMC Genomics, vol.19, issue.1, pp.1-13, 2018.

L. Taiz and E. Zeiger, Plant Physiology, 1998.

K. Takahagi, K. Inoue, and K. Mochida, Gene Co-Expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat, Frontiers in Plant Science, vol.9, pp.1-10, 2018.

M. Tan, D. Cheng, Y. Yang, G. Zhang, M. Qin et al., Co-Expression Network Analysis of the Transcriptomes of Rice Roots Exposed to Various Cadmium Stresses Reveals Universal Cadmium-Responsive Genes, BMC Plant Biology, vol.17, issue.1, pp.1-18, 2017.

T. Tan, H. Tian, R. Endo, T. Sano, M. Kurata et al., Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation, Plant Physiology, vol.176, issue.1, pp.773-89, 2018.

K. Tanaka, K. Murata, M. Yamazaki, K. Onosato, A. Miyao et al., Three Distinct Rice Cellulose Synthase Catalytic Subunit Genes Required for Cellulose Synthesis in the Secondary Wall, Plant Physiology, vol.133, issue.1, pp.73-83, 2003.

,

N. G. Taylor, R. M. Howells, A. K. Huttly, K. Vickers, and S. R. Turner, Interactions among Three Distinct CesA Proteins Essential for Cellulose Synthesis, Proceedings of the National Academy of Sciences, vol.100, issue.3, pp.1450-55, 2003.

R. Tenhaken, Cell Wall Remodeling under Abiotic Stress, Frontiers in Plant Science, vol.5, pp.1-9, 2015.

N. Terashima, H. G. Jung, D. R. Buxton, R. D. Hatfield, J. Ralph et al.,

. Takabe, Comprehensive Model of the Lignified Plant Cell Wall, 1993.

,

H. M. Tetreault, D. Erin, T. Scully, N. A. Gries, D. L. Palmer et al., Overexpression of the Sorghum Bicolor SbCCoAOMT Alters Cell Wall Associated Hydroxycinnamoyl Groups, PLoS ONE, vol.13, issue.10, pp.1-25, 2018.

,

K. Thera, Analyse des déterminants génétiques contrôlant la production et la composition de la tige chez le sorgho (Sorghum Bicolor [l.] Moench). Intégration des approches bi-et multiparentales, Unité de Recherche AGAP, 2017.

B. Thomma, B. Cammue, and K. Thevissen, Plant Defensins, Planta, vol.216, issue.2, pp.193-202, 2002.

D. Thompson, A. Regev, and S. Roy, Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution, Annual Review of Cell and Developmental Biology, vol.31, issue.1, pp.399-428, 2015.

P. K. Thornton, A. Whitbread, T. Baedeker, J. Cairns, L. Claessens et al., A Framework for Priority-Setting in Climate Smart Agriculture Research, Agricultural Systems, vol.167, pp.161-75, 2018.

,

T. Tian, Q. You, L. Zhang, X. Yi, H. Yan et al., Original Article SorghumFDB : Sorghum Functional Genomics Database with Multidimensional Network Analysis, pp.1-16, 2016.

S. Tingay, D. Mcelroy, R. Kalla, S. Fieg, M. Wang et al., Agrobacterium Tumefaciens-Mediated Barley Transformation, The Plant Journal, vol.11, issue.6, pp.1369-76, 1997.

Y. Tobimatsu and M. Schuetz, Lignin Polymerization: How Do Plants Manage the Chemistry so Well?, Current Opinion in Biotechnology, vol.56, pp.75-81, 2019.

,

D. Todaka, K. Nakashima, K. Maruyama, S. Kidokoro, Y. Osakabe et al., Rice Phytochrome-Interacting Factor-like Protein OsPIL1 Functions as a Key Regulator of, 2012.

, Internode Elongation and Induces a Morphological Response to Drought Stress, Proceedings of the National Academy of Sciences, vol.109, issue.39, pp.15947-52

,

B. T. Townsley, R. Neelima, J. Sinha, and . Kang, KNOX1 Genes Regulate Lignin Deposition and Composition in Monocots and Dicots, Frontiers in Plant Science, vol.4, 2013.

L. Tran, K. Phan, Y. Nakashima, S. D. Sakuma, Y. Simpson et al., Isolation and Functional Analysis of Arabidopsis Stress-Inducible NAC Transcription Factors That Bind to a Drought-Responsive Cis -Element in the Early Responsive to Dehydration Stress 1 Promoter, The Plant Cell, vol.16, issue.9, pp.2481-98, 2004.

