Silage maize as a potent candidate for sustainable animal husbandry development-perspectives and strategies for genetic enhancement

Maize is recognized as the queen of cereals, with an ability to adapt to diverse agroecologies (from 58^oN to 55^oS latitude) and the highest genetic yield potential among cereals. Under contemporary conditions of global climate change, C₄ maize crops offer resilience and sustainability to ensure food, nutritional security, and farmer livelihood. In the northwestern plains of India, maize is an important alternative to paddy for crop diversification in the wake of depleting water resources, reduced farm diversity, nutrient mining, and environmental pollution due to paddy straw burning. Owing to its quick growth, high biomass, good palatability, and absence of anti-nutritional components, maize is also one of the most nutritious non-legume green fodders. It is a high-energy, low-protein forage commonly used for dairy animals like cows and buffalos, often in combination with a complementary high-protein forage such as alfalfa. Maize is also preferred for silage over other fodders due to its softness, high starch content, and sufficient soluble sugars required for proper ensiling. With a rapid population increase in developing countries like China and India, there is an upsurge in meat consumption and, hence, the requirement for animal feed, which entails high usage of maize. The global maize silage market is projected to grow at a compound annual growth rate of 7.84% from 2021 to 2030. Factors such as increasing demand for sustainable and environment-friendly food sources coupled with rising health awareness are fueling this growth. With the dairy sector growing at about 4%-5% and the increasing shortage faced for fodder, demand for silage maize is expected to increase worldwide. The progress in improved mechanization for the provision of silage maize, reduced labor demand, lack of moisture-related marketing issues as associated with grain maize, early vacancy of farms for next crops, and easy and economical form of feed to sustain household dairy sector make maize silage a profitable venture. However, sustaining the profitability of this enterprise requires the development of hybrids specific for silage production. Little attention has yet been paid to breeding for a plant ideotype for silage with specific consideration of traits such as dry matter yield, nutrient yield, energy in organic matter, genetic architecture of cell wall components determining their digestibility, stalk standability, maturity span, and losses during ensiling. This review explores the available information on the underlying genetic mechanisms and gene/gene families impacting silage yield and quality. The trade-offs between yield and nutritive value in relation to crop duration are also discussed. Based on available genetic information on inheritance and molecular aspects, breeding strategies are proposed to develop maize ideotypes for silage for the development of sustainable animal husbandry.

Elucidating the multifunctional role of the cell wall components in the maize exploitation

BACKGROUND

Besides the use of maize grain as food and feed, maize stover can be a profitable by-product for cellulosic ethanol production, whereas the whole plant can be used for silage production. However, yield is reduced by pest damages, stem corn borers being one of the most important yield constraints. Overall, cell wall composition is key in determining the quality of maize biomass, as well as pest resistance. This study aims to evaluate the composition of the four cell wall fractions (cellulose, hemicellulose, lignin and hydroxycinnamates) in diverse maize genotypes and to understand how this composition influences the resistance to pests, ethanol capacity and digestibility.

RESULTS

The following results can be highlighted: (i) pests' resistant materials may show cell walls with low p-coumaric acid and low hemicellulose content; (ii) inbred lines showing cell walls with high cellulose content and high diferulate cross-linking may present higher performance for ethanol production; (iii) and inbreds with enhanced digestibility may have cell walls poor in neutral detergent fibre and diferulates, combined with a lignin polymer composition richer in G subunits.

CONCLUSIONS

Results evidence that there is no maize cell wall ideotype among the tested for optimal performance for various uses, and maize plants should be specifically bred for each particular application.

Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane

Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified in this species is still very low. The recently released sugarcane genome sequence has allowed the genome-wide characterization of the 11 gene families involved in the monolignol biosynthesis branch of the phenylpropanoid pathway. After an exhaustive analysis of sugarcane genomes, 438 haplotypes derived from 175 candidate genes from Saccharum spontaneum and 144 from Saccharum hybrid R570 were identified as associated with this biosynthetic route. The phylogenetic analyses, combined with the search for protein conserved residues involved in the catalytic activity of the encoded enzymes, were employed to identify the family members potentially involved in developmental lignification. Accordingly, 15 candidates were identified as bona fide lignin biosynthesis genes: PTAL1, PAL2, C4H4, 4CL1, HCT1, HCT2, C3'H1, C3'H2, CCoAOMT1, COMT1, F5H1, CCR1, CCR2, CAD2, and CAD7. For this core set of lignin biosynthetic genes, we searched for the chromosomal location, the gene expression pattern, the promoter cis-acting elements, and microRNA targets. Altogether, our results present a comprehensive characterization of sugarcane general phenylpropanoid and monolignol-specific genes, providing the basis for further functional studies focusing on lignin biosynthesis manipulation and biotechnological strategies to improve sugarcane biomass utilization.

Identification of genes from the general phenylpropanoid and monolignol-specific metabolism in two sugarcane lignin-contrasting genotypes

The phenylpropanoid pathway is an important route of secondary metabolism involved in the synthesis of different phenolic compounds such as phenylpropenes, anthocyanins, stilbenoids, flavonoids, and monolignols. The flux toward monolignol biosynthesis through the phenylpropanoid pathway is controlled by specific genes from at least ten families. Lignin polymer is one of the major components of the plant cell wall and is mainly responsible for recalcitrance to saccharification in ethanol production from lignocellulosic biomass. Here, we identified and characterized sugarcane candidate genes from the general phenylpropanoid and monolignol-specific metabolism through a search of the sugarcane EST databases, phylogenetic analysis, a search for conserved amino acid residues important for enzymatic function, and analysis of expression patterns during culm development in two lignin-contrasting genotypes. Of these genes, 15 were cloned and, when available, their loci were identified using the recently released sugarcane genomes from Saccharum hybrid R570 and Saccharum spontaneum cultivars. Our analysis points out that ShPAL1, ShPAL2, ShC4H4, Sh4CL1, ShHCT1, ShC3H1, ShC3H2, ShCCoAOMT1, ShCOMT1, ShF5H1, ShCCR1, ShCAD2, and ShCAD7 are strong candidates to be bona fide lignin biosynthesis genes. Together, the results provide information about the candidate genes involved in monolignol biosynthesis in sugarcane and may provide useful information for further molecular genetic studies in sugarcane.

