TY - JOUR AU - McCann, M. C. AU - Carpita, N. C. PY - 2015 DA - 2015// TI - Biomass recalcitrance: a multi-scale, multi-factor, and conversion-specific property JO - J Exp Bot VL - 66 UR - https://doi.org/10.1093/jxb/erv267 DO - 10.1093/jxb/erv267 ID - McCann2015 ER - TY - JOUR AU - Rudall, P. J. AU - Caddick, L. R. PY - 1994 DA - 1994// TI - Investigation of the presence of phenolic compounds in monocotyledonous cell walls, using UV fluorescence microscopy JO - Ann Bot VL - 74 UR - https://doi.org/10.1006/anbo.1994.1145 DO - 10.1006/anbo.1994.1145 ID - Rudall1994 ER - TY - JOUR AU - Brown, D. M. AU - Zeef, L. A. H. AU - Ellis, J. AU - Goodacre, R. AU - Turner, S. R. PY - 2005 DA - 2005// TI - Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics JO - Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.105.031542 DO - 10.1105/tpc.105.031542 ID - Brown2005 ER - TY - JOUR AU - Dharmawardhana, P. AU - Brunner, A. M. AU - Strauss, S. H. PY - 2010 DA - 2010// TI - Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa JO - BMC Genomics VL - 11 UR - https://doi.org/10.1186/1471-2164-11-150 DO - 10.1186/1471-2164-11-150 ID - Dharmawardhana2010 ER - TY - JOUR AU - Hefer, C. A. AU - Mizrachi, E. AU - Myburg, A. A. AU - Douglas, C. J. AU - Mansfield, S. D. PY - 2015 DA - 2015// TI - Comparative interrogation of the developing xylem transcriptomes of two wood-forming species: Populus trichocarpa and Eucalyptus grandis JO - New Phytol VL - 206 UR - https://doi.org/10.1111/nph.13277 DO - 10.1111/nph.13277 ID - Hefer2015 ER - TY - JOUR AU - McKinley, B. AU - Rooney, W. AU - Wilkerson, C. AU - Mullet, J. PY - 2016 DA - 2016// TI - Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum bicolor JO - Plant J VL - 88 UR - https://doi.org/10.1111/tpj.13269 DO - 10.1111/tpj.13269 ID - McKinley2016 ER - TY - JOUR AU - McCormick, R. F. AU - Truong, S. K. AU - Sreedasyam, A. AU - Jenkins, J. AU - Shu, S. AU - Sims, D. AU - Kennedy, M. AU - Amirebrahimi, M. AU - Weers, B. D. AU - McKinley, B. PY - 2018 DA - 2018// TI - The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization JO - Plant J VL - 93 UR - https://doi.org/10.1111/tpj.13781 DO - 10.1111/tpj.13781 ID - McCormick2018 ER - TY - JOUR AU - Yong, W. AU - Link, B. AU - O’Malley, R. AU - Tewari, J. AU - Hunter, C. T. AU - Lu, C. A. AU - Li, X. AU - Bleecker, A. B. AU - Koch, K. E. AU - McCann, M. C. PY - 2005 DA - 2005// TI - Genomics of plant cell wall biogenesis JO - Planta VL - 221 UR - https://doi.org/10.1007/s00425-005-1563-z DO - 10.1007/s00425-005-1563-z ID - Yong2005 ER - TY - JOUR AU - Penning, B. W. AU - Hunter, C. T. AU - Tayengwa, R. AU - Eveland, A. L. AU - Dugard, C. K. AU - Olek, A. T. AU - Vermerris, W. AU - Koch, K. E. AU - McCarty, D. R. AU - Davis, M. F. PY - 2009 DA - 2009// TI - Genetic resources for maize cell wall biology JO - Plant Physiol VL - 151 UR - https://doi.org/10.1104/pp.109.136804 DO - 10.1104/pp.109.136804 ID - Penning2009 ER - TY - JOUR AU - Tenaillon, M. I. AU - Sawkins, M. C. AU - Long, A. D. AU - Gaut, R. L. AU - Doebley, J. F. AU - Gaut, B. S. PY - 2001 DA - 2001// TI - Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) JO - Proc Natl Acad Sci U S A VL - 98 UR - https://doi.org/10.1073/pnas.151244298 DO - 10.1073/pnas.151244298 ID - Tenaillon2001 ER - TY - JOUR AU - Springer, N. M. AU - Ying, K. AU - Fu, Y. AU - Ji, T. M. AU - Yeh, C. T. AU - Jia, Y. AU - Wu, W. AU - Richmond, T. AU - Kitzman, J. AU - Rosenbaum, H. PY - 2009 DA - 2009// TI - Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000734 DO - 10.1371/journal.pgen.1000734 ID - Springer2009 ER - TY - JOUR AU - Penning, B. W. AU - Sykes, R. W. AU - Babcock, N. C. AU - Dugard, C. K. AU - Held, M. A. AU - Klimek, J. F. AU - Shreve, J. T. AU - Fowler, M. AU - Ziebell, A. AU - Davis, M. F. PY - 2014 DA - 2014// TI - Genetic determinants for enzymatic digestion of lignocellulosic biomass are independent of those for lignin abundance in a maize