D. Treutter, Significance of Flavonoids in Plant Resistance and Enhancement of Their Biosynthesis, Plant Biology, vol.7, issue.6, pp.581-91, 2005.

E. Tripoli, M. L. Guardia, S. Giammanco, D. D. Majo, and M. Giammanco, Citrus Flavonoids: Molecular Structure, Biological Activity and Nutritional Properties: A Review, vol.104, pp.466-79, 2007.

M. Tronchet, C. Balagué, T. Kroj, L. Jouanin, and D. R. , Cinnamyl Alcohol Dehydrogenases-C and D, Key Enzymes in Lignin Biosynthesis, Play an Essential Role in Disease Resistance in Arabidopsis, Molecular Plant Pathology, vol.11, issue.1, pp.83-92, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01203884

,

G. Trouche, D. Bastianelli, T. V. Hamadou, J. Chantereau, J. F. Rami et al., Exploring the Variability of a Photoperiod-Insensitive Sorghum Genetic Panel for Stem Composition and Related Traits in Temperate Environments, Field Crops Research, vol.166, pp.72-81, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02639951

G. Trouche, D. Bastianelli, T. Cao-hamadou, J. Chantereau, J. F. Rami et al., Exploring the Variability of a Photoperiod-Insensitive Sorghum Genetic Panel for Stem Composition and Related Traits in Temperate Environments, Field Crops Research, vol.166, pp.72-81, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02639951

T. Tzfira and V. Citovsky, Agrobacterium-Mediated Genetic Transformation of Plants: Biology and Biotechnology, Current Opinion in Biotechnology, vol.17, issue.2, pp.147-54, 2006.

,

H. Uchimiya, T. Fushimi, H. Hashimoto, H. Harada, K. Syono et al., Expression of a Foreign Gene in Callus Derived from DNA-Treated Protoplasts of Rice (Oryza Sativa L.), MGG Molecular & General Genetics, vol.204, issue.2, pp.204-211, 1986.

,

W. Underwood, The Plant Cell Wall: A Dynamic Barrier against Pathogen Invasion, Frontiers in Plant Science, vol.3, pp.1-6, 2012.

B. R. Urbanowicz, J. Maria, H. A. Peña, K. W. Moniz, and W. S. Moremen,

. York, Two Arabidopsis Proteins Synthesize Acetylated Xylan in Vitro, The Plant Journal, vol.80, issue.2, pp.197-206, 2014.

T. Vain, E. F. Crowell, H. Timpano, E. Biot, T. Desprez et al., The Cellulase KORRIGAN Is Part of the Cellulose Synthase Complex, Plant Physiology, vol.165, issue.4, pp.1521-1553, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01204117

E. R. Valdivia, T. María, C. Herrera, J. Gianzo, G. Fidalgo et al., Regulation of Secondary Wall Synthesis and Cell Death by NAC Transcription Factors in the Monocot Brachypodium Distachyon, Journal of Experimental Botany, vol.64, issue.5, pp.1333-1376, 2013.

J. P. Vandenbrink, V. Goff, H. Jin, W. Kong, A. H. Paterson et al., Identification of Bioconversion Quantitative Trait Loci in the Interspecific Cross Sorghum Bicolor ?? Sorghum Propinquum, Theoretical and Applied Genetics, vol.126, issue.9, pp.2367-80, 2013.

R. Vanholme, I. Cesarino, K. Rataj, Y. Xiao, L. Sundin et al., Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis, Science, vol.341, issue.6150, pp.1103-1109, 2013.

R. Vanholme, V. Storme, B. Vanholme, L. Sundin, J. Holst-christensen et al., A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis, Plant Cell, vol.24, issue.9, pp.3506-3535, 2012.

M. E. Vega-sánchez, D. Loqué, J. Lao, M. Catena, Y. Verhertbruggen et al., Engineering Temporal Accumulation of a Low Recalcitrance Polysaccharide Leads to Increased C6 Sugar Content in Plant Cell Walls, Plant Biotechnology Journal, vol.13, issue.7, pp.903-917, 2015.

. Vélez-bermúdez, J. E. Isabel-cristina, S. Salazar-henao, I. Fornalé, J. López-vidriero et al., A MYB/ZML Complex Regulates Wound-Induced Lignin Genes in Maize, The Plant Cell, vol.27, issue.11, pp.3245-59, 2015.

