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Title: Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development

Abstract

The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize ( Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at =95 reads per 20 M, and 693 of them at =500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17,more » but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6]; ORCiD logo [7]; ORCiD logo [8]; ORCiD logo [9]; ORCiD logo [10]
  1. Purdue Univ., West Lafayette, IN (United States). Dept. of Botany & Plant Pathology; Purdue Univ., West Lafayette, IN (United States). Dept. of Biological Sciences; USDA-ARS, Wooster, OH (United States). Wheat Quality Research Unit
  2. Purdue Univ., West Lafayette, IN (United States). Dept. of Botany & Plant Pathology; Dept. de Alimentos e Nutrição Experimental, Sao Paulo (Brazil)
  3. Purdue Univ., West Lafayette, IN (United States). Dept. of Botany & Plant Pathology
  4. Purdue Univ., West Lafayette, IN (United States). Genomics Core Facility
  5. Purdue Univ., West Lafayette, IN (United States). Bioinformatics Core Facility; Cleveland Clinic, Cleveland, OH (United States). Dept. of Internal Medicine
  6. Dept. de Alimentos e Nutrição Experimental, Sao Paulo (Brazil); Purdue Univ., West Lafayette, IN (United States). Bioinformatics Core Facility
  7. National Renewable Energy Lab. (NREL), Golden, CO (United States). National Bioenergy Center; Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  8. National Renewable Energy Lab. (NREL), Golden, CO (United States). National Bioenergy Center
  9. Purdue Univ., West Lafayette, IN (United States). Dept. of Biological Sciences; Plant Center for Plant Biology, West Lafayette, IN (United States)
  10. Purdue Univ., West Lafayette, IN (United States). Dept. of Botany & Plant Pathology; Purdue Univ., West Lafayette, IN (United States). Dept. of Biological Sciences; Purdue Center for Plant Biology, West Lafayette, IN (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1573961
Report Number(s):
NREL/JA-5100-74676
Journal ID: ISSN 1471-2164
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; Zea mays; maize; stem development; cell-wall biosynthesis; gene expression; transcript profiling; lignocellulosic biomass

Citation Formats

Penning, Bryan W., Shiga, Tânia M., Klimek, John F., SanMiguel, Philip J., Shreve, Jacob, Thimmapuram, Jyothi, Sykes, Robert W., Davis, Mark F., McCann, Maureen C., and Carpita, Nicholas C. Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development. United States: N. p., 2019. Web. doi:10.1186/s12864-019-6117-z.
Penning, Bryan W., Shiga, Tânia M., Klimek, John F., SanMiguel, Philip J., Shreve, Jacob, Thimmapuram, Jyothi, Sykes, Robert W., Davis, Mark F., McCann, Maureen C., & Carpita, Nicholas C. Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development. United States. doi:10.1186/s12864-019-6117-z.
Penning, Bryan W., Shiga, Tânia M., Klimek, John F., SanMiguel, Philip J., Shreve, Jacob, Thimmapuram, Jyothi, Sykes, Robert W., Davis, Mark F., McCann, Maureen C., and Carpita, Nicholas C. Tue . "Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development". United States. doi:10.1186/s12864-019-6117-z. https://www.osti.gov/servlets/purl/1573961.
@article{osti_1573961,
title = {Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development},
author = {Penning, Bryan W. and Shiga, Tânia M. and Klimek, John F. and SanMiguel, Philip J. and Shreve, Jacob and Thimmapuram, Jyothi and Sykes, Robert W. and Davis, Mark F. and McCann, Maureen C. and Carpita, Nicholas C.},
abstractNote = {The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize (Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at =95 reads per 20 M, and 693 of them at =500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.},
doi = {10.1186/s12864-019-6117-z},
journal = {BMC Genomics},
number = 1,
volume = 20,
place = {United States},
year = {2019},
month = {10}
}

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