recombinant inbred population JO - Plant Physiol VL - 165 UR - https://doi.org/10.1104/pp.114.242446 DO - 10.1104/pp.114.242446 ID - Penning2014 ER - TY - JOUR AU - Paschold, A. AU - Jia, Y. AU - Marcon, C. AU - Lund, S. AU - Larson, N. B. AU - Yeh, C. T. AU - Ossowski, S. AU - Lanz, C. AU - Nettleton, D. AU - Schnable, P. S. PY - 2012 DA - 2012// TI - Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.138461.112 DO - 10.1101/gr.138461.112 ID - Paschold2012 ER - TY - JOUR AU - Sekhon, R. S. AU - Lin, H. AU - Childs, K. L. AU - Hansey, C. N. AU - Buell, C. R. AU - Leon, N. AU - Kaeppler, S. M. PY - 2011 DA - 2011// TI - Genome-wide atlas of transcription during maize development JO - Plant J VL - 66 UR - https://doi.org/10.1111/j.1365-313X.2011.04527.x DO - 10.1111/j.1365-313X.2011.04527.x ID - Sekhon2011 ER - TY - JOUR AU - Schindelman, G. AU - Morikami, A. AU - Jung, J. AU - Baskin, T. I. AU - Carpita, N. C. AU - McCann, M. C. AU - Benfey, P. N. PY - 2001 DA - 2001// TI - The COBRA gene encodes a putative glycosylphosphatidyl-inositol anchored protein, which is polarly localized and necessary for oriented cell expansion in Arabidopsis JO - Genes Dev VL - 15 UR - https://doi.org/10.1101/gad.879101 DO - 10.1101/gad.879101 ID - Schindelman2001 ER - TY - JOUR AU - Roudier, F. AU - Fernandez, A. G. AU - Fujita, M. AU - Himmelspach, R. AU - Borner, G. H. H. AU - Schindelman, G. AU - Song, S. AU - Baskin, T. I. AU - Dupree, P. AU - Wasteneys, G. O. PY - 2005 DA - 2005// TI - COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation JO - Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.105.031732 DO - 10.1105/tpc.105.031732 ID - Roudier2005 ER - TY - JOUR AU - Sindhu, A. AU - Langewisch, T. AU - Olek, A. AU - Multani, D. S. AU - McCann, M. C. AU - Vermerris, W. AU - Carpita, N. C. AU - Johal, G. PY - 2007 DA - 2007// TI - Maize Brittle stalk2 encodes a COBRA-like protein expressed in early organ development but required for tissue flexibility at maturity JO - Plant Physiol VL - 145 UR - https://doi.org/10.1104/pp.107.102582 DO - 10.1104/pp.107.102582 ID - Sindhu2007 ER - TY - JOUR AU - Nicol, F. AU - His, I. AU - Jauneau, A. AU - Vernhettes, S. AU - Canut, H. AU - Hofte, H. PY - 1998 DA - 1998// TI - A plasma membrane-bound putative endo-1,4-β-D-glucanase is required for normal wall assembly and cell elongation in Arabidopsis JO - EMBO J VL - 17 UR - https://doi.org/10.1093/emboj/17.19.5563 DO - 10.1093/emboj/17.19.5563 ID - Nicol1998 ER - TY - JOUR AU - Buchanan, M. AU - Burton, R. A. AU - Dhugga, K. S. AU - Rafalski, A. J. AU - Tingey, S. V. AU - Shirley, N. J. AU - Fincher, G. B. PY - 2012 DA - 2012// TI - Endo-(1,4)-β-glucanase gene families in the grasses: temporal and spatial co-transcription of orthologous genes JO - BMC Plant Biol VL - 12 UR - https://doi.org/10.1186/1471-2229-12-235 DO - 10.1186/1471-2229-12-235 ID - Buchanan2012 ER - TY - JOUR AU - Carpita, N. C. AU - Gibeaut, D. M. PY - 1993 DA - 1993// TI - Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth JO - Plant J VL - 3 UR - https://doi.org/10.1111/j.1365-313X.1993.tb00007.x DO - 10.1111/j.1365-313X.1993.tb00007.x ID - Carpita1993 ER - TY - JOUR AU - Brown, D. M. AU - Zhang, Z. AU - Stephens, E. AU - Dupree, P. AU - Turner, S. R. PY - 2009 DA - 2009// TI - Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis JO - Plant J VL - 57 UR - https://doi.org/10.1111/j.1365-313X.2008.03729.x DO - 10.1111/j.1365-313X.2008.03729.x ID - Brown2009 ER - TY - JOUR AU - Gille, S. AU - Pauly, M. PY - 2012 DA - 2012// TI - O-acetylation of plant cell wall polysaccharides JO - Frontiers Plant Sci VL - 3 UR - https://doi.org/10.3389/fpls.2012.00012 DO - 10.3389/fpls.2012.00012 ID - Gille2012 ER - TY - JOUR AU - Gao, Y. AU - He, C. AU - Zhang, D. AU - Liu, X. AU - Xu, Z. AU - Tian, Y. AU - Liu, X. -. H. AU - Zang, S. AU - Pauly, M. AU - Zhou, Y. AU - Zhang, B. PY - 2017 DA - 2017// TI - Two trichome birefringence-like proteins