,

W. Vermerris, Survey of Genomics Approaches to Improve Bioenergy Traits in Maize, Sorghum and SugarcaneFree Access, Journal of Integrative Plant Biology, vol.53, issue.2, pp.105-124, 2011.

,

W. Vermerris, A. Saballos, G. Ejeta, N. S. Mosier, M. R. Ladisch et al., Molecular Breeding to Enhance Ethanol Production from Corn and Sorghum Stover, Crop Science, vol.47, 2007.

,

P. Veronese, M. T. Ruiz, M. A. Coca, A. Hernandez-lopez, H. Lee et al.,

B. Ibeas and . Damsz, In Defense against Pathogens. Both Plant Sentinels and Foot Soldiers Need to Know the Enemy: Fig. 1, Plant Physiology, vol.131, issue.4, pp.1580-90, 2003.

,

L. T. Vo, J. Girones, C. Beloli, L. Chupin, E. D. Giuseppe et al., Processing and Properties of Sorghum Stem Fragment-Polyethylene Composites, Industrial Crops and Products, vol.107, pp.386-98, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01541489

,

L. A. Voesenek, T. D. Colmer, R. Pierik, F. F. Millenaar, and A. J. Peeters, How Plants Cope with Complete Submergence, New Phytologist, vol.170, issue.2, pp.213-239, 2006.

,

J. Vogel, Unique Aspects of the Grass Cell Wall, Current Opinion in Plant Biology, vol.11, issue.3, pp.301-308, 2008.

R. A. Vreeburg, J. Joris, A. J. Benschop, T. D. Peeters, and A. H. Colmer,

M. Ammerlaan, T. M. Staal, and . Elzenga, Ethylene Regulates Fast Apoplastic Acidification and Expansin A Transcription during Submergence-Induced Petiole Elongation in Rumex Palustris, The Plant Journal, vol.43, issue.4, pp.597-610, 2005.

K. Wakabayashi, K. Soga, and T. Hoson, Phenylalanine Ammonia-Lyase and Cell Wall Peroxidase Are Cooperatively Involved in the Extensive Formation of Ferulate Network in Cell Walls of Developing Rice Shoots, Journal of Plant Physiology, vol.169, issue.3, pp.262-67, 2012.

C. Waldron, E. B. Murphy, J. L. Roberts, G. D. Gustafson, S. L. Armour et al., Resistance to Hygromycin B, Plant Molecular Biology, vol.5, issue.2, pp.103-111, 1985.

,

Y. Wan and P. G. Lemaux, Generation of Large Numbers of Independently Transformed Fertile Barley Plants, Plant Physiology, vol.104, issue.1, pp.37-48, 1994.

H. Wang, U. Avci, J. Nakashima, M. G. Hahn, F. Chen et al., Mutation of WRKY Transcription Factors Initiates Pith Secondary Wall Formation and Increases Stem Biomass in Dicotyledonous Plants, Proceedings of the National Academy of Sciences, vol.107, issue.51, pp.22338-22381, 2010.

H. Wang, M. Tucker, and Y. Ji, Recent Development in Chemical Depolymerization of Lignin: A Review, Journal of Applied Chemistry, vol.2013, pp.1-9, 2013.

,

H. Wang, M. L. Russa, and L. S. Qi, CRISPR/Cas9 in Genome Editing and Beyond, Annual Review of Biochemistry, vol.85, issue.1, pp.227-64, 2016.

H. Wang, L. Gu, X. Zhang, M. Liu, H. Jiang et al., Global Transcriptome and Weighted Gene Co-Expression Network Analyses Reveal Hybrid-Specific Modules and Candidate Genes Related to Plant Height Development in Maize, Plant Molecular Biology, vol.98, issue.3, pp.187-203, 2018.

,

. Wang, R. A. Huan-zhong, and . Dixon, On-Off Switches for Secondary Cell Wall Biosynthesis, Molecular Plant, vol.5, issue.2, pp.297-303, 2012.

H. Wang, U. Avci, J. Nakashima, G. Michael, F. Hahn et al., Mutation of WRKY Transcription Factors Initiates Pith Secondary Wall Formation and Increases Stem Biomass in Dicotyledonous Plants, Proceedings of the National Academy of Sciences of the United States of America, vol.107, issue.51, pp.22338-22381, 2010.

