Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits

Conformational Rearrangements in the Redox Cycling of NADPH-Cytochrome P450 Reductase from Sorghum bicolor Explored with FRET and Pressure-Perturbation Spectroscopy

Simple Summary

NADPH-cytochrome P450 reductase (CPR) enzymes are known to undergo an ample conformational transition between the closed and open states in the process of their redox cycling. To explore the conformational landscape of CPR from the potential biofuel crop Sorghum bicolor (SbCPR), we incorporated a FRET donor/acceptor pair into the enzyme and employed rapid scanning stop-flow and pressure perturbation spectroscopy to characterize the equilibrium between its open and closed states at different stages of the redox cycle. Our results suggest the presence of several open conformational sub-states differing in the system volume change associated with the opening transition (ΔV⁰). Although the closed conformation always predominates in the conformational landscape, the population of the open conformations increases by order of magnitude upon the two-electron reduction and the formation of the disemiquinone state of the enzyme. In addition to elucidating the functional choreography of plant CPRs, our study demonstrates the high exploratory potential of a combination of the pressure-perturbation approach with the FRET-based monitoring of protein conformational transitions.

Abstract

NADPH-cytochrome P450 reductase (CPR) from Sorghum bicolor (SbCPR) serves as an electron donor for cytochrome P450 essential for monolignol and lignin production in this biofuel crop. The CPR enzymes undergo an ample conformational transition between the closed and open states in their functioning. This transition is triggered by electron transfer between the FAD and FMN and provides access of the partner protein to the electron-donating FMN domain. To characterize the electron transfer mechanisms in the monolignol biosynthetic pathway better, we explore the conformational transitions in SbCPR with rapid scanning stop-flow and pressure-perturbation spectroscopy. We used FRET between a pair of donor and acceptor probes incorporated into the FAD and FMN domains of SbCPR, respectively, to characterize the equilibrium between the open and closed states and explore its modulation in connection with the redox state of the enzyme. We demonstrate that, although the closed conformation always predominates in the conformational landscape, the population of open state increases by order of magnitude upon the formation of the disemiquinone state. Our results are consistent with several open conformation sub-states differing in the volume change (ΔV⁰) of the opening transition. While the ΔV⁰ characteristic of the oxidized enzyme is as large as −88 mL/mol, the interaction of the enzyme with the nucleotide cofactor and the formation of the double-semiquinone state of CPR decrease this value to −34 and −18 mL/mol, respectively. This observation suggests that the interdomain electron transfer in CPR increases protein hydration, while promoting more open conformation. In addition to elucidating the functional choreography of plant CPRs, our study demonstrates the high exploratory potential of a combination of the pressure-perturbation approach with the FRET-based monitoring of protein conformational transitions.

Functional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin composition

Plant NADPH-dependent cytochrome P450 reductase (CPR) is a multidomain enzyme that donates electrons for hydroxylation reactions catalyzed by class II cytochrome P450 monooxygenases involved in the synthesis of many primary and secondary metabolites. These P450 enzymes include trans-cinnamate-4-hydroxylase, p-coumarate-3′-hydroxylase, and ferulate-5-hydroxylase involved in monolignol biosynthesis. Because of its role in monolignol biosynthesis, alterations in CPR activity could change the composition and overall output of lignin. Therefore, to understand the structure and function of three CPR subunits from sorghum, recombinant subunits SbCPR2a, SbCPR2b, and SbCPR2c were subjected to X-ray crystallography and kinetic assays. Steady-state kinetic analyses demonstrated that all three CPR subunits supported the oxidation reactions catalyzed by SbC4H1 (CYP73A33) and SbC3′H (CYP98A1). Furthermore, comparing the SbCPR2b structure with the well-investigated CPRs from mammals enabled us to identify critical residues of functional importance and suggested that the plant flavin mononucleotide–binding domain might be more flexible than mammalian homologs. In addition, the elucidated structure of SbCPR2b included the first observation of NADP⁺ in a native CPR. Overall, we conclude that the connecting domain of SbCPR2, especially its hinge region, could serve as a target to alter biomass composition in bioenergy and forage sorghums through protein engineering.

Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations

The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single- nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Surprisingly, only 110 (1.56%) SNPs under selection were common in both populations, while the majority (98.4%) were unique to each population. This result indicated that high and low RPR phenotypes are produced by biologically distinct mechanisms. Remarkably, regions harboring lignin and polysaccharide genes were preferentially selected in high and low RPR populations, respectively. The preferential selection was manifested as higher lignification and increased saccharification of the high and low RPR stalks, respectively. The evolution of distinct gene classes according to the direction of selection was unexpected in the context of parallel evolution and demonstrated that selection for a trait, albeit in different directions, does not necessarily act on the same genes. Tricin, a grass-specific monolignol that initiates the incorporation of lignin in the cell walls, emerged as a key determinant of RPR. Integration of selection mapping and transcriptomic analyses with published genetic studies of RPR identified several candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, ZmEXPA2, ZmIAA41 and hk5. These findings provide a foundation for an enhanced understanding of RPR and the improvement of stalk lodging resistance.