mediate xylan acetylation, which is essential for leaf blight resistance in rice JO - Plant Physiol VL - 173 UR - https://doi.org/10.1104/pp.16.01618 DO - 10.1104/pp.16.01618 ID - Gao2017 ER - TY - JOUR AU - Molinari, H. B. C. AU - Pellny, T. K. AU - Freeman, J. AU - Shewry, P. R. AU - Mitchell, R. A. C. PY - 2013 DA - 2013// TI - Grass cell wall feruloylation: distribution of bound ferulate and candidate gene expression in Brachypodium distachyon JO - Frontiers Plant Sci. VL - 4 UR - https://doi.org/10.3389/fpls.2013.00050 DO - 10.3389/fpls.2013.00050 ID - Molinari2013 ER - TY - JOUR AU - Rautengarten, C. AU - Ebert, B. AU - Ouellet, M. AU - Nafisi, M. AU - Baidoo, E. E. K. AU - Benke, P. AU - Stranne, M. AU - Mukhopadhyay, A. AU - Keasling, J. D. AU - Sakuragi, Y. AU - Scheller, H. V. PY - 2012 DA - 2012// TI - Arabidopsis Deficient in Cutin Ferulate encodes a transferase required for feruloylation of ω-hydroxy fatty acids in cutin polyester JO - Plant Physiol VL - 158 UR - https://doi.org/10.1104/pp.111.187187 DO - 10.1104/pp.111.187187 ID - Rautengarten2012 ER - TY - JOUR AU - Smith, B. G. AU - Harris, P. J. PY - 1999 DA - 1999// TI - The polysaccharide composition of Poales cell walls: Poaceae cell walls are not unique JO - Biochem Syst Ecol VL - 27 UR - https://doi.org/10.1016/S0305-1978(98)00068-4 DO - 10.1016/S0305-1978(98)00068-4 ID - Smith1999 ER - TY - JOUR AU - Carpita, N. C. AU - Defernez, M. AU - Findlay, K. AU - Wells, B. AU - Shoue, D. A. AU - Catchpole, G. AU - Wilson, R. H. AU - McCann, M. C. PY - 2001 DA - 2001// TI - Cell wall architecture of the elongating maize coleoptile JO - Plant Physiol VL - 127 UR - https://doi.org/10.1104/pp.010146 DO - 10.1104/pp.010146 ID - Carpita2001 ER - TY - JOUR AU - McCann, M. C. AU - Defernez, M. AU - Urbanowicz, B. R. AU - Tewari, J. C. AU - Langewisch, T. AU - Olek, A. AU - Wells, B. AU - Wilson, R. H. AU - Carpita, N. C. PY - 2007 DA - 2007// TI - Neural network analyses of infrared spectra for classifying cell wall architectures JO - Plant Physiol VL - 143 UR - https://doi.org/10.1104/pp.106.093054 DO - 10.1104/pp.106.093054 ID - McCann2007 ER - TY - JOUR AU - Vega-Sanchez, M. AU - Verhertbruggen, Y. AU - Scheller, H. V. AU - Ronald, P. PY - 2013 DA - 2013// TI - Abundance of mixed linkage glucan in mature tissues and secondary cell walls of grasses JO - Plant Signal Behav VL - 8 UR - https://doi.org/10.4161/psb.23143 DO - 10.4161/psb.23143 ID - Vega-Sanchez2013 ER - TY - JOUR AU - Takenaka, Y. AU - Kato, K. AU - Ogawa-Ohnishi, M. AU - Tsuruhama, K. AU - Kajiura, H. AU - Yagyu, K. AU - Takeda, A. AU - Takeda, Y. AU - Kunieda, T. AU - Hara-Nishimura, I. PY - 2018 DA - 2018// TI - Pectin RG-I rhamnosyl-transferases represent a novel plant-specific glycosyltransferase family JO - Nat Plants VL - 4 UR - https://doi.org/10.1038/s41477-018-0217-7 DO - 10.1038/s41477-018-0217-7 ID - Takenaka2018 ER - TY - JOUR AU - Wang, Y. AU - Mortimer, J. C. AU - Jonathan, D. AU - Dupree, P. AU - Keegstra, K. PY - 2013 DA - 2013// TI - Identification of an additional protein involved in mannan biosynthesis JO - Plant J VL - 73 UR - https://doi.org/10.1111/tpj.12019 DO - 10.1111/tpj.12019 ID - Wang2013 ER - TY - JOUR AU - Stonebloom, S. AU - Ebert, B. AU - Xiong, G. AU - Pattathil, S. AU - Birdseye, D. AU - Lao, J. AU - Pauly, M. AU - Hahn, M. G. AU - Heazlewood, J. L. AU - Scheller, H. V. PY - 2016 DA - 2016// TI - A DUF-246 family glycosyltransferase-like gene affects male fertility and the biosynthesis of pectic arabinogalactans JO - BMC Plant Biol VL - 16 UR - https://doi.org/10.1186/s12870-016-0780-x DO - 10.1186/s12870-016-0780-x ID - Stonebloom2016 ER - TY - JOUR AU - Cosgrove, D. J. PY - 2000 DA - 2000// TI - Loosening of plant cell walls by expansins JO - Nature. VL - 407 UR - https://doi.org/10.1038/35030000 DO - 10.1038/35030000 ID - Cosgrove2000 ER - TY - JOUR AU - Rose, J. K. C. AU - Braam, J. AU - Fry, S. C. AU - Nishitani, K. PY - 2002 DA - 2002// TI - The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: current perspectives and a new unifying nomenclature JO - Plant Cell Physiol VL - 43 UR - https://doi.org/10.1093/pcp/pcf171 DO - 10.1093/pcp/pcf171 ID - Rose2002 ER - TY - JOUR AU - Liseron-Monfils, C. AU - Lewis, T. AU - Ashlock, D. AU - McNicholas, P. D. AU - Fauteux, F. AU - Stromvik, M. AU - Raizada, M. N. PY - 2013 DA - 2013// TI - Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the maize development atlas JO - BMC Plant Biol VL - 13 UR - https://doi.org/10.1186/1471-2229-13-42 DO - 10.1186/1471-2229-13-42 ID - Liseron-Monfils2013 ER - TY - JOUR AU - Mahony, S. AU - Benos, P. V. PY - 2007 DA - 2007// TI - STAMP: a web tool for exploring DNA-binding motif similarities JO - Nucl Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm272 DO - 10.1093/nar/gkm272 ID - Mahony2007 ER - TY - JOUR AU - Chow, C. N. AU - Lee, T. Y. AU - Hung, Y. C. AU - Li, G. Z. AU - Tseng, K. C. AU - Liu, Y. H. AU - Kuo, P. L. AU - Zheng, H. Q. AU - Chang, W. C. PY - 2019 DA - 2019// TI - PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky1081 DO - 10.1093/nar/gky1081 ID - Chow2019 ER - TY - JOUR AU - Grotewald, E. AU - Drummond, B. J. AU - Bowen, B. AU - Peterson, T. PY - 1994 DA - 1994// TI - The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset JO - Cell. VL - 76 UR - https://doi.org/10.1016/0092-8674(94)90117-1 DO - 10.1016/0092-8674(94)90117-1 ID - Grotewald1994 ER - TY - JOUR AU - Patzlaf, A. AU - McInnis, S. AU - Courtenay, A. AU - Surman, C. AU - Newman, L. J. AU - Smith, C. AU - Bevan, M. W. AU - Mansfield, S. AU - Whetten, R. W. AU - Sederoff, R. R. AU - Campbell, M. M. PY - 2003 DA - 2003// TI - Characterization of a pine MYB that regulates lignification JO - Plant J VL - 36 UR - https://doi.org/10.1046/j.1365-313X.2003.01916.x DO - 10.1046/j.1365-313X.2003.01916.x ID - Patzlaf2003 ER - TY - JOUR AU - Patzlaf, A. AU - Newman, L. J. AU - Dubos, C. AU - Whetten, R. W. AU - Smith, C. AU - McInnis, S. AU - Bevan, M. W. AU - Sederoff, R. R. AU - Campbell, M. M. PY - 2003 DA - 2003// TI - Characterization of Pt MYB1, an R2R3-MYB from pine xylem JO - Plant Mol Biol VL - 53 UR - https://doi.org/10.1023/B:PLAN.0000019066.07933.d6 DO - 10.1023/B:PLAN.0000019066.07933.d6 ID - Patzlaf2003 ER - TY - JOUR AU - Kaothien, P. AU - Shimokawatoko, Y. AU - Kawaoka, A. AU - Yoshida, K. AU - Shinmyo, A. PY - 2000 DA - 2000// TI - A cis-element containing PAL-box functions in the expression of the wound-inducible peroxidase gene of horseradish JO - Plant Cell Rep VL - 19 UR - https://doi.org/10.1007/s002990050773 DO - 10.1007/s002990050773 ID - Kaothien2000 ER - TY - JOUR AU - Kawaoka, A. AU - Kaothien, P. AU - Yoshida, K. AU - Endo, S. AU - Yamada, K. AU - Ebinuma, H. PY - 2000 DA - 2000// TI - Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis JO - Plant J VL - 22 UR - https://doi.org/10.1046/j.1365-313x.2000.00737.x DO - 10.1046/j.1365-313x.2000.00737.x ID - Kawaoka2000 ER - TY - JOUR AU - Lis, M. AU - Walther, D. PY - 2016 DA - 2016// TI - The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-016-2549-x DO - 10.1186/s12864-016-2549-x ID - Lis2016 ER - TY - JOUR AU - Muthamilarasan, M. AU - Mangu, V. R. AU - Zandkarimi, H. AU - Prasad, M. AU - Niranjan, B. N. PY - 2016 DA - 2016// TI - Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet, and their expression in rice JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep24008 DO - 10.1038/srep24008 ID - Muthamilarasan2016 ER - TY - JOUR AU - Zhang, L. AU - Yu, S. AU - Zuo, K. AU - Luo, L. AU - Tang, K. PY - 2012 DA - 2012// TI - Identification of gene modules associated with drought response in rice by network-based analysis JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0033748 DO - 10.1371/journal.pone.0033748 ID - Zhang2012 ER - TY - JOUR AU - Sircar, S. AU - Parekh, N. PY - 2015 DA - 2015// TI - Functional characterization of drought responsive