,

M. L. Wang, C. Zhu, N. A. Barkley, Z. Chen, J. E. Erpelding et al.,

M. R. Murray, T. Tuinstra, G. A. Tesso, J. Pederson, and . Yu, Genetic Diversity and Population Structure Analysis of Accessions in the US Historic Sweet Sorghum Collection, Theoretical and Applied Genetics, vol.120, issue.1, pp.13-23, 2009.

,

Y. Wang, A. Acharya, M. Burrell, P. E. Robert-r-klein, K. H. Klein et al., Mapping and Candidate Genes Associated with Saccharification Yield in Sorghum, Genome, vol.56, issue.11, pp.659-65, 2013.

Y. Wang, A. Hong, A. M. Acharya, R. R. Burrell, P. E. Klein et al., Mapping and Candidate Genes Associated with Saccharification Yield in Sorghum, Genome, vol.56, issue.11, pp.659-65, 2013.

Z. Wang, H. Xing, L. Dong, H. Zhang, C. Han et al., Egg Cell-Specific Promoter-Controlled CRISPR/Cas9 Efficiently Generates Homozygous Mutants for Multiple Target Genes in Arabidopsis in a Single Generation, 2015.

, Genome Biology, vol.16, issue.1, p.144

. Waters, T. Mark, and J. A. Langdale, The Making of a Chloroplast, The EMBO Journal, vol.28, pp.2861-73, 2009.

Z. M. Wei and Z. H. Xu, Regeneration of Plants from Protoplasts of Sorghum (Sorghum Vulgare), pp.123-154, 1993.

O. Wilkins, H. Nahal, J. Foong, N. J. Provart, and M. M. Campbell, Expansion and Diversification of the Populus R2R3-MYB Family of Transcription Factors, Plant Physiology, vol.149, issue.2, pp.981-93, 2009.

V. Willemsen, M. Bauch, T. Bennett, A. Campilho, H. Wolkenfelt et al., The NAC Domain Transcription Factors FEZ and SOMBRERO Control the Orientation of Cell Division Plane in Arabidopsis Root Stem Cells, Developmental Cell, vol.15, issue.6, pp.913-935, 2008.

J. R. Wilson and R. D. Hatfield, Structural and Chemical Changes of Cell Wall Types during Stem Development: Consequences for Fibre Degradation by Rumen Microflora, Australian Journal of Agricultural Research, vol.48, issue.2, p.165, 1997.

F. Winchell, M. Brass, A. Manzo, A. Beldados, V. Perna et al., On the Origins and Dissemination of Domesticated Sorghum and Pearl Millet across Africa and into India: A View from the Butana Group of the Far Eastern Sahel, African Archaeological Review, vol.35, issue.4, pp.483-505, 2018.

,

P. J. Wittkopp, Variable Gene Expression in Eukaryotes: A Network Perspective, Journal of Experimental Biology, vol.210, issue.9, pp.1567-75, 2007.

W. Wohlleben, W. Arnold, I. Broer, D. Hillemann, E. Strauch et al., Nucleotide Sequence of the Phosphinothricin N-Acetyltransferase Gene from Streptomyces Viridochromogenes Tü494 and Its Expression in Nicotiana Tabacum, Gene, vol.70, issue.1, pp.25-37, 1988.

, , pp.90101-90102

S. Wolf, H. Hematy, and . Hofte, Growth Control and Cell Wall Signaling in Plants, Annu Rev Plant Biol, vol.63, pp.381-407, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01053127

A. Wu, C. Rihouey, M. Seveno, E. Hörnblad, . Sunil-kumar et al., The Arabidopsis IRX10 and IRX10-LIKE Glycosyltransferases Are Critical for Glucuronoxylan Biosynthesis during Secondary Cell Wall Formation, The Plant Journal, vol.57, issue.4, pp.718-749, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02128741

,

E. Wu, B. Lenderts, K. Glassman, M. Berezowska-kaniewska, H. Christensen et al., Optimized Agrobacterium-Mediated Sorghum Transformation Protocol and Molecular Data of Transgenic Sorghum Plants, In Vitro Cellular and Developmental Biology -Plant, vol.50, issue.1, pp.9-18, 2014.

