Abstract
BackgroundThe 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.ResultsHigh-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.ConclusionsLarge 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.
Highlights
The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families
Xylan, and lignin contents increase in maize rind tissue during internode development Maize stem development began at the fifth-leaf stage and culminated with tassel formation after five weeks
Identification of gene family members for biosynthetic enzymes of cellulose, xylan and lignin in stems We identified over 70 families and sub-groups of cell wall-related genes that function in nucleotide-sugar and monolignol substrate generation, synthesis and glycosyl transfer, growth, and hydrolysis and transglycosylation in maize B73 (Additional file 1: Dataset 1)
Summary
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. The disassembly of lignocellulosic biomass to release sugars and aromatics, as substrates for fuels and chemicals, could be enhanced by the ability to modulate both the composition and the interactions of the polymers of cell walls [1]. Secondary walls are thickened and lignified in specific cell types that contribute to substantial amounts of biomass. Genome-wide transcript-profiling technologies have been used to identify suites of genes involved in deposition of thickened and lignified secondary walls in Arabidopsis and poplar [3,4,5] and in the synthesis and assembly of grass-specific wall components abundant in C4 grass species [6, 7]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
