title: Cell Wall Composition and Candidate Biosynthesis Gene Expression During Rice Development.
abstract: Cell walls of grasses, including cereal crops and biofuel grasses, comprise the majority of plant biomass and intimately influence plant growth, development and physiology. However, the functions of many cell wall synthesis genes, and the relationships among and the functions of cell wall components remain obscure. To better understand the patterns of cell wall accumulation and identify genes that act in grass cell wall biosynthesis, we characterized 30 samples from aerial organs of rice (Oryza sativa cv. Kitaake) at 10 developmental time points, 3-100 d post-germination. Within these samples, we measured 15 cell wall chemical components, enzymatic digestibility and 18 cell wall polysaccharide epitopes/ligands. We also used quantitative reverse transcription-PCR to measure expression of 50 glycosyltransferases, 15 acyltransferases and eight phenylpropanoid genes, many of which had previously been identified as being highly expressed in rice. Most cell wall components vary significantly during development, and correlations among them support current understanding of cell walls. We identified 92 significant correlations between cell wall components and gene expression and establish nine strong hypotheses for genes that synthesize xylans, mixed linkage glucan and pectin components. This work provides an extensive analysis of cell wall composition throughout rice development, identifies genes likely to synthesize grass cell walls, and provides a framework for development of genetically improved grasses for use in lignocellulosic biofuel production and agriculture.
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
authors.forename: Fan
authors.initials: F
authors.lastname: Lin
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Chithra
authors.initials: C
authors.lastname: Manisseri
authors.affiliation: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Fagerström
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Peck
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.|Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA.|Monsanto Company, Chesterfield Village Campus, Chesterfield, MO 63017, USA.
authors.forename: Miguel E
authors.initials: ME
authors.lastname: Vega-Sánchez
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Williams
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Chiniquy
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
authors.forename: Prasenjit
authors.initials: P
authors.lastname: Saha
authors.affiliation: Bioenergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
authors.forename: Sivakumar
authors.initials: S
authors.lastname: Pattathil
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Conlin
authors.affiliation: Department of Statistics, Oklahoma State University, Stillwater, OK 74078, USA.
authors.forename: Lan
authors.initials: L
authors.lastname: Zhu
authors.affiliation: Bioenergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Hahn
authors.affiliation: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark.
authors.forename: William G T
authors.initials: WG
authors.lastname: Willats
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.|Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Henrik V
authors.initials: HV
authors.lastname: Scheller
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.|Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark.
authors.forename: Pamela C
authors.initials: PC
authors.lastname: Ronald
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA lbartley@ou.edu.|Joint BioEnergy Institute, Emeryville, CA 94608, USA.|Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark.
authors.forename: Laura E
authors.initials: LE
authors.lastname: Bartley
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics*; D002473:Cell Wall / Q000378:metabolism*; D016000:Cluster Analysis; D000939:Epitopes / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D005936:Glucans / Q000378:metabolism; D008024:Ligands; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D025341:Principal Component Analysis
chemical_list: D000939:Epitopes; D005936:Glucans; D008024:Ligands
keywords: 
  Oryza sativa
  ; Acyltransferase; Cell wall; Glycosyltransferase; Grass; Mixed linkage glucan; Xylan