Canopy reflectance, stalk sugar and juice yields in specialty corn hybrids as affected by nitrogen management strategies

BACKGROUND

The newly developed sugarcorn is conceived for dual-purpose use as a potential biofuel feedstock and a high-energy silage crop. Its agronomic traits are, however, not fully appraised under the umbrella of nitrogen (N) management and with canopy reflectance indicator. A 3-year field study was conducted to examine the responses of silage biomass, stalk sugar concentration, sugar and juice yields to various N applications; and determine the quantitative relationships between canopy reflectance, expressed as the normalized difference vegetation index (NDVI), and stalk sucrose or other sugar measures in a dual-purpose sugarcorn (cv. 'CO384xC103'), in comparison with a commercial leafy silage-specific hybrid (cv. 'Pride A5892G3 EDF').

RESULTS

The moderate N rate, 125 kg ha^-1 , produced similar stalk sucrose, silage and grain yields, compared to the high rate (250 kg N ha^-1 ), regardless of application methods. The NDVI signatures measured at the V8-V10 stage exhibited significant (P < 0.01) and exponential relationships with stalk sucrose concentrations, sucrose and juice yields at the R3 stage, and with silage yield at approximately 65% whole-plant moisture, the optimum silage-harvest window.

CONCLUSION

The results indicate that the moderate N rate, 125 kg ha^-1 , which is recommended for conventional grain corn production in the region, was likely close to the economic optimum N rate for leafy silage-specific and sugarcorn. Canopy reflectance, measured at the early growth stages, can be used as a potential indicator of sugar and silage production, and this quantitative relationship necessitates further evaluation with more genotypes and under wide environmental conditions. © 2019 Her Majesty the Queen in Right of Canada Journal of The Science of Food and Agriculture © 2019 Society of Chemical Industry.

Influence of a novel bm3 corn silage hybrid with floury kernel genetics on lactational performance and feed efficiency of Holstein cows

Dry matter intake, lactation performance, and chewing behavior of multiparous Holstein cows (n = 15) fed diets containing a novel bm3 corn silage hybrid with floury kernel genetics were compared with cows fed diets containing commercially available conventional and bm3 hybrids using a replicated 3 × 3 Latin square design with 28-d periods. Cows were housed in tiestalls, milked 3 times/d, and fed a total mixed ration containing 49.0% (dry matter basis) of (1) a conventional corn silage hybrid (CONV); (2) a brown midrib bm3 hybrid (BMR); or (3) a bm3 hybrid with floury kernel genetics (BMRFL). All diets contained 6.3% hay crop silage and 44.7% concentrate. Dietary nutrient composition averaged 32.7% neutral detergent fiber (NDF) and 26.3 starch (% of dry matter). Data were analyzed by ANOVA using the MIXED procedure in SAS (SAS Institute Inc., Cary, NC). The dry matter intake was greater for cows fed BMR (28.0 kg/d) compared with CONV (26.8 kg/d), whereas dry matter intake for cows fed BMRFL was intermediate (27.6 kg/d). Energy-corrected milk (ECM) yield was greater for cows fed BMR (50.3 kg/d) and BMRFL (51.8 kg/d) compared with CONV (47.2 kg/d). Milk fat yield was higher for cows fed BMRFL (1.87 kg/d) compared with CONV (1.74 kg/d) and BMR (1.80 kg/d). Milk protein yield was greater for cows fed BMR (1.49 kg/d) and BMRFL (1.54 kg/d) compared with CONV (1.36 kg/d). Milk urea-N was reduced for cows fed BMR (11.61 mg/dL) and BMRFL (11.16 mg/dL) compared with CONV (13.60 mg/dL). Feed efficiency (ECM/dry matter intake) was higher for cows fed BMRFL (1.87) compared with CONV (1.76) and BMR (1.79). Milk N efficiency was greatest for cows fed BMRFL (40.4%) followed by BMR (38.1%) and finally CONV (35.3%). Cows fed CONV chewed 5 min more per kilograms of NDF consumed than cows fed either of the BMR hybrids. No differences were observed among diets in apparent total-tract digestibility of NDF (58.1%) or starch (99.3%). Overall lactational performance was enhanced for cows fed diets containing both BMR and BMRFL hybrids versus CONV. In addition, feeding the BMRFL corn silage improved efficiency of component-corrected milk production and milk N efficiency compared with the CONV and BMR silages.

Low Lignin Mutants and Reduction of Lignin Content in Grasses for Increased Utilisation of Lignocellulose

Biomass rich in lignocellulose from grasses is a major source for biofuel production and animal feed. However, the presence of lignin in cell walls limits its efficient utilisation such as in its bioconversion to biofuel. Reduction of the lignin content or alteration of its structure in crop plants have been pursued, either by regulating genes encoding enzymes in the lignin biosynthetic pathway using biotechnological techniques or by breeding naturally-occurring low lignin mutant lines. The aim of this review is to provide a summary of these studies, focusing on lignin (monolignol) biosynthesis and composition in grasses and, where possible, the impact on recalcitrance to bioconversion. An overview of transgenic crops of the grass family with regulated gene expression in lignin biosynthesis is presented, including the effect on lignin content and changes in the ratio of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units. Furthermore, a survey is provided of low-lignin mutants in grasses, including cereals in particular, summarising their origin and phenotypic traits together with genetics and the molecular function of the various genes identified.

Genetic and Quantitative Trait Locus Analysis of Cell Wall Components and Forage Digestibility in the Zheng58 × HD568 Maize RIL Population at Anthesis Stage

The plant cell wall plays vital roles in various aspects of the plant life cycle. It provides a basic structure for cells and gives mechanical rigidity to the whole plant. Some complex cell wall components are involved in signal transduction during pathogenic infection and pest infestations. Moreover, the lignification level of cell walls strongly influences the digestibility of forage plants. To determine the genetic bases of cell wall components and digestibility, quantitative trait locus (QTL) analyses for six related traits were performed using a recombinant inbred line (RIL) population from a cross between Zheng58 and HD568. Eight QTL for in vitro neutral detergent fiber (NDF) digestibility were observed, out of which only two increasing alleles came from HD568. Three QTL out of ten with alleles increasing in vitro dry matter digestibility also originated from HD568. Five-ten QTL were detected for lignin, cellulose content, acid detergent fiber, and NDF content. Among these results, 29.8% (14/47) of QTL explained >10% of the phenotypic variation in the RIL population, whereas 70.2% (33/47) explained ≤10%. These results revealed that in maize stalks, a few large-effect QTL and a number of minor-effect QTL contributed to most of the genetic components involved in cell wall biosynthesis and digestibility.

Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne

In monocots, lignin content has a strong impact on the digestibility of the cell wall fraction. Engineering lignin biosynthesis requires a profound knowledge of the role of paralogues in the multigene families that constitute the monolignol biosynthesis pathway. We applied a bioinformatics approach for genome-wide identification of candidate genes in Lolium perenne that are likely to be involved in the biosynthesis of monolignols. More specifically, we performed functional subtyping of phylogenetic clades in four multigene families: 4CL, COMT, CAD and CCR. Essential residues were considered for functional clade delineation within these families. This classification was complemented with previously published experimental evidence on gene expression, gene function and enzymatic activity in closely related crops and model species. This allowed us to assign functions to novel identified L. perenne genes, and to assess functional redundancy among paralogues. We found that two 4CL paralogues, two COMT paralogues, three CCR paralogues and one CAD gene are prime targets for genetic studies to engineer developmentally regulated lignin in this species. Based on the delineation of sequence conservation between paralogues and a first analysis of allelic diversity, we discuss possibilities to further study the roles of these paralogues in lignin biosynthesis, including expression analysis, reverse genetics and forward genetics, such as association mapping. We propose criteria to prioritise paralogues within multigene families and certain SNPs within these genes for developing genotyping assays or increasing power in association mapping studies. Although L. perenne was the target of the analyses presented here, this functional subtyping of phylogenetic clades represents a valuable tool for studies investigating monolignol biosynthesis genes in other monocot species.

Measuring the Mechanical Properties of Plant Cell Walls

The size, shape and stability of a plant depend on the flexibility and integrity of its cell walls, which, at the same time, need to allow cell expansion for growth, while maintaining mechanical stability. Biomechanical studies largely vanished from the focus of plant science with the rapid progress of genetics and molecular biology since the mid-twentieth century. However, the development of more sensitive measurement tools renewed the interest in plant biomechanics in recent years, not only to understand the fundamental concepts of growth and morphogenesis, but also with regard to economically important areas in agriculture, forestry and the paper industry. Recent advances have clearly demonstrated that mechanical forces play a crucial role in cell and organ morphogenesis, which ultimately define plant morphology. In this article, we will briefly review the available methods to determine the mechanical properties of cell walls, such as atomic force microscopy (AFM) and microindentation assays, and discuss their advantages and disadvantages. But we will focus on a novel methodological approach, called cellular force microscopy (CFM), and its automated successor, real-time CFM (RT-CFM).

Helicoverpa zea (Lepidoptera: Noctuidae) and Spodoptera frugiperda (Lepidoptera: Noctuidae) Responses to Sorghum bicolor (Poales: Poaceae) Tissues From Lowered Lignin Lines

The presence of lignin within biomass impedes the production of liquid fuels. Plants with altered lignin content and composition are more amenable to lignocellulosic conversion to ethanol and other biofuels but may be more susceptible to insect damage where lignin is an important resistance factor. However, reduced lignin lines of switchgrasses still retained insect resistance in prior studies. Therefore, we hypothesized that sorghum lines with lowered lignin content will also retain insect resistance. Sorghum excised leaves and stalk pith Sorghum bicolor (L.) Moench (Poales: Poaceae) from near isogenic brown midrib (bmr) 6 and 12 mutants lines, which have lowered lignin content and increased lignocellulosic ethanol conversion efficiency, were examined for insect resistance relative to wild-type (normal BTx623). Greenhouse and growth chamber grown plant tissues were fed to first-instar larvae of corn earworms, Helicoverpa zea (Boddie) and fall armyworms Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), two sorghum major pests. Younger bmr leaves had significantly greater feeding damage in some assays than wild-type leaves, but older bmr6 leaves generally had significantly less damage than wild-type leaves. Caterpillars feeding on the bmr6 leaves often weighed significantly less than those feeding on wild-type leaves, especially in the S. frugiperda assays. Larvae fed the pith from bmr stalks had significantly higher mortality compared with those larvae fed on wild-type pith, which suggested that bmr pith was more toxic. Thus, reducing lignin content or changing subunit composition of bioenergy grasses does not necessarily increase their susceptibility to insects and may result in increased resistance, which would contribute to sustainable production.

Reduced lignin content and altered lignin composition in the warm season forage grass Paspalum dilatatum by down-regulation of a Cinnamoyl CoA reductase gene

C4 grasses are favoured as forage crops in warm, humid climates. The use of C4 grasses in pastures is expected to increase because the tropical belt is widening due to global climate change. While the forage quality of Paspalum dilatatum (dallisgrass) is higher than that of other C4 forage grass species, digestibility of warm-season grasses is, in general, poor compared with most temperate grasses. The presence of thick-walled parenchyma bundle-sheath cells around the vascular bundles found in the C4 forage grasses are associated with the deposition of lignin polymers in cell walls. High lignin content correlates negatively with digestibility, which is further reduced by a high ratio of syringyl (S) to guaiacyl (G) lignin subunits. Cinnamoyl-CoA reductase (CCR) catalyses the conversion of cinnamoyl CoA to cinnemaldehyde in the monolignol biosynthetic pathway and is considered to be the first step in the lignin-specific branch of the phenylpropanoid pathway. We have isolated three putative CCR1 cDNAs from P. dilatatum and demonstrated that their spatio-temporal expression pattern correlates with the developmental profile of lignin deposition. Further, transgenic P. dilatatum plants were produced in which a sense-suppression gene cassette, delivered free of vector backbone and integrated separately to the selectable marker, reduced CCR1 transcript levels. This resulted in the reduction of lignin, largely attributable to a decrease in G lignin.

Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations

The caffeic acid 3-O-methytransferase (COMT) gene is a prime candidate for cell wall digestibility improvement based on the characterization of brown midrib-3 mutants. We compared the genetic diversity and linkage disequilibrium at this locus between exotic populations sampled within the Germplasm Enhancement of Maize (GEM) project and 70 inbred lines. In total, we investigated 55 exotic COMT alleles and discovered more than 400 polymorphisms in a 2.2 kb region with pairwise nucleotide diversity (π) up to 0.017, much higher than reported π values of various genes in inbred lines. The ratio of non-synonymous to synonymous SNPs was 3:1 in exotic populations, and significantly higher than the 1:1 ratio for inbred lines. Selection tests detected selection signature in this gene in both pools, but with different evolution patterns. The linkage disequilibrium decay in exotic populations was at least four times more rapid than for inbred lines with r²>0.1 persisting only up to 100 bp. In conclusion, the alleles sampled in the GEM Project offer a valuable genetic resource to broaden genetic variation for the COMT gene, and likely other genes, in inbred background. Moreover, the low linkage disequilibrium makes this material suitable for high resolution association analyses.