,

Y. Wu, R. E. Sharp, D. M. Durachko, and D. J. Cosgrove, Growth Maintenance of the Maize Primary Root at Low Water Potentials Involves Increases in Cell-Wall Extension Properties, Expansin Activity, and Wall Susceptibility to Expansins, Plant Physiology, vol.111, issue.3, pp.765-72, 1996.

W. A. Wuddineh, M. Mazarei, J. Zhang, G. B. Turner, R. W. Sykes et al.,

M. F. Decker, M. K. Davis, C. Udvardi, and . Stewart, Identification and Overexpression of a Knotted1-Like Transcription Factor in Switchgrass (Panicum Virgatum L.) for Lignocellulosic Feedstock Improvement, Frontiers in Plant Science, vol.7, 2016.

,

J. Xia, Y. Zhao, P. Burks, M. Pauly, and P. J. Brown, A Sorghum NAC Gene Is Associated with Variation in Biomass Properties and Yield Potential, Plant Direct, vol.2, issue.7, pp.1-11, 2018.

W. Xiao, Y. Yang, and J. Yu, ZmNST3 and ZmNST4 Are Master Switches for Secondary Wall Deposition in Maize (Zea Mays L.), Plant Science, vol.266, pp.83-94, 2018.

,

Q. Xie, . Frugis, N. Colgan, and . Chua, Arabidopsis NAC1 Transduces Auxin Signal Downstream of TIR1 to Promote Lateral Root Development, Genes & Development, vol.14, issue.23, pp.3024-3060, 2000.

Z. Xin and J. Browse, Cold Comfort Farm: The Acclimation of Plants to Freezing Temperatures, Plant, Cell & Environment, vol.23, issue.9, pp.893-902, 2000.

Z. Xin, M. L. Wang, N. A. Barkley, G. Burow, C. Franks et al., Applying Genotyping (TILLING) and Phenotyping Analyses to Elucidate Gene Function in a Chemically Induced Sorghum Mutant Population, BMC Plant Biology, vol.8, issue.1, p.103, 2008.

Y. Xiong, T. Liu, C. Tian, S. Sun, J. Li et al., Transcription Factors in Rice: A Genome-Wide Comparative Analysis between Monocots and Eudicots, Plant Molecular Biology, vol.59, issue.1, pp.191-203, 2005.

H. Xu, A. Ding, S. Chen, P. Marowa, D. Wang et al., Genome-Wide Analysis of Sorghum GT47 Family Reveals Functional Divergences of MUR3-Like Genes, Frontiers in Plant Science, vol.9, 2018.

T. Yamada, K. Kuroda, Y. Jitsuyama, D. Takezawa, K. Arakawa et al., Roles of the Plasma Membrane and the Cell Wall in the Responses of Plant Cells to Freezing, Planta, vol.215, issue.5, pp.770-78, 2002.

M. Yamaguchi, M. Kubo, H. Fukuda, and T. Demura, VASCULAR, 2008.

M. Yamaguchi, N. Mitsuda, M. Ohtani, M. Ohme-takagi, K. Kato et al., VASCULAR-RELATED NAC-DOMAIN 7 Directly Regulates the Expression of a Broad Range of Genes for Xylem Vessel Formation, Plant Journal, vol.66, issue.4, pp.579-90, 2011.

,

M. Yamaguchi, M. Ohtani, N. Mitsuda, M. Kubo, M. Ohme-takagi et al., VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation in Arabidopsis, The Plant Cell, vol.22, issue.4, pp.1249-63, 2010.

M. Yamaguchi, H. Fujimoto, K. Hirano, S. Araki-nakamura, K. Ohmae-shinohara et al., Sorghum Dw1, an Agronomically Important Gene for Lodging Resistance, Encodes a Novel Protein Involved in Cell Proliferation, Scientific Reports, vol.6, p.28366, 2016.

C. Yang, D. Li, X. Liu, C. Ji, L. Hao et al., OsMYB103L, an R2R3-MYB Transcription Factor, Influences Leaf Rolling and Mechanical Strength in Rice (Oryza Sativa L.), BMC Plant Biology, vol.14, issue.1, p.158, 2014.

L. Yang, X. Zhao, F. Yang, D. Fan, Y. Jiang et al., PtrWRKY19, a Novel WRKY Transcription Factor, Contributes to the Regulation of Pith Secondary Wall Formation in Populus Trichocarpa, Scientific Reports, vol.6, issue.1, p.18643, 2016.

