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November 19, 2009

Maize cell wall genes identified, giving boost to biofuel research

WEST LAFAYETTE, Ind. - Purdue University scientists have helped identify and group the genes thought to be responsible for cell wall development in maize, an effort that expands their ability to discover ways to produce the biomass best suited for biofuels production.

The Purdue scientists, led by Nicholas Carpita, a professor of plant cell biology, published their findings on the 750 cell wall genes in the journal Plant Physiology on Thursday (Nov. 19). They also were co-authors on a study, published Thursday (Nov. 19) in Science, that for the first time sequenced the genome of maize.

In discovering the some 32,000 genes of maize, scientists can better study the function of individual genes and how each affects all aspects of the plant's development. Purdue's scientists are particularly interested in the genes that regulate cellulose, lignin and other parts of plant's cell walls.

"This gives us an inventory of the genes that could become possible targets for modification in the production of biomass," Carpita said. "We want to be able to control the structure of the cell walls."

Carpita and Maureen McCann, a professor of biology and a co-author on both papers, are part of Purdue's C3Bio research project, which is aimed at using thermal and chemical catalysts to create biofuels that utilize more of a plant's carbon. The team hopes to engineer catalysts or catalytic sites into plants and use heat or chemical catalysts to directly convert the biomass into fuel.

"The grasses, including maize, make a unique kind of cell wall," Carpita said. "Beyond the cell wall genes, having a complete genome will enable us to identify developmental controls, such as genes that delay flowering to continue production of biomass, or alter pathways so that plants accumulate more sugar in the stem."

The annotation of the maize cell wall genes also led to the discovery of more than 80 mutants involved in cell wall production. Scientists can grow plants that have a gene mutation and compare them to those without the mutation to understand how changes in the gene functions in biomass accumulation or quality in maize.

"Discovering the genome sequence of maize is a huge step forward in getting at the functions of genes that will be useful in developing new bioenergy crops," McCann said. "We will be able to identify mutants in key genes of interest and then assess how mutation changes the plant cell wall and if those changes are useful."

Researchers found that maize's cell wall genes were more similar to those of rice than to Arabidopsis, a plant often used as a model in scientific experiments.  

"Now we're starting to see differences in the families of related genes and how those genes are expressed," said Bryan Penning, McCann's lab manager and a co-author on both papers. "Now that we have the sequence, we can start building a reservoir of data on the expression patterns of the cell wall genes."

The next step in using the data collected will include testing the mutant genes and exploring how expression of particular genes can be regulated to produce desired characteristics in a maize plant.

Other Purdue scientists involved in the Science paper were Phillip San Miguel, director of the Agricultural Genomics Center, and Richard Westerman, a systems manager and senior programmer in horticulture and landscape architecture. Purdue researchers collaborated with the University of Florida and the National Renewable Energy Laboratory.

Writer: Brian Wallheimer, 765-496-2050, bwallhei@purdue.edu

Sources: Nicholas Carpita, 765-494-4653, carpita@purdue.edu

Maureen McCann, 765-496-1779, mmccann@purdue.edu

Bryan Penning, 765-494-7924, bpenning@purdue.edu

Ag Communications: (765) 494-8415;
Steve Leer, sleer@purdue.edu
Agriculture News Page


ABSTRACT

Genetic Resources for Maize Cell Wall Biology 

Bryan W. Penning, Charles T. Hunter III, Reuben Tayengwa, Andrea L. Eveland, Christopher K. Dugard, Anna T. Olek, Wilfred Vermerris, Karen E. Koch, Donald R. McCarty, Mark F. Davis, Steven R. Thomas, Maureen C. McCann, and Nicholas C. Carpita

Grass species represent a major source of food, feed, and �ber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression pro�les, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript pro�le data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-speci�c genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of �eld-grown lines by near-infrared (NIR) spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis- molecular beam mass spectrometry con�rmed that several NIR mutants had altered carbohydrate-lignin compositions.


 


ABSTRACT

The B73 Maize Genome: Complexity, Diversity and Dynamics

Patrick S. Schnable, Doreen Ware, Robert S. Fulton, Joshua C. Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A. Graves, Patrick Minx, Amy Denise Reily, Laura Courtney, Scott S. Kruchowski, Chad Tomlinson, Cindy Strong, Kim Delehaunty, Catrina Fronick, Bill Courtney, Susan M. Rock, Eddie Belter, Feiyu Du, Kyung Kim, Rachel M. Abbott, Marc Cotton, Andy Levy, Pamela Marchetto, Kerri Ochoa, Stephanie M. Jackson, Barbara Gillam, Weizu Chen, Le Yan, Jamey Higginbotham, Marco Cardenas, Jason Waligorski, Elizabeth Applebaum, Lindsey Phelps, Jason Falcone, Krishna Kanchi, Thynn Thane, Adam Scimone, Nay Thane, Jessica Henke, Tom Wang, Jessica Ruppert, Neha Shah, Kelsi Rotter, Jennifer Hodges, Elizabeth Ingenthron, Matt Cordes, Sara Kohlberg, Jennifer Sgro, Brandon Delgado, Kelly Mead, Asif Chinwalla, Shawn Leonard, Kevin Crouse, Kristi Collura, Dave Kudrna, Jennifer Currie, Ruifeng He, Angelina Angelova, Shanmugam Rajasekar, Teri Mueller, Rene Lomeli, Gabriel Scara, Ara Ko, Krista Delaney, Marina Wissotski, Georgina Lopez, David Campos, Michele Braidotti, Elizabeth Ashley, Wolfgang Golser, HyeRan Kim, SeungHee Lee, Jinke Lin, Zeljko Dujmic, Woojin Kim, Jayson Talag, Andrea Zuccolo, Chuanzhu Fan, Aswathy Sebastian, Melissa Kramer, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Beth Miller, Claude Ambroise, Stephanie Muller, Will Spooner, Apurva Narechania, Liya Ren, Sharon Wei, Sunita Kumari, Ben Faga, Michael Levy, Linda McMahan, Peter Van Buren, Matthew W. Vaughn, Kai Ying, Cheng-Ting Yeh,, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia,, W. Brad Barbazuk, Regina S. Baucom,, Thomas P. Brutnell, Nicholas C. Carpita, Cristian Chaparro, Jer-Ming Chia, Jean-Marc Deragon, James C. Estill, Yan Fu, Jeffrey A. Jeddeloh, Yujun Han,, Hyeran Lee, Pinghua Li, Damon R. Lisch, Sanzhen Liu, Zhijie Liu, Dawn Holligan Nagel, Maureen C. McCann, Phillip San Miguel, Alan M. Myers, Dan Nettleton, John Nguyen, Bryan W. Penning, Lalit Ponnala, Kevin L. Schneider, David C. Schwartz, Anupma Sharma, Carol Soderlund, Nathan M. Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K. Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L. Bennetzen, R. Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G. Presting, Sue Wessler, Srinivas Aluru, Robert A. Martienssen, Sandra W. Clifton, W. Richard McCombie, Rod A. Wing and Richard K. Wilson

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.


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