Stability analysis of a high fibre yield and low lignin content "thick stem" mutant in tossa jute (Corchorus olitorius L.)

A “thick stem” mutant of Corchorus olitorius L. was induced at M₂ (0.50%, 4 h, EMS) and the true breeding mutant is assessed across generations (M₅ to M₇) considering morphometric traits as well as SEM analysis of pollen grains and raw jute fibres, stem anatomy, cytogenetical attributes, and lignin content in relation to control. Furthermore, single fibre diameter and tensile strength are also analysed. The objective is to assess the stability of mutant for its effective exploration for raising a new plant type in tossa jute for commercial exploitation and efficient breeding. The mutant trait is monogenic recessive to normal. Results indicate that “thick stem” mutant is stable across generations (2n = 14) with distinctive high seed and fibre yield and significantly low lignin content. Stem anatomy of the mutant shows significant enhancement in fibre zone, number of fibre pyramids and fibre bundles per pyramid, and diameter of fibre cell in relation to control. Moreover, tensile strength of mutant fibre is significantly higher than control fibre and the trait is inversely related to fibre diameter. However the mutant is associated with low germination frequency, poor seed viability, and high pollen sterility, which may be eliminated through mutational approach followed by rigorous selection and efficient breeding.

Lignin: characterization of a multifaceted crop component

Lignin is a plant component with important implications for various agricultural disciplines. It confers rigidity to cell walls, and is therefore associated with tolerance to abiotic and biotic stresses and the mechanical stability of plants. In animal nutrition, lignin is considered an antinutritive component of forages as it cannot be readily fermented by rumen microbes. In terms of energy yield from biomass, the role of lignin depends on the conversion process. It contains more gross energy than other cell wall components and therefore confers enhanced heat value in thermochemical processes such as direct combustion. Conversely, it negatively affects biological energy conversion processes such as bioethanol or biogas production, as it inhibits microbial fermentation of the cell wall. Lignin from crop residues plays an important role in the soil organic carbon cycling, as it constitutes a recalcitrant carbon pool affecting nutrient mineralization and carbon sequestration. Due to the significance of lignin in several agricultural disciplines, the modification of lignin content and composition by breeding is becoming increasingly important. Both mapping of quantitative trait loci and transgenic approaches have been adopted to modify lignin in crops. However, breeding goals must be defined considering the conflicting role of lignin in different agricultural disciplines.

Genetic and physical fine mapping of the novel brown midrib gene bm6 in maize (Zea mays L.) to a 180 kb region on chromosome 2

Brown midrib mutants in maize are known to be associated with reduced lignin content and increased cell wall digestibility, which leads to better forage quality and higher efficiency of cellulosic biomass conversion into ethanol. Four well known brown midrib (bm) mutants, named bm1-4, were identified several decades ago. Additional recessive brown midrib mutants have been identified by allelism tests and designated as bm5 and bm6. In this study, we determined that bm6 increases cell wall digestibility and decreases plant height. bm6 was confirmed onto the short arm of chromosome 2 by a small mapping set with 181 plants from a F(2) segregating population, derived from crossing B73 and a bm6 mutant line. Subsequently, 960 brown midrib individuals were selected from the same but larger F(2) population for genetic and physical mapping. With newly developed markers in the target region, the bm6 gene was assigned to a 180 kb interval flanked by markers SSR_308337 and SSR_488638. In this region, ten gene models are predicted in the maize B73 sequence. Analysis of these ten genes as well as genes in the syntenic rice region revealed that four of them are promising candidate genes for bm6. Our study will facilitate isolation of the underlying gene of bm6 and advance our understanding of brown midrib gene functions.

Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes

BACKGROUND

For cellulosic biofuels processes, suitable characterization of the lignin remaining within the cell wall and correlation of quantified properties of lignin to cell wall polysaccharide enzymatic deconstruction is underrepresented in the literature. This is particularly true for grasses which represent a number of promising bioenergy feedstocks where quantification of grass lignins is particularly problematic due to the high fraction of p-hydroxycinnamates. The main focus of this work is to use grasses with a diverse range of lignin properties, and applying multiple lignin characterization platforms, attempt to correlate the differences in these lignin properties to the susceptibility to alkaline hydrogen peroxide (AHP) pretreatment and subsequent enzymatic deconstruction.

RESULTS

We were able to determine that the enzymatic hydrolysis of cellulose to to glucose (i.e. digestibility) of four grasses with relatively diverse lignin phenotypes could be correlated to total lignin content and the content of p-hydroxycinnamates, while S/G ratios did not appear to contribute to the enzymatic digestibility or delignification. The lignins of the brown midrib corn stovers tested were significantly more condensed than a typical commercial corn stover and a significant finding was that pretreatment with alkaline hydrogen peroxide increases the fraction of lignins involved in condensed linkages from 88-95% to ~99% for all the corn stovers tested, which is much more than has been reported in the literature for other pretreatments. This indicates significant scission of β-O-4 bonds by pretreatment and/or induction of lignin condensation reactions. The S/G ratios in grasses determined by analytical pyrolysis are significantly lower than values obtained using either thioacidolysis or 2DHSQC NMR due to presumed interference by ferulates.

CONCLUSIONS

It was found that grass cell wall polysaccharide hydrolysis by cellulolytic enzymes for grasses exhibiting a diversity of lignin structures and compositions could be linked to quantifiable changes in the composition of the cell wall and properties of the lignin including apparent content of the p-hydroxycinnamates while the limitations of S/G estimation in grasses is highlighted.