The potential of resilient carbon dynamics for stabilizing crop reproductive development and productivity during heat stress

Impaired carbon metabolism and reproductive development constrain crop productivity during heat stress. Reproductive development is energy intensive, and its requirement for respiratory substrates rises as associated metabolism increases with temperature. Understanding how these processes are integrated and the extent to which they contribute to the maintenance of yield during and following periods of elevated temperatures is important for developing climate-resilient crops. Recent studies are beginning to demonstrate links between processes underlying carbon dynamics and reproduction during heat stress, consequently a summation of research that has been reported thus far and an evaluation of purported associations are needed to guide and stimulate future research. To this end, we review recent studies relating to source-sink dynamics, non-foliar photosynthesis and net carbon gain as pivotal in understanding how to improve reproductive development and crop productivity during heat stress. Rapid and precise phenotyping during narrow phenological windows will be important for understanding mechanisms underlying these processes, thus we discuss the development of relevant high-throughput phenotyping approaches that will allow for more informed decision-making regarding future crop improvement.

Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/).

Natural Variation of Lignocellulosic Components in Miscanthus Biomass in China

Lignocellulose content is an important factor affecting the conversion efficiency of biomass energy plants. In this study, 179 Miscanthus accessions in China were used to determine the content of lignocellulose components in stems via acid hydrolysis and high-performance liquid chromatography. Results showed that the average lignocellulose content of wild Miscanthus germplasm resources was 80.27 ± 6.51%, and the average content of cellulose, hemicellulose, lignin, extracts, and total ash was 38.38 ± 3.52, 24.23 ± 4.21, 17.66 ± 1.56, 14.50 ± 5.60, and 2.53 ± 0.59%, respectively. The average lignocellulose content of M. sinensis, M. floridulus, M. nudipes, M. sacchariflorus, M. lutarioriparius, and the hybrids was 77.94 ± 6.06, 75.16 ± 4.98, 75.68 ± 3.02, 83.71 ± 4.78, 81.50 ± 5.23, and 74.72 ± 7.13%, respectively. In all the tested materials, the highest cellulose content was 48.52%, and the lowest was 29.79%. Hemicellulose had the maximum content of 34.23% and a minimum content of 15.71%. The highest lignin content was 23.75%, and the lowest was 13.01%. The lignocellulosic components of different ploidy materials were compared. The content of lignocellulosic components of diploid M. sacchariflorus was higher than that of tetraploid M. sacchariflorus, and the content of lignocellulosic components of diploid M. lutarioriparius was lower than that of tetraploid M. lutarioriparius. Analysis of the relationship between the changes in lignocellulosic components and geographical locations of Miscanthus showed that the holocellulose and hemicellulose content was significantly positive correlated with the latitude of the original growth location. Results indicated that the lignocellulosic components of Miscanthus resources in China are rich in genetic diversity.

Engineering grass biomass for sustainable and enhanced bioethanol production

Bioethanol from lignocellulosic biomass is a promising step for the future energy requirements. Grass is a potential lignocellulosic biomass which can be utilised for biorefinery-based bioethanol production. Grass biomass is a suitable feedstock for bioethanol production due to its all the year around production, requirement of less fertile land and noninterference with food system. However, the processes involved, i.e. pretreatment, enzymatic hydrolysis and fermentation for bioethanol production from grass biomass, are both time consuming and costly. Developing the grass biomass in planta for enhanced bioethanol production is a promising step for maximum utilisation of this valuable feedstock and, thus, is the focus of the present review. Modern breeding techniques and transgenic processes are attractive methods which can be utilised for development of the feedstock. However, the outcomes are not always predictable and the time period required for obtaining a robust variety is generation dependent. Sophisticated genome editing technologies such as synthetic genetic circuits (SGC) or clustered regularly interspaced short palindromic repeats (CRISPR) systems are advantageous for induction of desired traits/heritable mutations in a foreseeable genome location in the 1st mutant generation. Although, its application in grass biomass for bioethanol is limited, these sophisticated techniques are anticipated to exhibit more flexibility in engineering the expression pattern for qualitative and qualitative traits. Nevertheless, the fundamentals rendered by the genetics of the transgenic crops will remain the basis of such developments for obtaining biorefinery-based bioethanol concepts from grass biomass. Grasses which are abundant and widespread in nature epitomise attractive lignocellulosic feedstocks for bioethanol production. The complexity offered by the grass cell wall in terms of lignin recalcitrance and its binding to polysaccharides forms a barricade for its commercialization as a biofuel feedstock. Inspired by the possibilities for rewiring the genetic makeup of grass biomass for reduced lignin and lignin-polysaccharide linkages along with increase in carbohydrates, innovative approaches for in planta modifications are forging ahead. In this review, we highlight the progress made in the field of transgenic grasses for bioethanol production and focus our understanding on improvements of simple breeding techniques and post-harvest techniques for development in shortening of lignin-carbohydrate and carbohydrate-carbohydrate linkages. Further, we discuss about the designer lignins which are aimed for qualitable lignins and also emphasise on remodelling of polysaccharides and mixed-linkage glucans for enhancing carbohydrate content and in planta saccharification efficiency. As a final point, we discuss the role of synthetic genetic circuits and CRISPR systems in targeted improvement of cell wall components without compromising the plant growth and health. It is anticipated that this review can provide a rational approach towards a better understanding of application of in planta genetic engineering aspects for designing synthetic genetic circuits which can promote grass feedstocks for biorefinery-based bioethanol concepts.

