Analysis of a Modern Hybrid and an Ancient Sugarcane Implicates a Complex Interplay of Factors in Affecting Recalcitrance to Cellulosic Ethanol Production

Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content

Sugarcane, with its exceptional carbon dioxide assimilation, biomass and sugar yield, has a high potential for the production of bio-energy, bio-plastics and high-value products in the food and pharmaceutical industries. A crucial challenge for long-term economic viability and environmental sustainability is also to optimize the production of biomass composition and carbon sequestration. Sugarcane varieties such as KQ228 and Q253 are highly utilized in the industry. These varieties are characterized by a high early-season sugar content associated with high yield. In order to investigate these correlations, 1,440 internodes were collected and combined to generate a set of 120 samples in triplicate across 24 sugarcane cultivars at five different development stages. Weighted gene co-expression network analysis (WGCNA) was used and revealed for the first time two sets of co-expressed genes with a distinct and opposite correlation between fibre and sugar content. Gene identification and metabolism pathways analysis was used to define these two sets of genes. Correlation analysis identified a large number of interconnected metabolic pathways linked to sugar content and fibre content. Unsupervised hierarchical clustering of gene expression revealed a stronger level of segregation associated with the genotypes than the stage of development, suggesting a dominant genetic influence on biomass composition and facilitating breeding selection. Characterization of these two groups of co-expressed key genes can help to improve breeding program for high fibre, high sugar species or plant synthetic biology.

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.

Relationship between sugarcane culm and leaf biomass composition and saccharification efficiency

BACKGROUND

Lignocellulosic biomass is recognized as a promising renewable feedstock for the production of biofuels. However, current methods for converting biomass into fermentable sugars are considered too expensive and inefficient due to the recalcitrance of the secondary cell wall. Biomass composition can be modified to create varieties that are efficiently broken down to release cell wall sugars. This study focused on identifying the key biomass components influencing plant cell wall recalcitrance that can be targeted for selection in sugarcane, an important and abundant source of biomass.

RESULTS

Biomass composition and the amount of glucan converted into glucose after saccharification were measured in leaf and culm tissues from seven sugarcane genotypes varying in fiber composition after no pretreatment and dilute acid, hydrothermal and ionic liquid pretreatments. In extractives-free sugarcane leaf and culm tissue, glucan, xylan, acid-insoluble lignin (AIL) and acid-soluble lignin (ASL) ranged from 20 to 32%, 15% to 21%, 14% to 20% and 2% to 4%, respectively. The ratio of syringyl (S) to guaiacyl (G) content in the lignin ranged from 1.5 to 2.2 in the culm and from 0.65 to 1.1 in the leaf. Hydrothermal and dilute acid pretreatments predominantly reduced xylan content, while the ionic liquid (IL) pretreatment targeted AIL reduction. The amount of glucan converted into glucose after 26 h of pre-saccharification was highest after IL pretreatment (42% in culm and 63.5% in leaf) compared to the other pretreatments. Additionally, glucan conversion in leaf tissues was approximately 1.5-fold of that in culm tissues. Percent glucan conversion varied between genotypes but there was no genotype that was superior to all others across the pretreatment groups. Path analysis revealed that S/G ratio, AIL and xylan had the strongest negative associations with percent glucan conversion, while ASL and glucan content had strong positive influences.

CONCLUSION

To improve saccharification efficiency of lignocellulosic biomass, breeders should focus on reducing S/G ratio, xylan and AIL content and increasing ASL and glucan content. This will be key for the development of sugarcane varieties for bioenergy uses.

Fate of p-hydroxycinnamates and structural characteristics of residual hemicelluloses and lignin during alkaline-sulfite chemithermomechanical pretreatment of sugarcane bagasse

BACKGROUND

Preparing multiple products from lignocellulosic biomass feedstock enhances the profit and sustainability of future biorefineries. Grasses are suitable feedstocks for biorefineries as they permit a variety of possible by-products due to their particular chemical characteristics and morphology. Elucidating the fate of p-hydroxycinnamates (ferulates-FAs and p-coumarates-pCAs) and major structural components during bioprocessing helps to discriminate the sources of recalcitrance in grasses and paves the way for the recovery of p-hydroxycinnamates, which have multiple applications. To address these subjects, we assessed sugarcane bagasse biorefining under alkaline-sulfite chemithermomechanical (AS-CTM) pretreatment and enzymatic saccharification.

RESULTS

The mass balances of the major bagasse components were combined with 2D-NMR structural evaluation of process solids to advance our understanding of sugarcane bagasse changes during biorefining. AS-CTM pretreatment provided a high yield and thoroughly digestible substrates. The pretreated material was depleted in acetyl groups, but retained 62 and 79% of the original lignin and xylan, respectively. Forty percent of the total FAs and pCAs were also retained in pretreated material. After pretreatment and enzymatic hydrolysis, the residual solids contained mostly lignin and ester-linked pCAs, with minor amounts of FAs and non-digested polysaccharides. Saponification of the residual solids, at a higher alkali load, cleaved all the ester linkages in the pCAs; nevertheless, a significant fraction of the pCAs remained attached to the saponified solids, probably to lignin, through 4-O ether-linkages.