Characterization of European forage maize lines for stover composition and associations with polymorphisms within O-methyltransferase genes

Cell wall components, such as lignin, cellulose, and hemicelluloses, play an important role in the conversion efficiency of corn stover into ethanol. Understanding the molecular basis of cell wall formation is fundamental for marker assisted selection to develop lines more suitable for ethanol production. In this study, we evaluated a set of 40 European forage maize lines for cellulose, lignin, total hemicellulose, glucuronoarabinoxylan (GAX), and monosaccharides, such as arabinose (ara), xylose (xyl), and glucuronic acid (GlcA). The most significant correlations were observed between hemicelluloses and GAX (0.9), and hemicelluloses and cellulose (-0.81). Cell wall digestibility (CWD, estimated by digestible neutral detergent fiber, DNDF) was negatively correlated with Xyl (-0.34). The association analysis between the evaluated traits and polymorphisms within ten "lignin" genes revealed significant associations between polymorphisms within CCoAOMT1, CCoAOMT2, 4CL2 and C4H, and cellulose/xyl, cellulose, cellulose, and GclA, respectively. None of the QTPs identified in this study corresponded to previously reported CWD QTPs.

Effect of reduced ferulate-mediated lignin/arabinoxylan cross-linking in corn silage on feed intake, digestibility, and milk production

Cross-linking of lignin to arabinoxylan by ferulates limits in vitro rumen digestibility of grass cell walls. The effect of ferulate cross-linking on dry matter intake (DMI), milk production, and in vivo digestibility was investigated in ad libitum and restricted-intake digestion trials with lambs, and in a dairy cow performance trial using the low-ferulate sfe corn mutant. Silages of 5 inbred corn lines were fed: W23, 2 W23sfe lines (M04-4 and M04-21), B73, and B73bm3. As expected, the W23sfe silages contained fewer ferulate ether cross-links and B73bm3 silage had a lower lignin concentration than the respective genetic controls. Silages were fed as the sole ingredient to 4 lambs per silage treatment. Lambs were confined to metabolism crates and fed ad libitum for a 12-d adaptation period followed by a 5-d collection period of feed refusals and feces. Immediately following the ad libitum feeding trial, silage offered was limited to 2% of body weight. After a 2-d adaptation to restricted feeding, feed refusals and feces were collected for 5 d. Seventy Holstein cows were blocked by lactation, days in milk, body weight, and milk production and assigned to total mixed ration diets based on the 5 corn silages. Diets were fed for 28 d and data were collected on weekly DMI and milk production and composition. Fecal grab samples were collected during the last week of the lactation trial for estimation of feed digestibility using acid-insoluble ash as a marker. Silage, total mixed ration, feed refusals, and fecal samples were analyzed for crude protein, starch, neutral detergent fiber (NDF), cell wall polysaccharides, and lignin. The W23sfe silages resulted in lower DMI in the ad libitum trial than the W23 silage, but DMI did not differ in the restricted trial. No differences were observed for NDF or cell wall polysaccharide digestibility by lambs with restricted feeding, but the amount of NDF digested daily increased for lambs fed the M04-21 W23sfe silage ad libitum. Lambs were less selective against NDF and lignin when offered W23sfe silages. The B73bm3 silage did not affect DMI or digestibility of cell walls at the restricted feeding level, but total daily NDF digested was greater at ad libitum intake. Intake, milk production, and cell wall digestibility were greater for cows fed diets containing W23sfe silages than for those fed W23 silage. Although milk production was greater for the B73bm3 diet, DMI and cell wall digestibility were not altered. Cows were less selective against cell wall material when fed both W23sfe and B73bm3 silages. Reduced ferulate cross-linking in sfe corn silage is a new genetic mechanism for improving milk production.

Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.)

BACKGROUND

OMT (O-methyltransferase) genes are involved in lignin biosynthesis, which relates to stover cell wall digestibility. Reduced lignin content is an important determinant of both forage quality and ethanol conversion efficiency of maize stover.

RESULTS

Variation in genomic sequences coding for COMT, CCoAOMT1, and CCoAOMT2 was analyzed in relation to stover cell wall digestibility for a panel of 40 European forage maize inbred lines, and re-analyzed for a panel of 34 lines from a published French study. Different methodologies for association analysis were performed and compared. Across association methodologies, a total number of 25, 12, 1, 6 COMT polymorphic sites were significantly associated with DNDF, OMD, NDF, and WSC, respectively. Association analysis for CCoAOMT1 and CCoAOMT2 identified substantially fewer polymorphic sites (3 and 2, respectively) associated with the investigated traits. Our re-analysis on the 34 lines from a published French dataset identified 14 polymorphic sites significantly associated with cell wall digestibility, two of them were consistent with our study. Promising polymorphisms putatively causally associated with variability of cell wall digestibility were inferred from the total number of significantly associated SNPs/Indels.

CONCLUSIONS

Several polymorphic sites for three O-methyltransferase loci were associated with stover cell wall digestibility. All three tested genes seem to be involved in controlling DNDF, in particular COMT. Thus, considerable variation among Bm3 wildtype alleles can be exploited for improving cell-wall digestibility. Target sites for functional markers were identified enabling development of efficient marker-based selection strategies.

Polymorphisms in monolignol biosynthetic genes are associated with biomass yield and agronomic traits in European maize (Zea mays L.)

BACKGROUND

Reduced lignin content leads to higher cell wall digestibility and, therefore, better forage quality and increased conversion of lignocellulosic biomass into ethanol. However, reduced lignin content might lead to weaker stalks, lodging, and reduced biomass yield. Genes encoding enzymes involved in cell wall lignification have been shown to influence both cell wall digestibility and yield traits.

RESULTS

In this study, associations between monolignol biosynthetic genes and plant height (PHT), days to silking (DTS), dry matter content (DMC), and dry matter yield (DMY) were identified by using a panel of 39 European elite maize lines. In total, 10 associations were detected between polymorphisms or tight linkage disequilibrium (LD) groups within the COMT, CCoAOMT2, 4CL1, 4CL2, F5H, and PAL genomic fragments, respectively, and the above mentioned traits. The phenotypic variation explained by these polymorphisms or tight LD groups ranged from 6% to 25.8% in our line collection. Only 4CL1 and F5H were found to have polymorphisms associated with both yield and forage quality related characters. However, no pleiotropic polymorphisms affecting both digestibility of neutral detergent fiber (DNDF), and PHT or DMY were discovered, even under less stringent statistical conditions.

CONCLUSION

Due to absence of pleiotropic polymorphisms affecting both forage yield and quality traits, identification of optimal monolignol biosynthetic gene haplotype(s) combining beneficial quantitative trait polymorphism (QTP) alleles for both quality and yield traits appears possible within monolignol biosynthetic genes. This is beneficial to maximize forage and bioethanol yield per unit land area.