,

Z. Yang and B. Rannala, Molecular Phylogenetics: Principles and Practice, Nature Reviews Genetics, vol.13, issue.5, pp.303-317, 2012.

C. Yanhui, Y. Xiaoyuan, H. Kun, L. Meihua, L. Jigang et al., The MYB Transcription Factor Superfamily of Arabidopsis: Expression Analysis and Phylogenetic Comparison with the Rice MYB Family, Plant Molecular Biology, vol.60, issue.1, pp.107-131, 2006.

T. Yazawa, H. Kawahigashi, T. Matsumoto, and H. Mizuno, Simultaneous Transcriptome Analysis of Sorghum and Bipolaris Sorghicola by Using RNA-Seq in Combination with De Novo Transcriptome Assembly, PLoS ONE, vol.8, issue.4, 2013.

Y. Ye, B. Liu, M. Zhao, K. Wu, W. Cheng et al., CEF1/OsMYB103L Is Involved in GA-Mediated Regulation of Secondary Wall Biosynthesis in Rice, Plant Molecular Biology, vol.89, issue.4-5, pp.385-401, 2015.

T. H. Yeats and J. K. Rose, The Biochemistry and Biology of Extracellular Plant Lipid-Transfer Proteins (LTPs), Protein Science, vol.17, issue.2, pp.191-98, 2008.

,

L. Yepes, H. S. Marcela, and . Aldwinckle, Micropropagation of Thirteen Malus Cultivars and Rootstocks, and Effect of Antibiotics on Proliferation, Plant Growth Regulation, vol.15, issue.1, pp.55-67, 1994.

Y. Yin, J. Huang, and Y. Xu, The Cellulose Synthase Superfamily in Fully Sequenced Plants and Algae, BMC Plant Biology, vol.9, issue.1, p.99, 2009.

S. -. Yoo, Y. Dong, J. Cho, and . Sheen, Arabidopsis Mesophyll Protoplasts: A Versatile Cell System for Transient Gene Expression Analysis, Nature Protocols, vol.2, issue.7, pp.1565-72, 2007.

K. Yoshida, S. Sakamoto, T. Kawai, Y. Kobayashi, K. Sato et al., Engineering the Oryza Sativa Cell Wall with Rice NAC Transcription Factors Regulating Secondary Wall Formation, Frontiers in Plant Science, vol.4, pp.1-12, 2013.

J. You, L. Zhang, B. Song, X. Qi, and Z. Chan, Systematic Analysis and Identification of Stress-Responsive Genes of the NAC Gene Family in Brachypodium Distachyon, PLoS ONE, vol.10, issue.3, pp.1-20, 2015.

H. Yu, B. Jiao, and C. Liang, High-Quality Rice RNA-Seq-Based Co-Expression Network for Predicting Gene Function and Regulation, BioRxiv, 2017.

J. M. Zale, S. Agarwal, S. Loar, and C. M. Steber, Evidence for Stable Transformation of Wheat by Floral Dip in Agrobacterium Tumefaciens, Plant Cell Reports, vol.28, issue.6, pp.903-916, 2009.

,

A. Zang, X. Xu, S. Neill, and W. Cai, Overexpression of OsRAN2 in Rice and Arabidopsis Renders Transgenic Plants Hypersensitive to Salinity and Osmotic Stress, Journal of Experimental Botany, vol.61, issue.3, pp.777-89, 2010.

B. Zhang, T. Zhao, W. Yu, B. Kuang, Y. Yao et al., Functional Conservation of the Glycosyltransferase Gene GT47A in the Monocot Rice, Journal of Plant Research, vol.127, issue.3, pp.423-455, 2014.

,

D. Zhang, M. Hrmova, C. Hua-wan, C. Wu, J. Balzen et al., Members of a New Group of Chitinase-like Genes Are Expressed Preferentially in Cotton Cells with Secondary Walls, Plant Molecular Biology, vol.54, issue.3, pp.353-72, 2004.

,

J. Zhang, M. Xie, G. A. Tuskan, W. Muchero, and J. Chen, Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants, Frontiers in Plant Science, vol.9, 2018.

L. Zhang, C. Leng, H. Luo, X. Wu, Z. Liu et al., Sweet Sorghum Originated through Selection of Dry , a Plant-Specific NAC Transcription Factor Gene, The Plant Cell, vol.30, issue.10, pp.2286-2307, 2018.