modules and genes in Oryza sativa: a network-based approach JO - Front Genet VL - 6 UR - https://doi.org/10.3389/fgene.2015.00256 DO - 10.3389/fgene.2015.00256 ID - Sircar2015 ER - TY - JOUR AU - Demura, T. AU - Ye, Z. -. H. PY - 2010 DA - 2010// TI - Regulation of plant biomass production JO - Curr Opin Plant Biol VL - 13 UR - https://doi.org/10.1016/j.pbi.2010.03.002 DO - 10.1016/j.pbi.2010.03.002 ID - Demura2010 ER - TY - JOUR AU - Zhong, R. AU - Lee, C. AU - Ye, Z. -. H. PY - 2010 DA - 2010// TI - Evolutionary conservation of the transcriptional network regulating secondary cell wall biosynthesis JO - Trends Plant Sci VL - 15 UR - https://doi.org/10.1016/j.tplants.2010.08.007 DO - 10.1016/j.tplants.2010.08.007 ID - Zhong2010 ER - TY - JOUR AU - Zhao, Q. AU - Dixon, R. A. PY - 2011 DA - 2011// TI - Transcriptional networks for lignin biosynthesis: more complex than we thought? JO - Trends Plant Sci VL - 16 UR - https://doi.org/10.1016/j.tplants.2010.12.005 DO - 10.1016/j.tplants.2010.12.005 ID - Zhao2011 ER - TY - JOUR AU - Gibeaut, D. M. AU - Carpita, N. C. PY - 1991 DA - 1991// TI - Tracing cell-wall biogenesis in intact cells and plants. Selective turnover and alteration of soluble and cell-wall polysaccharides in grasses JO - Plant Physiol VL - 97 UR - https://doi.org/10.1104/pp.97.2.551 DO - 10.1104/pp.97.2.551 ID - Gibeaut1991 ER - TY - JOUR AU - Barrière, Y. AU - Guillet, C. AU - Goffner, D. AU - Pichon, M. PY - 2003 DA - 2003// TI - Genetic variation and breeding strategies for improved cell wall digestibility in annual forage crops JO - A review Animal Res VL - 52 UR - https://doi.org/10.1051/animres:2003018 DO - 10.1051/animres:2003018 ID - Barrière2003 ER - TY - JOUR AU - Jung, H. J. G. AU - Samac, D. A. AU - Sarath, G. PY - 2012 DA - 2012// TI - (2012) modifying crops to increase cell wall digestibility JO - Plant Sci VL - 185 UR - https://doi.org/10.1016/j.plantsci.2011.10.014 DO - 10.1016/j.plantsci.2011.10.014 ID - Jung2012 ER - TY - JOUR AU - Li, X. AU - Weng, J. -. K. AU - Chapple, C. PY - 2008 DA - 2008// TI - Improvement of biomass through lignin modification JO - Plant J VL - 54 UR - https://doi.org/10.1111/j.1365-313X.2008.03457.x DO - 10.1111/j.1365-313X.2008.03457.x ID - Li2008 ER - TY - STD TI - Harrington MJ, Mutwil M, Barrière, Sibout R. Molecular biology of lignification in grasses. In: Jouanin L, Lapierre C, editors. Advances in botanical research, Vol. 61. Elsevier, Ltd; 2012, p. 77–112. ID - ref54 ER - TY - JOUR AU - Vermerris, W. AU - Abril, A. PY - 2015 DA - 2015// TI - Enhancing cellulose utilization for fuels and chemicals by genetic modification of plant cell wall architecture JO - Curr Opin Biotech VL - 32 UR - https://doi.org/10.1016/j.copbio.2014.11.024 DO - 10.1016/j.copbio.2014.11.024 ID - Vermerris2015 ER - TY - JOUR AU - Biswal, A. K. AU - Atmodjo, M. A. AU - Li, M. AU - Baxter, H. L. AU - Yoo, C. G. AU - Pu, Y. Q. AU - Lee, Y. C. AU - Mazarei, M. AU - Black, I. M. AU - Zhang, J. Y. PY - 2018 DA - 2018// TI - Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis JO - Nat Biotech VL - 36 UR - https://doi.org/10.1038/nbt.4067 DO - 10.1038/nbt.4067 ID - Biswal2018 ER - TY - STD TI - Yang H, Benatti MR, Karva RA, Fox A, Meilan R, Carpita NC, McCann MC. Rhamnogalacturonan I-lyase expression in transgenic poplar wood facilitates cell-cell separation for biomass use in review. ID - ref57 ER - TY - JOUR AU - Vergara, C. E. AU - Carpita, N. C. PY - 2001 DA - 2001// TI - β-D-glycan synthases and the CesA gene family: Lessons to be learned from the mixed-linkage (1→3),(1→4)-β-D-glucan synthase JO - Plant Mol Biol VL - 47 UR - https://doi.org/10.1023/A:1010631431620 DO - 10.1023/A:1010631431620 ID - Vergara2001 ER - TY - JOUR AU - Tanaka, K. AU - Murata, K. AU - Yamazaki, M. AU - Onosato, K. AU - Miyao, A. AU - Hirochika, H. PY - 2003 DA - 2003// TI - Three distinct rice cellulose synthase catalytic subunit genes required for cellulose synthesis