Advances in maize genomics and their value for enhancing genetic gains from breeding

Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products.

Forage quality and composition measurements as predictors of ethanol yield from maize (Zea mays L.) stover

BACKGROUND

Improvement of biofeedstock quality for cellulosic ethanol production will be facilitated by inexpensive and rapid methods of evaluation, such as those already employed in the field of ruminant nutrition. Our objective was to evaluate whether forage quality and compositional measurements could be used to estimate ethanol yield of maize stover as measured by a simplified pretreatment and simultaneous saccharification and fermentation assay. Twelve maize varieties selected to be diverse for stover digestibility and composition were evaluated.

RESULTS

Variation in ethanol yield was driven by glucan convertibility rather than by glucan content. Convertibility was highly correlated with ruminal digestibility and lignin content. There was no relationship between structural carbohydrate content (glucan and neutral detergent fiber) and ethanol yield. However, when these variables were included in multiple regression equations including convertibility or neutral detergent fiber digestibility, their partial regression coefficients were significant and positive. A regression model including both neutral detergent fiber and its ruminal digestibility explained 95% of the variation in ethanol yield.

CONCLUSION

Forage quality and composition measurements may be used to predict cellulosic ethanol yield to guide biofeedstock improvement through agronomic research and plant breeding.

Expression of cell wall related genes in basal and ear internodes of silking brown-midrib-3, caffeic acid O-methyltransferase (COMT) down-regulated, and normal maize plants

BACKGROUND

Silage maize is a major forage and energy resource for cattle feeding, and several studies have shown that lignin content and structure are the determining factors in forage maize feeding value. In maize, four natural brown-midrib mutants have modified lignin content, lignin structure and cell wall digestibility. The greatest lignin reduction and the highest cell wall digestibility were observed in the brown-midrib-3 (bm3) mutant, which is disrupted in the caffeic acid O-methyltransferase (COMT) gene.

RESULTS

Expression of cell wall related genes was investigated in basal and ear internodes of normal, COMT antisens (AS225), and bm3 maize plants of the INRA F2 line. A cell wall macro-array was developed with 651 gene specific tags of genes specifically involved in cell wall biogenesis. When comparing basal (older lignifying) and ear (younger lignifying) internodes of the normal line, all genes known to be involved in constitutive monolignol biosynthesis had a higher expression in younger ear internodes. The expression of the COMT gene was heavily reduced, especially in the younger lignifying tissues of the ear internode. Despite the fact that AS225 transgene expression was driven only in sclerenchyma tissues, COMT expression was also heavily reduced in AS225 ear and basal internodes. COMT disruption or down-regulation led to differential expressions of a few lignin pathway genes, which were all over-expressed, except for a phenylalanine ammonia-lyase gene. More unexpectedly, several transcription factor genes, cell signaling genes, transport and detoxification genes, genes involved in cell wall carbohydrate metabolism and genes encoding cell wall proteins, were differentially expressed, and mostly over-expressed, in COMT-deficient plants.

CONCLUSION

Differential gene expressions in COMT-deficient plants highlighted a probable disturbance in cell wall assembly. In addition, the gene expressions suggested modified chronology of the different events leading to cell expansion and lignification with consequences far beyond the phenylpropanoid metabolism. The reduced availability of monolignols and S units in bm3 or AS225 plants led to plants also differing in cell wall carbohydrate, and probably protein, composition. Thus, the deficiency in a key-enzyme of the lignin pathway had correlative effects on the whole cell wall metabolism. Furthermore, the observed differential expression between bm3 and normal plants indicated the possible involvement in the maize lignin pathway of genes which up until now have not been considered to play this role.

Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint x Flint maize recombinant inbred line population

Background

Cell-wall digestibility is the major target for improving the feeding value of forage maize. An understanding of the molecular basis for cell-wall digestibility is crucial towards breeding of highly digestible maize.

Results

865 candidate ESTs for cell-wall digestibility were selected according to the analysis of expression profiles in 1) three sets of brown-midrib isogenic lines in the genetic background of inbreds 1332 (1332 and 1332 bm3), 5361 (5361 and 5361 bm3), and F2 (F2, F2 bm1, F2 bm2, and F2 bm3), 2) the contrasting extreme lines of FD (Flint × Dent, AS08 × AS 06), DD1 (Dent × Dent, AS11 × AS09), and DD2 (Dent × Dent, AS29 × AS30) mapping populations, and 3) two contrasting isogenic inbreds, AS20 and AS21. Out of those, 439 ESTs were assembled on our "Forage Quality Array", a small microarray specific for cell wall digestibility related experiments. Transcript profiles of 40 lines of a Flint × Flint population were monitored using the Forage Quality Array, which were contrasting for cell wall digestibility. Using t-tests (p < 0.01), the expression patterns of 102 ESTs were significantly different between high and low quality groups. Using interval mapping, eQTL (LOD ≥ 2.4) were detected for 20% (89 of 439) of the spotted ESTs. On average, these eQTL explained 39% of the transcription variation of the corresponding ESTs. Only 26% (23 of 89) ESTs detected a single eQTL. eQTL hotspots, containing greater than 5% of the total number of eQTL, were located in chromosomal bins 1.07, 1.12, 3.05, 8.03, and 9.04, respectively. Bin 3.05 was co-localized with a cell-wall digestibility related QTL cluster.

Conclusion

102 candidate genes for cell-wall digestibility were validated by genetical genomics approach. Although the cDNA array highlights gene types (the tested gene and any close family members), trans-acting factors or metabolic bottlenecks seem to play the major role in controlling heritable variation of gene expression related to cell-wall digestibility, since no in silico mapped ESTs were in the same location as their own eQTL. Transcriptional variation was generally found to be oligogenic rather than monogenic inherited due to only 26% ESTs detected a single eQTL in the present study. One eQTL hotspot was co-localized with cell wall digestibility related QTL cluster on bins 3.05, implying that in this case the gene(s) underlying QTL and eQTL are identical. As the field of genetical genomics develops, it is expected to significantly improve our knowledge about complex traits, such as cell wall degradability. Comprehensive knowledge of the lignin pathway and cell wall biogenesis will allow plant breeders to choose the best genomic targets controlling these characters, for improving forage digestibility through genetic engineering or marker-assisted selection.