,

W. Zhang and R. Wu, Efficient Regeneration of Transgenic Plants from Rice Protoplasts and Correctly Regulated Expression of the Foreign Gene in the Plants, Theoretical and Applied Genetics, vol.76, issue.6, pp.835-875, 1988.

Y. Zhang, J. Su, S. Duan, Y. Ao, J. Dai et al., A Highly Efficient Rice Green Tissue Protoplast System for Transient Gene Expression and Studying Light/Chloroplast-Related Processes, Plant Methods, vol.7, issue.1, p.30, 2011.

,

J. Zhao and R. A. Dixon, MATE Transporters Facilitate Vacuolar Uptake of Epicatechin 3?-O -Glucoside for Proanthocyanidin Biosynthesis in Medicago Truncatula and Arabidopsis, The Plant Cell, vol.21, issue.8, pp.2323-2363, 2009.

K. Zhao and L. E. Bartley, Comparative Genomic Analysis of the R2R3 MYB Secondary Cell Wall Regulators of Arabidopsis, BMC Plant Biology, vol.14, issue.1, p.135, 2014.

Q. Zhao and R. A. Dixon, Transcriptional Networks for Lignin Biosynthesis: More Complex than We Thought?, Trends in Plant Science, vol.16, issue.4, pp.227-260, 2011.

,

W. Zhao, P. Langfelder, T. Fuller, J. Dong, A. Li et al., Weighted Gene Coexpression Network Analysis: State of the Art, Journal of Biopharmaceutical Statistics, vol.20, issue.2, pp.281-300, 2010.

Z. Zhao, T. Cai, L. Tagliani, M. Miller, N. Wang et al., Agrobacterium -Mediated Sorghum Transformation, pp.789-98, 1991.

X. Zheng, D. Yi, L. Shao, and C. Li, In Silico Genome-Wide Identification, Phylogeny and Expression Analysis of the R2R3-MYB Gene Family in Medicago Truncatula, Journal of Integrative Agriculture, vol.16, issue.7, pp.61521-61527, 2017.

H. Zhong, W. Wang, and M. Sticklen, In Vitro Morphogenesis of Sorghum Bicolor (L.) Moench: Efficient Plant Regeneration from Shoot Apices, Journal of Plant Physiology, vol.153, issue.5-6, pp.719-745, 1998.

R. Zhong, C. Lee, J. Zhou, R. L. Mccarthy, and Z. Ye, A Battery of Transcription Factors Involved in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis, The Plant Cell Online, vol.20, issue.10, pp.2763-82, 2008.

R. Zhong, E. A. Richardson, and Z. Ye, The MYB46 Transcription Factor Is a Direct Target of SND1 and Regulates Secondary Wall Biosynthesis in Arabidopsis, The Plant Cell Online, vol.19, issue.9, pp.2776-92, 2007.

. Zhong, D. H. Ruiqin, W. H. Burk, Z. Morrison, and . Ye, A Kinesin-Like Protein Is Essential for Oriented Deposition of Cellulose Microfibrils and Cell Wall Strength, The Plant Cell, vol.14, issue.12, pp.3101-3118, 2002.

R. Zhong, T. Demura, and Z. Ye, SND1, a NAC Domain Transcription Factor, Is a Key Regulator of Secondary Wall Synthesis in Fibers of Arabidopsis, The Plant Cell Online, vol.18, issue.11, pp.3158-70, 2006.

R. Zhong, C. Lee, R. L. Mccarthy, K. Cromwell, E. G. Reeves et al., Transcriptional Activation of Secondary Wall Biosynthesis by Rice and Maize NAC and MYB Transcription Factors, Plant and Cell Physiology, vol.52, issue.10, pp.1856-71, 2011.

,

R. Zhong, C. Lee, and Z. Hua-ye, Global Analysis of Direct Targets of Secondary Wall NAC Master Switches in Arabidopsis, Molecular Plant, vol.3, issue.6, pp.1087-1103, 2010.

,

R. Zhong, C. Lee, and Z. Ye, Evolutionary Conservation of the Transcriptional Network Regulating Secondary Cell Wall Biosynthesis, Trends in Plant Science, vol.15, issue.11, pp.625-657, 2010.

. Zhong, R. L. Ruiqin, M. Mccarthy, Z. Haghighat, and . Hua-ye, The Poplar MYB Master Switches Bind to the SMRE Site and Activate the Secondary Wall Biosynthetic Program during Wood Formation, PLoS ONE, vol.8, issue.7, pp.18-21, 2013.