CONCLUSION

AS-CTM pretreatment provided soundly digestible substrates, which retain substantial amounts of xylans and lignin. Acetyl groups were depleted, but 40% of the total FAs and pCAs remained in pretreated material. Ester-linked pCAs detected in pretreated material also resisted to the enzymatic hydrolysis step. Only a more severe saponification reaction cleaved ester linkages of pCAs from residual solids; nevertheless, pCAs remained attached to the core lignin through 4-O ether-linkages, suggesting the occurrence of an alkali-stable fraction of pCAs in sugarcane bagasse.

Methyl jasmonate and salicylic acid are able to modify cell wall but only salicylic acid alters biomass digestibility in the model grass Brachypodium distachyon

In addition to playing a key role in the response to environmental changes, cell walls are also considered as a valuable feedstock for cellulosic ethanol. Here we explored the effects of the stress-response hormones, salicylic acid and methyl jasmonate, on cell wall biosynthesis and biomass digestibility in Brachypodium distachyon, a species recently considered as a suitable model for biomass conversion. We found that in response to salicylic acid or methyl jasmonate treatment, plant growth was reduced coupled with significant changes in cell wall composition. Cellulose content increased in response to methyl jasmonate whereas a reduction in lignin content was found after salicylic acid application. Moreover, hemicellulose composition was altered and increases in caffeic acid, ferulic acid and p-coumaric acid content were detected in response to both treatments. The hormonal profile and the expression pattern of genes involved in cell wall biosynthesis were also modified. Biomass digestibility was reduced in leaf tissue after salicylic acid treatment and was negatively correlated with ferulic acid and p-coumaric acid content. The results obtained here aid in our understanding of cell wall dynamics in response to stress and will enable the development of new strategies to improve cell wall digestibility in bioenergy feedstock.

Biotechnological Strategies to Improve Plant Biomass Quality for Bioethanol Production

The transition from an economy dependent on nonrenewable energy sources to one with higher diversity of renewables will not be a simple process. It requires an important research effort to adapt to the dynamics of the changing energy market, sort costly processes, and avoid overlapping with social interest markets such as food and livestock production. In this review, we analyze the desirable traits of raw plant materials for the bioethanol industry and the molecular biotechnology strategies employed to improve them, in either plants already under use (as maize) or proposed species (large grass families). The fundamentals of these applications can be found in the mechanisms by which plants have evolved different pathways to manage carbon resources for reproduction or survival in unexpected conditions. Here, we review the means by which this information can be used to manipulate these mechanisms for commercial uses, including saccharification improvement of starch and cellulose, decrease in cell wall recalcitrance through lignin modification, and increase in plant biomass.

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.

Genome-wide association analysis of forage quality in maize mature stalk

BACKGROUND

Plant digestibility of silage maize (Zea mays L.) has a large influence on nutrition intake for animal feeding. Improving forage quality will enhance the utilization efficiency and feeding value of forage maize. Dissecting the genetic basis of forage quality will improve our understanding of the complex nature of cell wall biosynthesis and degradation, which is also helpful for breeding good quality silage maize.

RESULTS

Acid detergent fiber (ADF), neutral detergent fiber (NDF) and in vitro dry matter digestibility (IVDMD) of stalk were evaluated in a diverse maize population, which is comprised of 368 inbred lines and planted across seven environments. Using a mixed model accounting for population structure and polygenic background effects, a genome-wide association study was conducted to identify single nucleotide polymorphisms (SNPs) significantly associated with forage quality. Scanning 559,285 SNPs across the whole genome, 73, 41 and 82 SNPs were found to be associated with ADF, NDF, and IVDMD, respectively. Each significant SNP explained 4.2 %-6.2 % of the phenotypic variation. Underlying these associated loci, 56 genes were proposed as candidate genes for forage quality.

CONCLUSIONS

Of all the candidate genes proposed by GWAS, we only found a C3H gene (ZmC3H2) that is directly involved in cell wall component biosynthesis. The candidate genes found in this study are mainly involved in signal transduction, stress resistance, and transcriptional regulation of cell wall biosynthetic gene expression. Adding high digestibility maize into the association panel would be helpful for increasing genetic variability and identifying more genes associated with forage quality traits. Cloning and functional validation of these genes would be helpful for understanding the molecular mechanism of the fiber content and digestibility. These findings provide us new insights into cell wall formation and deposition.

Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane

Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. Expression of sugar transporters might explain sucrose differences among genotypes, but an unexpected differential expression of histones were also identified between high and low Brix° genotypes. Lignin biosynthetic genes and bioenergetics-related genes were up-regulated in the high lignin genotype, suggesting that these genes are important for S. spontaneum to allocate carbon to lignin, while S. officinarum allocates it to sucrose storage. Co-expression network analysis identified 18 transcription factors possibly related to cell wall biosynthesis while in silico analysis detected cis-elements involved in cell wall biosynthesis in their promoters. Our results provide information to elucidate regulatory networks underlying traits of interest that will allow the improvement of sugarcane for biofuel and chemicals production.