Comparison of maize brown-midrib isogenic lines by cellular UV-microspectrophotometry and comparative transcript profiling

The molecular mechanisms underlying cell wall digestibility in maize (Zea mays L.) have been studied in three sets of maize brown-midrib isogenic lines in the genetic background of inbreds 1332 (1332 and 1332 bm3), 5361 (5361 and 5361 bm3), and F2 (F2, F2 bm1, F2 bm2, and F2 bm3). Two complementary approaches, SSH (suppression subtractive hybridization) and microarray-based expression profiling, were used to isolate and identify candidate genes in isogenic lines for bm mutants. Metabolic pathway analysis revealed that transcriptional events caused by altering the expression of a single bm gene involve all metabolic and signaling pathways. 53 ESTs were differentially expressed in all three isogenic bm3 comparisons, whereas 32 ESTs were consistently differentially expressed in different bm isogenic lines in F2 background. About 70% ESTs isolated by SSH were not present on the unigene microarray, demonstrating the usefulness of the SSH procedure to identify genes related to cell wall digestibility. Together with lignin analysis by cellular UV-microspectrophotometry, expression profiling in isogenic bm lines proved to be useful to understand alterations at the sub-cellular and molecular level with respect to lignin composition. The down-regulation of COMT affected the expression of CCoAOMT genes and caused a reduced content both of G and S units in bm3 mutants.

In search of a maize ideotype for cell wall enzymatic degradability using histological and biochemical lignin characterization

Grass cell wall degradability is conventionally related to the lignin content and to the ferulic-mediated cross-linking of lignins to polysaccharides. To better understand the variations in degradability, 22 maize inbred lines were subjected to image analyses of Fasga- and Mäule-stained stem sections and to chemical analyses of lignins and p-hydroxycinnamic acids. For the first time, the nearness of biochemical and histological estimates of lignin levels was established. Combination of histological and biochemical traits could explain 89% of the variations for cell wall degradability and define a maize ideotype for cell wall degradability. In addition to a reduced lignin level, such an ideotype would contain lignins richer in syringyl than in guaiacyl units and preferentially localized in the cortical region rather than in the pith. Such enrichment in syringyl units would favor wall degradability in grasses, contrary to dicots, and could be related to the fact that grass syringyl units are noticeably p-coumaroylated. This might affect the interaction capabilities of lignins and polysaccharides.

Genetic and molecular basis of grass cell wall biosynthesis and degradability. II. Lessons from brown-midrib mutants

The brown-midrib mutants of maize have a reddish-brown pigmentation of the leaf midrib and stalk pith, associated with lignified tissues. These mutants progressively became models for lignification genetics and biochemical studies in maize and grasses. Comparisons at silage maturity of bm1, bm2, bm3, bm4 plants highlighted their reduced lignin, but also illustrated the biochemical specificities of each mutant in p-coumarate, ferulate ester and etherified ferulate content, or syringyl/guaiacyl monomer ratio after thioacidolysis. Based on the current knowledge of the lignin pathway, and based on presently developed data and discussions, C3H and CCoAOMT activities are probably major hubs in controlling cell-wall lignification (and digestibility). It is also likely that ferulates arise via the CCoAOMT pathway.

A Comparison of Processed Conventional Corn Silage to Unprocessed and Processed Brown Midrib Corn Silage on Intake, Digestion, and Milk Production by Dairy Cows

We studied the effects of mechanical processing and type of hybrid on the nutritive value of corn silage for lactating cows. Treatments were brown midrib (BMR) corn silage that was unprocessed (U-BMR), BMR corn silage that was processed (P-BMR), and a conventional corn silage that was processed (P-7511). All silages were harvested at a theoretical chop length of 19 mm. The chemical compositions of the silages were similar among treatments except that BMR silages were lower in lignin and higher in protein than P-7511. Brown midrib silages had greater 30-h in situ and in vitro NDF digestion than did P-7511, and processing had no effect on 30-h in situ and in vitro fiber digestion, but it increased in situ starch digestion after 3 and 12 h of incubation. Both processed silages had a smaller proportion of particles >1.91 cm and fewer whole corn kernels compared with unprocessed silage. Lactating cows were fed a total mixed ration (TMR) consisting of 42% of each silage type, 40% concentrate, 10% alfalfa silage, and 8% alfalfa hay (DM basis). Cows fed TMR containing P-BMR ate more DM and produced more milk than cows fed P-7511. At feeding, the TMR containing U-BMR had a larger proportion of particles >1.91 cm when compared with the TMR of cows fed processed silages, and after 24 h the difference was even greater, indicating that cows fed unprocessed corn silage sorted more. Cows fed TMR with P-7511 and P-BMR had greater total tract digestibility of organic matter, crude protein, and starch compared with cows fed U-BMR. In vivo digestibility of neutral detergent fiber was greatest for cows fed P-BMR when compared with the other treatments.

Variation in cell wall composition among forage maize (Zea mays L.) inbred lines and its impact on digestibility: analysis of neutral detergent fiber composition by pyrolysis-gas chromatography-mass spectrometry

Cell wall digestibility is an important determinant of forage quality, but the relationship between cell wall composition and digestibility is poorly understood. We analyzed the neutral detergent fiber (NDF) fraction of nine maize inbred lines and one brown midrib3 mutant with pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS). Among 29 pyrolysis fragments that were quantified, two carbohydrate-derived and six lignin-derived fragments showed statistically significant genetic variation. The pyrolysis products 4-vinyl phenol and 2,6-dimethoxy-4-vinyl phenol were negatively correlated with digestibility, whereas furfural and 3-(4-hydroxyphenyl)-3-oxopropanal showed a positive correlation with digestibility. Linear discriminant analysis of the pyrolysis data resulted in the resolution of groups of inbred lines with different digestibility properties based on their chemical composition. These analyses reveal that digestibility is governed by complex interactions between different cell wall compounds, but that several pyrolysis fragments can be used as markers to distinguish between maize lines with different digestibility.