,

. Zhong, E. A. Ruiqin, Z. Richardson, and . Hua-ye, Two NAC Domain Transcription Factors, SND1 and NST1, Function Redundantly in Regulation of Secondary Wall Synthesis in Fibers of Arabidopsis, Planta, vol.225, issue.6, pp.1603-1614, 2007.

R. Zhong and Z. Hua-ye, Secondary Cell Walls: Biosynthesis, Patterned Deposition and Transcriptional Regulation, Plant and Cell Physiology, vol.56, issue.2, pp.195-214, 2015.

,

R. Zhong and Z. Ye, The Arabidopsis NAC Transcription Factor NST2, 2015.

, Functions Together with SND1 and NST1 to Regulate Secondary Wall Biosynthesis in Fibers of Inflorescence Stems, Plant Signaling & Behavior, vol.10, issue.2, pp.1-7

,

R. Zhong and Z. Ye, MYB46 and MYB83 Bind to the SMRE Sites and Directly Activate a Suite of Transcription Factors and Secondary Wall Biosynthetic Genes, Plant and Cell Physiology, vol.53, issue.2, pp.368-80, 2012.

R. Zhong and Z. Hua-ye, Regulation of Cell Wall Biosynthesis, Current Opinion in Plant Biology, vol.10, issue.6, pp.564-72, 2007.

R. Zhong, Y. Yuan, J. J. Spiekerman, J. T. Guley, J. C. Egbosiuba et al., Functional Characterization of NAC and MYB Transcription Factors Involved in Regulation of Biomass Production in Switchgrass (Panicum Virgatum), PLoS ONE, vol.10, issue.8, pp.1-24, 2015.

H. Zhou, B. Liu, D. P. Weeks, M. H. Spalding, and B. Yang, Large Chromosomal Deletions and Heritable Small Genetic Changes Induced by CRISPR/Cas9 in Rice, Nucleic Acids Research, vol.42, issue.17, pp.10903-10917, 2014.

J. Zhou, C. Lee, R. Zhong, and Z. Ye, MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis, The Plant Cell Online, vol.21, issue.1, pp.248-66, 2009.

J. Zhou, R. Zhong, and Z. Hua-ye, Arabidopsis NAC Domain Proteins, VND1 to VND5, Are Transcriptional Regulators of Secondary Wall Biosynthesis in Vessels, PLoS ONE, vol.9, issue.8, 2014.

X. Zhou and M. Stephens, Genome-Wide Efficient Mixed-Model Analysis for Association Studies, Nature Genetics, vol.44, issue.7, pp.821-845, 2012.

X. Zhou, X. Shen, C. T. Hittinger, and A. Rokas, Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets, Molecular Biology and Evolution, vol.35, issue.2, pp.486-503, 2018.

C. Zhu, M. Gore, E. S. Buckler, and J. Yu, Status and Prospects of Association Mapping in Plants, The Plant Genome Journal, vol.1, issue.1, p.5, 2008.

,

G. Zhu, G. Chen, J. Zhu, Y. Zhu, X. Lu et al., Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium Distachyon L, PLoS ONE, vol.10, issue.10, pp.1-23, 2015.

,

J. Zhu, S. Alvarez, E. L. Marsh, M. E. Lenoble, I. Cho et al., Cell Wall Proteome in the Maize Primary Root Elongation Zone. II. Region-Specific Changes in Water Soluble and Lightly Ionically Bound Proteins under Water Deficit, Plant Physiology, vol.145, issue.4, pp.1533-1581, 2007.

, Les niveaux de seuils (0,8 et 200) sont définis comme recommandés dans la FAQ de WGCNA (au-dessus de 0.8 et en dessous des centaines) afin de conserver le pouvoir aussi faible que possible. Pour nos analyses un pouvoir de 12 a été utilisé. (B) Répartition des gènes dans les modules identifiés par l'analyse de réseaux de co-expression, Annexe SII-1: (A) Free topological index de WGCNA afin de choisir les pouvoir en utilisant la correspondance avec les modèles de scale independence et de mean connectivity

, Annexe SII-2: GO-terms liés aux parois agrégés par mot-clé. Afin de faciliter l'analyse d'enrichissement en GO-term, une agrégation des GO-terms liés aux parois a été réalisée

, Mot-clé GO-term ID Processus Biologiques Annoté 1