in the secondary wall JO - Plant Physiol VL - 133 UR - https://doi.org/10.1104/pp.103.022442 DO - 10.1104/pp.103.022442 ID - Tanaka2003 ER - TY - JOUR AU - Appenzeller, L. AU - Doblin, M. AU - Barreiro, R. AU - Wang, H. Y. AU - Niu, X. M. AU - Kollipara, K. AU - Carrigan, L. AU - Tomes, D. AU - Chapman, M. AU - Dhugga, K. S. PY - 2004 DA - 2004// TI - Cellulose synthesis in maize: isolation and expression analysis of the cellulose synthase (CesA) gene family JO - Cellulose VL - 11 UR - https://doi.org/10.1023/B:CELL.0000046417.84715.27 DO - 10.1023/B:CELL.0000046417.84715.27 ID - Appenzeller2004 ER - TY - JOUR AU - Taylor, N. G. PY - 2008 DA - 2008// TI - Cellulose biosynthesis and deposition in higher plants JO - New Phytol VL - 178 UR - https://doi.org/10.1111/j.1469-8137.2008.02385.x DO - 10.1111/j.1469-8137.2008.02385.x ID - Taylor2008 ER - TY - JOUR AU - Gonneau, M. AU - Desprez, T. AU - Guillot, A. AU - Vernhettes, S. AU - Höfte, H. PY - 2014 DA - 2014// TI - Catalytic subunit stoichiometry within the cellulose synthase complex JO - Plant Physiol VL - 166 UR - https://doi.org/10.1104/pp.114.250159 DO - 10.1104/pp.114.250159 ID - Gonneau2014 ER - TY - JOUR AU - Hill, J. L. AU - Hammudi, M. B. AU - Tien, M. PY - 2014 DA - 2014// TI - The Arabidopsis cellulose synthase complex: a proposed hexamer of CESA trimers in an equimolar stoichiometry JO - Plant Cell VL - 26 UR - https://doi.org/10.1105/tpc.114.131193 DO - 10.1105/tpc.114.131193 ID - Hill2014 ER - TY - JOUR AU - Zhang, X. AU - Dominguez, P. G. AU - Kumar, M. AU - Bygdell, J. AU - Miroshnichenko, S. AU - Sundberg, B. AU - Wingsle, G. AU - Niittyläa, T. PY - 2018 DA - 2018// TI - (2018) cellulose synthase stoichiometry in aspen differs from Arabidopsis and Norway spruce JO - Plant Physiol VL - 177 UR - https://doi.org/10.1104/pp.18.00394 DO - 10.1104/pp.18.00394 ID - Zhang2018 ER - TY - JOUR AU - Okekeogbu, I. O. AU - Pattathil, S. AU - Fernández-Niño, S. M. G. AU - Penning, B. W. AU - Lao, J. AU - Heazlewood, J. L. AU - Hahn, M. G. AU - McCann, M. C. AU - Carpita, N. C. PY - 2019 DA - 2019// TI - Glycome and proteomic components of Golgi membranes are common between two angiosperms with distinct cell wall structures JO - Plant Cell VL - 31 UR - https://doi.org/10.1105/tpc.18.00755 DO - 10.1105/tpc.18.00755 ID - Okekeogbu2019 ER - TY - JOUR AU - Peña, M. J. AU - Zhong, R. AU - Zhou, G. K. AU - Richardson, E. A. AU - O’Neill, M. A. AU - Darvill, A. G. AU - York, W. S. AU - Ye, Z. H. PY - 2007 DA - 2007// TI - Arabidopsis irregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis JO - Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.106.049320 DO - 10.1105/tpc.106.049320 ID - Peña2007 ER - TY - JOUR AU - Brown, D. M. AU - Goubet, F. AU - Wong, V. W. AU - Goodacre, R. AU - Stephens, E. AU - Dupree, P. AU - Turner, S. R. PY - 2007 DA - 2007// TI - Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis JO - Plant J VL - 52 UR - https://doi.org/10.1111/j.1365-313X.2007.03307.x DO - 10.1111/j.1365-313X.2007.03307.x ID - Brown2007 ER - TY - JOUR AU - Brown, D. M. AU - Zhang, Z. AU - Stephens, E. AU - Dupree, P. AU - Turner, S. R. PY - 2009 DA - 2009// TI - Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis JO - Plant J VL - 57 UR - https://doi.org/10.1111/j.1365-313X.2008.03729.x DO - 10.1111/j.1365-313X.2008.03729.x ID - Brown2009 ER - TY - JOUR AU - Wu, A. M. AU - Rihouey, C. AU - Seveno, M. AU - Hörnblad, E. AU - Singh, S. K. AU - Matsunaga, T. AU - Ishii, T. AU - Lerouge, P. AU - Marchant, A. PY - 2009 DA - 2009// TI - The Arabidopsis IRX10 and IRX10-LIKE glycosyltransferases are critical for glucuronoxylan biosynthesis during secondary cell wall formation JO - Plant J VL - 57 UR - https://doi.org/10.1111/j.1365-313X.2008.03724.x DO - 10.1111/j.1365-313X.2008.03724.x ID - Wu2009 ER - TY - JOUR AU - Anders, N. AU - Wilkinson, M. D. AU - Lovegrove, A. AU - Freeman, J. AU - Tryfona, T. AU - Peliny, T. K. AU - Weimar, T. AU - Mortimer, J. C. AU - Stott, K. AU - Baker, J. M. PY - 2012 DA - 2012// TI - Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1115858109 DO - 10.1073/pnas.1115858109 ID - Anders2012 ER - TY - JOUR AU - Chiniquy, D. AU - Sharma, V. AU - Schultink, A. AU - Baidoo, E. E. AU - Rautengarten, C. AU - Cheng, K. AU - Carroll, A. AU - Ulvskov, P. AU - Harholt, J. AU - Keasling, J. D. PY - 2012 DA - 2012// TI - XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1202079109 DO - 10.1073/pnas.1202079109 ID - Chiniquy2012 ER - TY - JOUR AU - Wang, Q. AU - Dooner, H. K. PY - 2006 DA - 2006// TI - Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0603080103 DO - 10.1073/pnas.0603080103 ID - Wang2006 ER - TY - JOUR AU - Swanson-Wagner, R. A. AU - Eichten, S. R. AU - Kumari, S. AU - Tiffin, P. AU - Stein, J. C. AU - Ware, D. AU - Springer, N. M. PY - 2010 DA - 2010// TI - Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.109165.110 DO - 10.1101/gr.109165.110 ID - Swanson-Wagner2010 ER - TY - STD TI - Paschold A, Larson NB, Marcon C, Schnable JC, Yeh C-T, Lanz C, Nettleton D, Piepho H-P, Schnable PS, Hochholdinger F. Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids. Plant Cell. 2014;26:3939–48. ID - ref74 ER - TY - STD TI - Baldauf JA, Marcon C, Paschold A, Hochholdinger F. Nonsyntenic genes drive tissue-specific dynamics of differential, nonadditive, and allelic expression patterns in maize hybrids. Plant Physiol. 2016;171:1144–55. ID - ref75 ER - TY - JOUR AU - Jiang, L. AU - Lv, Y. AU - Li, T. AU - Zhao, H. AU - Zhang, T. PY - 2015 DA - 2015// TI - Identification and characterization of presence/absence variation in maize genotype Mo17 JO - Genes Genom VL - 37 UR - https://doi.org/10.1007/s13258-015-0272-7 DO - 10.1007/s13258-015-0272-7 ID - Jiang2015 ER - TY - JOUR AU - Beló, A. AU - Beatty, M. K. AU - Hondred, D. AU - Fengler, K. A. AU - Li, B. PY - 2005 DA - 2005// TI - Rafalski a (2010) allelic genome structural variations in maize detected by array comparative genome hybridization JO - Theor Appl Genet VL - 2 ID - Beló2005 ER - TY - JOUR AU - Morgante, M. AU - Brunner, S. AU - Pea, G. AU - Fengler, K. AU - Zuccolo, A. PY - 2005 DA - 2005// TI - Rafalski a (2005) gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize JO - Nat Genet VL - 9 UR - https://doi.org/10.1038/ng1615 DO - 10.1038/ng1615 ID - Morgante2005 ER - TY - JOUR AU - Liu, K. AU - Goodman, M. AU - Muse, S. AU - Smith, J. S. AU - Buckler, E. AU - Doebley, J. PY - 2003 DA - 2003// TI - Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites JO - Genetics VL - 165 ID - Liu2003 ER - TY - JOUR AU - Lu, F. AU - Romay, M. C. AU - Glaubitz, J. C. AU - Bradbury, P. J. AU - Elshire, R. J. AU - Wang, T. AU - Li, Y. AU - Li, Y. AU - Semagn, K. AU - Zhang, X. PY - 2015 DA - 2015// TI - High-resolution genetic mapping of maize pan-genome sequence anchors JO - Nat Commun VL - 6 UR - https://doi.org/10.1038/ncomms7914 DO - 10.1038/ncomms7914 ID - Lu2015 ER - TY - JOUR AU - Romay, M. C. AU - Millard, M. J. AU - Glaubitz, J. C. AU - Peiffer, J. A. AU - Swarts, K. L. AU - Casstevens, T. M. AU - Elshire, R. J. AU - Acharya, C. B. AU - Mitchell, S. E. AU - Flint-Garcia, S. A. PY - 2013 DA - 2013// TI - Comprehensive genotyping of the USA national maize inbred seed bank JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-6-r55 DO - 10.1186/gb-2013-14-6-r55 ID - Romay2013 ER - TY - JOUR AU - Lu, F. AU - Romay, M. C. AU - Glaubitz, J. C. AU - Bradbury, P. J. AU - Elshire, R. J. AU - Wang, T. AU - Li, Y. AU - Li, Y. AU - Semagn, K. AU - Zhang, X. PY - 2015 DA - 2015// TI - High-resolution genetic mapping of maize pan-genome sequence anchors JO - Nat Commun VL - 6 UR - https://doi.org/10.1038/ncomms7914 DO - 10.1038/ncomms7914 ID - Lu2015 ER - TY - JOUR AU - Tian, F. AU - Bradbury, P. J. AU - Brown, P. J. AU - Hung, H. AU - Sun, Q. AU - Flint-Garcia, S. AU - Rocheford, T. R. AU - McMullen, M. D. AU - Holland, J. B. AU - Buckler, E. S. PY - 2011 DA - 2011// TI - Genome-wide association study of leaf architecture in the maize nested association mapping population JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.746 DO - 10.1038/ng.746 ID - Tian2011 ER - TY - JOUR AU - Buckler, E. S. AU - Holland, B. AU - Bradbury, P. J. AU - Acharya, C. B. AU - Brown, P. J. AU - Browne, C. AU - Ersoz, E. AU - Flint-Garcia, S. AU - Garcia, A. AU - Glaubitz, J. C. PY - 2009 DA - 2009// TI - The genetic architecture of maize flowering time JO - Science VL - 325 UR - https://doi.org/10.1126/science.1174276 DO - 10.1126/science.1174276 ID - Buckler2009 ER - TY - STD TI - Peiffer JA, Romay MC, Gore MA, Flint-Garcia SA, Zhang Z, Millard MJ, Gardner CAC, McMullen MD, Holland JB, Peter J. Bradbury PJ, Buckler ES. The genetic architecture of maize height. Genetics 2014;196(4):1337–1356. ID - ref85 ER - TY - JOUR AU - Penning, B. W. AU - Sykes, R. W. AU - Babcock, N. C. AU - Dugard, C. K. AU - Klimek, J. F. AU - Gamblin, D. AU - Davis, M. AU - Filley, T. R. AU - Mosier, N. S. AU - Weil, C. F. PY - 2014 DA - 2014// TI - Validation of PyMBMS as a high-throughput screen for lignin abundance in lignocellulosic biomass of grasses JO - Bioenerg Res VL - 7 UR - https://doi.org/10.1007/s12155-014-9410-3 DO - 10.1007/s12155-014-9410-3 ID - Penning2014 ER - TY - JOUR AU - Dubois, M. AU - Gilles, K. A. AU - Hamilton, J. K. AU - Rebers, P. A. PY - 1956 DA - 1956// TI - Smith F JO - Colorimetric method for determination of sugars and related substances Anal Chem VL - 28 ID - Dubois1956 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Li, P. AU - Ponnala, L. AU - Gandotra, N. AU - Wang, L. AU - Si, Y. AU - Tausta, S. L. AU - Kebrom, T. H. AU - Provart, N. AU - Patel, R. AU - Myers, C. R. PY - 2010 DA - 2010// TI - The developmental dynamics of the maize leaf transcriptome JO - Nature Genet VL - 42 UR - https://doi.org/10.1038/ng.703 DO - 10.1038/ng.703 ID - Li2010 ER - TY - JOUR AU - Chang, Y. M. AU - Liu, W. Y. AU - Shih, A. C. C. AU - Shen, M. N. AU - Lu, C. H. AU - Lu, M. Y. J. AU - Yang, H. W. AU - Wang, T. Y. AU - Chen, S. C. C. AU - Chen, S. M. PY - 2012 DA - 2012// TI - Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis JO - Plant Physiol VL - 160 UR - https://doi.org/10.1104/pp.112.203810 DO - 10.1104/pp.112.203810 ID - Chang2012 ER - TY - JOUR AU - Sturn, A. AU - Quackenbush, J. AU - Trajanoski, Z. PY - 2002 DA - 2002// TI - Genesis: cluster analysis of microarray data JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.1.207 DO - 10.1093/bioinformatics/18.1.207 ID - Sturn2002 ER - TY - STD TI - R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2016. [https://www.R-project.org/]. UR - https://www.r-project.org/ ID - ref92 ER - TY - STD TI - Kassambara A, Mundt F. Factoextra: Extract and Visualize the Results of Multivariate Data Analyses. R package version 1.0.4, 2017. [https://CRAN.R-project.org/package=factoextra]. UR - https://cran.r-project.org/package=factoextra ID - ref93 ER - TY - JOUR AU - Robinson, M. D. AU - McCarthy, D. J. AU - Smyth, G. K. PY - 2010 DA - 2010// TI - edgeR: a bioconductor package for differential expression analysis of digital gene expression data JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp616 DO - 10.1093/bioinformatics/btp616 ID - Robinson2010 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Chenna, R. AU - Sugawara, H. AU - Koike, T. AU - Lopez, R. AU - Gibson, T. J. PY - 2003 DA - 2003// TI - Multiple sequence alignment with the Clustal series of programs JO - Nucl Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg500 DO - 10.1093/nar/gkg500 ID - Chenna2003 ER - TY - JOUR AU - Chevenet, F. AU - Brun, C. AU - Banuls, A. L. AU - Jacq, B. AU - Christen, R. PY - 2006 DA - 2006// TI - TreeDyn: towards dynamic graphics and annotations for analyses of trees JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-439 DO - 10.1186/1471-2105-7-439 ID - Chevenet2006 ER -