The expression of phenylpropanoid and related genes was investigated in bm1, bm2, bm3, and bm4 near-isogenic maize plants at the 4-5 leaf stage using a gene-specific cell wall macro-array. The bm3 mutant, which is mutated in the caffeic acid O-methyltransferase (COMT) gene, exhibited the lowest number of differentially expressed genes. Although no other phenylpropanoid gene had an altered expression, two distinct OMT and two cytochrome P450 genes were overexpressed suggesting the activation of alternative hydroxylation/methylation pathways. The bm1 mutant had the highest number of differentially expressed genes, all of which were under-expressed. Bm1 mutant plants were affected not only in cinnamyl alcohol dehydrogenase (bm1 related CAD) gene expression as expected, but also in the expression of other CAD/SAD gene family members and several regulatory genes including MYB, ARGONAUTE and HDZip. As originally believed, the bm1 mutation could be localized at the CAD locus, but more probably in a gene that regulates the expression of the CAD gene family. The profile of under-expressed genes in the bm2 mutant is nearly similar to that of bm1. These genes fell under several functional categories including phenylpropanoid metabolism, transport and trafficking, transcription factors and regulatory genes. As the bm2 mutant exhibited a lower guaiacyl (G) unit lignin content, the bm2 mutation could affect a regulatory gene involved, perhaps indirectly, in the regulation, conjugation or transport of coniferaldehyde, or the establishment of G-rich maize tissues. The pattern of gene expression in bm4 plants, characterized by the over-expression of phenylpropanoid and methylation genes, suggests that the bm4 mutation likely also affects a gene involved in the regulation of lignification.

Plants are constantly facing rapid changes in evaporative demand and soil water content, which affect their water status and growth. In apparent contradiction to a hydraulic hypothesis, leaf elongation rate (LER) declined in the morning and recovered upon soil rehydration considerably quicker than transpiration rate and leaf water potential (typical half-times of 30 min versus 1–2 h). The morning decline of LER began at very low light and transpiration and closely followed the stomatal opening of leaves receiving direct light, which represent a small fraction of leaf area. A simulation model in maize (Zea mays) suggests that these findings are still compatible with a hydraulic hypothesis. The small water flux linked to stomatal aperture would be sufficient to decrease water potentials of the xylem and growing tissues, thereby causing a rapid decline of simulated LER, while the simulated water potential of mature tissues declines more slowly due to a high hydraulic capacitance. The model also captured growth patterns in the evening or upon soil rehydration. Changes in plant hydraulic conductance partly counteracted those of transpiration. Root hydraulic conductivity increased continuously in the morning, consistent with the transcript abundance of Zea maize Plasma Membrane Intrinsic Protein aquaporins. Transgenic lines underproducing abscisic acid, with lower hydraulic conductivity and higher stomatal conductance, had a LER declining more rapidly than wild-type plants. Whole-genome transcriptome and phosphoproteome analyses suggested that the hydraulic processes proposed here might be associated with other rapidly occurring mechanisms. Overall, the mechanisms and model presented here may be an essential component of drought tolerance in naturally fluctuating evaporative demand and soil moisture.

Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution.

Association mapping of sequence polymorphisms underlying the phenotypic variability of quantitative agronomical traits is now a widely used method in plant genetics. However, due to the common presence of a complex genetic structure within the plant diversity panels, spurious associations are expected to be highly frequent. Several methods have thus been suggested to control for panel structure. They mainly rely on ad hoc criteria for selecting the number of ancestral groups; which is often not evident for the complex panels that are commonly used in maize. It was thus necessary to evaluate the effect of the selected structure models on the association mapping results. A real maize data set (342 maize inbred lines and 12,000 SNPs) was used for this study. The panel structure was estimated using both Bayesian and dimensional reduction methods, considering an increasing number of ancestral groups. Effect on association tests depends in particular on the number of ancestral groups and on the trait analyzed. The results also show that using a high number of ancestral groups leads to an over-corrected model in which all causal loci vanish. Finally the results of all models tested were combined in a meta-analysis approach. In this way, robust associations were highlighted for each analyzed trait.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-010-1519-y) contains supplementary material, which is available to authorized users.

