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

Autor: Penning BW; Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.; Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.; Present Address: USDA-ARS, Wheat Quality Research Unit, 1680 Madison Avenue, Wooster, OH, 44691, USA., Shiga TM; Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.; Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil., Klimek JF; Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA., SanMiguel PJ; Genomics Core Facility, Purdue University, 170 South University Street, Purdue University, West Lafayette, IN, 47907, USA., Shreve J; Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA.; Present Address: Department of Internal Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA., Thimmapuram J; Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil.; Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA., Sykes RW; National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.; Present Address: Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, Los Alamos, NM, 87545, USA., Davis MF; National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA., McCann MC; Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.; Purdue Center for Plant Biology, West Lafayette, USA., Carpita NC; Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. carpita@purdue.edu.; Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. carpita@purdue.edu.; Purdue Center for Plant Biology, West Lafayette, USA. carpita@purdue.edu.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2019 Oct 29; Vol. 20 (1), pp. 785. Date of Electronic Publication: 2019 Oct 29.
DOI: 10.1186/s12864-019-6117-z
Abstrakt: Background: 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.
Results: 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.
Conclusions: 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.
Databáze: MEDLINE
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