Down-regulation of caffeic acid o-methyltransferase in maize revisited using a transgenic approach

Transgenic maize (Zea mays) plants were generated with a construct harboring a maize caffeic acid O-methyltransferase (COMT) cDNA in the antisense (AS) orientation under the control of the maize Adh1 (alcohol dehydrogenase) promoter. Adh1-driven beta-glucuronidase expression was localized in vascular tissues and lignifying sclerenchyma, indicating its suitability in transgenic experiments aimed at modifying lignin content and composition. One line of AS plants, COMT-AS, displayed a significant reduction in COMT activity (15%-30% residual activity) and barely detectable amounts of COMT protein as determined by western-blot analysis. In this line, transgenes were shown to be stably integrated in the genome and transmitted to the progeny. Biochemical analysis of COMT-AS showed: (a) a strong decrease in Klason lignin content at the flowering stage, (b) a decrease in syringyl units, (c) a lower p-coumaric acid content, and (d) the occurrence of unusual 5-OH guaiacyl units. These results are reminiscent of some characteristics already observed for the maize bm3 (brown-midrib3) mutant, as well as for COMT down-regulated dicots. However, as compared with bm3, COMT down-regulation in the COMT-AS line is less severe in that it is restricted to sclerenchyma cells. To our knowledge, this is the first time that an AS strategy has been applied to modify lignin biosynthesis in a grass species.

Bt corn has a higher lignin content than non-Bt corn

Bt corn has been genetically modified to express the Cry1Ab protein of Bacillus thuringiensis to kill lepidopteran pests. Fluorescence microscopy and staining with toluidine blue indicated a higher content of lignin in the vascular bundle sheaths and in the sclerenchyma cells surrounding the vascular bundle in all ten Bt corn hybrids, representing three different transformation events, studied than of their respective non-Bt isolines. Chemical analysis confirmed that the lignin content of all hybrids of Bt corn, whether grown in a plant growth room or in the field, was significantly higher (33-97% higher) than that of their respective non-Bt isolines. As lignin is a major structural component of plant cells, modifications in lignin content may have ecological implications.

Lignification in transgenic poplars with extremely reduced caffeic acid O-methyltransferase activity

Transgenic poplars (Populus tremula x Populus alba) were obtained by introduction of a sense homologous transgene encoding caffeic acid O-methyltransferase (COMT) under the control either of the cauliflower mosaic virus double 35S promoter or of the eucalyptus cinnamyl alcohol dehydrogenase promoter. Although these constructs conferred a moderate overexpression of COMT in some lines, a transgenic line with the double 35S promoter was found where COMT activity in woody tissues was close to zero due to a gene-silencing phenomenon. For the first time in COMT down-regulated trees, this alteration substantially reduced lignin level in 6-month-old trees (17% decrease). Lignin structure was found to be strongly altered, with a two times higher content in condensed bonds, an almost complete lack of syringyl units, and the incorporation of 5-hydroxyguaiacyl units to the most remarkable extent reported so far. Consistent with the higher cellulose content and with the higher condensation degree of the lignin, the impact of the transformation on the kraft-pulping performances of the poplar trees positively affected the pulp yield (10% relative increase), but made lignins less amenable to industrial degradations.

Structural alterations of lignins in transgenic poplars with depressed cinnamyl alcohol dehydrogenase or caffeic acid O-methyltransferase activity have an opposite impact on the efficiency of industrial kraft pulping

We evaluated lignin profiles and pulping performances of 2-year-old transgenic poplar (Populus tremula x Populus alba) lines severely altered in the expression of caffeic acid/5-hydroxyferulic acid O-methyltransferase (COMT) or cinnamyl alcohol dehydrogenase (CAD). Transgenic poplars with CAD or COMT antisense constructs showed growth similar to control trees. CAD down-regulated poplars displayed a red coloration mainly in the outer xylem. A 90% lower COMT activity did not change lignin content but dramatically increased the frequency of guaiacyl units and resistant biphenyl linkages in lignin. This alteration severely lowered the efficiency of kraft pulping. The Klason lignin level of CAD-transformed poplars was slightly lower than that of the control. Whereas CAD down-regulation did not change the frequency of labile ether bonds or guaiacyl units in lignin, it increased the proportion of syringaldehyde and diarylpropane structures and, more importantly with regard to kraft pulping, of free phenolic groups in lignin. In the most depressed line, ASCAD21, a substantially higher content in free phenolic units facilitated lignin solubilization and fragmentation during kraft pulping. These results point the way to genetic modification of lignin structure to improve wood quality for the pulp industry.

Biochemistry and molecular biology of lignification

Lignins, which result from the dehydrogenative polymerization of cinnamyl alcohols, are complex heteropolymers deposited in the walls of specific cells of higher plants. Lignins have probably been associated to land colonization by plants but several aspects concerning their biosynthesis, structure and function are still only partially understood. This review focuses on the modern physicochemical methods of structural analysis of lignins, and on the new approaches of molecular biology and genetic engineering applied to lignification. The principles, advantages and limitations of three important analytical tools for studying lignin structure are presented. They include carbon 13 nuclear magnetic resonance, analytical pyrolysis and thioacidolysis. The use of these methods is illustrated by several examples concerning the characterization of grass lignins,'lignin-like'materials in protection barriers of plants and lignins produced by cell suspension cultures. Our present limited knowledge of the spatio temporal deposition of lignins during cell wall differentiation including the nature of the wall components associated to lignin deposition and of the cross-links between the different wall polymers is briefly reviewed. Emphasis is placed on the phenylpropanoid pathway enzymes and their corresponding genes which are described in relation to their potential roles in the quantitative and qualitative control of lignification. Recent findings concerning the promoter sequence elements responsible for the vascular expression of some of these genes are presented. A section is devoted to the enzymes specifically involved in the synthesis of monolignols: cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase. The recent characterization of the corresponding cDNAs/genes offers new possibilities for a better understanding of the regulation of lignification. Finally, at the level of the synthesis, the potential involvement of peroxidases and laccases in the polymerization of monolignols is critically discussed. In addition to previously characterized naturally occurring lignin mutants, induced lignin mutants have been obtained during the last years through genetic engineering. Some examples include plants transformed by O-methyltransferase and cinnamyl alcohol dehydrogenase antisense constructs which exhibit modified lignins. Such strategies offer promising perspectives in gaining a better understanding of lignin metabolism and functions and represent a realistic way to improve plant biomass. Contents Summary 203 I. Introduction 204 II. Main structural features of lignins 205 III. Lignification and cell wall differentiation: spatio-temporal deposition of lignins and inter-relations with other wall components 213 IV. Enzymes and genes involved in the biosynthesis and polymerization of monolignols 216 V. Lignin mutants as a way to improve plant biomass and to explore lignin biochemistry and metabolism 226 VI. Concluding remarks 229 Acknowledgements 230 References 230.