Both for cattle nutrition and biofuel production, the improvement in maize (Zea mays L.) cell wall degradability depends on understanding the genetic mechanisms involved in the biosynthesis of phenylpropanoids. Most of the genes involved in monolignol and p‐hydroxycinnamate biosynthesis are known, but many belong to multigene families. A macro‐array with cell wall gene specific tags was used to characterize the different gene expression profiles in maize ear internode at four stages from 7 d before silking to 15 d after silking. Gene expression profiles were related to biochemical variation observed for lignin content, lignin structure, and esterified and etherified ferulic acid content. Most of the significantly expressed genes had a maximum at the first stages of sampling with their expression decreasing rapidly thereafter. A few genes had a second later expression peak. In each multigene family, only a restricted number of genes were expressed during maize cell wall formation in the below‐ear internode. Genes for three phenylalanine ammonia‐lyases, two cinnamate 4‐hydroxylases, two 4‐coumarate:coenzyme A ligases, three caffeoyl‐CoA O‐methyltransferases, but only one cinnamoyl‐CoA reductase, two cinnamyl alcohol dehydrogenases, one ferulate 5‐hydroxylase, the only caffeic acid O‐methyltransferase, and a ZRP4‐like O‐methyltransferase were significantly expressed. These genes are likely the most important ones in maize stem lignification, and hence are priority targets in maize breeding.

Grasses, which are currently at the basis of cattle feeding, will, in the near future, be a major source of cell wall carbohydrates for sustainable biofuel production. The association of lignins with other matrix components, together with linkages between cell wall carbohydrates, greatly influences cell wall properties, including the degradability of structural polysaccharides by micro-organisms in animal rumen or industrial fermenters. The improvement in biofuel production from plants is based on the understanding of the cell wall composition and assembly, and on the discovery of genetic and genomic mechanisms involved in each component biosynthesis and their depositions in each lignified tissue. While nearly 40 QTL have been shown for lignin content, only seven locations appeared of greater importance in investigated genetic resources. Expression studies highlighted that several genes in the lignin pathway are less expressed in lines with higher cell wall degradability. However, only a few lignin pathway genes mapped in QTL positions, and the fully relevant candidates might be genes involved in regulation of lignin pathway genes, or in regulation of lignified tissue assembly.

Lignocellulosic biomass is an abundant byproduct from cereal crops that can potentially be valorized as a feedstock to produce biomaterials. Zea mays CINNAMYL ALCOHOL DEHYDROGENASE 2 (ZmCAD2) is involved in lignification, and is a promising target to improve the cellulose-to-glucose conversion of maize stover. Here, we analyzed a field-grown zmcad2 Mutator transposon insertional mutant. Zmcad2 mutant plants had an 18% lower Klason lignin content, whereas their cellulose content was similar to that of control lines. The lignin in zmcad2 mutants contained increased levels of hydroxycinnamaldehydes, i.e. the substrates of ZmCAD2, ferulic acid and tricin. Ferulates decorating hemicelluloses were not altered. Phenolic profiling further revealed that hydroxycinnamaldehydes are partly converted into (dihydro)ferulic acid and sinapic acid and their derivatives in zmcad2 mutants. Syringyl lactic acid hexoside, a metabolic sink in CAD-deficient dicot trees, appeared not to be a sink in zmcad2 maize. The enzymatic cellulose-to-glucose conversion efficiency was determined after 10 different thermochemical pre-treatments. Zmcad2 yielded significantly higher conversions compared with controls for almost every pre-treatment. However, the relative increase in glucose yields after alkaline pre-treatment was not higher than the relative increase when no pre-treatment was applied, suggesting that the positive effect of the incorporation of hydroxycinnamaldehydes was leveled off by the negative effect of reduced p-coumarate levels in the cell wall. Taken together, our results reveal how phenolic metabolism is affected in CAD-deficient maize, and further support mutating CAD genes in cereal crops as a promising strategy to improve lignocellulosic biomass for sugar-platform biorefineries.

The western corn rootworm (WCR) Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) remains one of the economically most important pests of maize (Zea mays) due to its adaptive capabilities to pest management options. This includes the ability to develop resistance to some of the commercial pesticidal proteins originating from different strains of Bacillus thuringiensis. Although urgently needed, the discovery of new, environmentally safe agents with new modes of action is a challenge. In this study we report the discovery of a new family of binary pesticidal proteins isolated from several Chryseobacterium species. These novel binary proteins, referred to as GDI0005A and GDI0006A, produced as recombinant proteins, prevent growth and increase mortality of WCR larvae, as does the bacteria. These effects were found both in susceptible and resistant WCR colonies to Cry3Bb1 and Cry34Ab1/Cry35Ab1 (reassigned Gpp34Ab1/Tpp35Ab1). This suggests GDI0005A and GDI0006A may not share the same binding sites as those commercially deployed proteins and thereby possess a new mode of action. This paves the way towards the development of novel biological or biotechnological management solutions urgently needed against rootworms.