An NIRS-based assay of chemical composition and biomass digestibility for rapid selection of Jerusalem artichoke clones

BACKGROUND

High-throughput evaluation of lignocellulosic biomass feedstock quality is the key to the successful commercialization of bioethanol production. Currently, wet chemical methods for the determination of chemical composition and biomass digestibility are expensive and time-consuming, thus hindering comprehensive feedstock quality assessments based on these biomass specifications. To find the ideal bioethanol feedstock, we perform a near-infrared spectroscopic (NIRS) assay to rapidly and comprehensively analyze the chemical composition and biomass digestibility of 59 Jerusalem artichoke (Helianthus tuberosus L., abbreviated JA) clones collected from 24 provinces in six regions of China.

RESULTS

The distinct geographical distribution of JA accessions generated varied chemical composition as well as related biomass digestibility (after soluble sugars extraction and mild alkali pretreatment). Notably, the soluble sugars, cellulose, hemicellulose, lignin, ash, and released hexoses, pentoses, and total carbohydrates were rapidly and perfectly predicted by partial least squares regression coupled with model population analyses (MPA), which exhibited significantly higher predictive performance than controls. Subsequently, grey relational grade analysis was employed to correlate chemical composition and biomass digestibility with feedstock quality score (FQS), resulting in the assignment of tested JA clones to five feedstock quality grades (FQGs). Ultimately, the FQGs of JA clones were successfully classified using partial least squares-discriminant analysis model coupled with MPA, attaining a significantly higher correct rate of 97.8% in the calibration subset and 91.1% in the validation subset.

CONCLUSIONS

Based on the diversity of JA clones, the present study has not only rapidly and precisely examined the biomass composition and digestibility with MPA-optimized NIRS models but has also selected the ideal JA clones according to FQS. This method provides a new insight into the selection of ideal bioethanol feedstock for high-efficiency bioethanol production.

High yielding tropical energy crops for bioenergy production: Effects of plant components, harvest years and locations on biomass composition

The composition of lignocellulosic feedstock, which depends on crop type, crop management, locations and plant parts, significantly affects the conversion efficiency of biomass into biofuels and biobased products. Thus, this study examined the composition of different parts of two high yielding tropical energy crops, Energycane and Napier grass, collected across three locations and years. Significantly higher fiber content was found in the leaves of Energycane than stems, while fiber content was significantly higher in the stems than the leaves of Napier grass. Similarly, fiber content was higher in Napier grass than Energycane. Due to significant differences in biomass composition between the plant parts within a crop type, neither biological conversion, including anaerobic digestion, nor thermochemical pretreatment alone is likely to efficiently convert biomass components into biofuels and biobased products. However, combination of anaerobic digestion with thermochemical conversion technologies could efficiently utilize biomass components in generating biofuels and biobased products.

Transcriptomics and proteomics reveal genetic and biological basis of superior biomass crop Miscanthus

Miscanthus is a rhizomatous C4 grass which is considered as potential high-yielding energy crop with the low-nutrient requirements, high water-use efficiency, and capability of C mitigation. To better understand the genetic basis, an integrative analysis of the transcriptome and proteome was performed to identify important genes and pathways involved in Miscanthus leaves. At the transcript level, 64,663 transcripts in M. lutarioriparius, 97,043 in M. sacchariflorus, 97,043 in M. sinensis, 67,323 in M. floridulus and 70,021 in M. × giganteus were detected by an RNA sequencing approach. At the protein level, 1964 peptide-represented proteins were identified and 1933 proteins differed by 1.5-fold or more in their relative abundance, as indicated by iTRAQ (isobaric tags for relative and absolute quantitation) analysis. Phylogenies were constructed from the nearly taxa of Miscanthus. A large number of genes closely related to biomass production were found. And SSR markers and their corresponding primers were derived from Miscanthus transcripts and 90% of them were successfully detected by PCR amplification among Miacanthus species. These similarities and variations on the transcriptional and proteomic level between Miscanthus species will serve as a resource for research in Miscanthus and other lignocellulose crops.

Genetic engineering of grass cell wall polysaccharides for biorefining

Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry.

Sweet sorghum as biofuel feedstock: recent advances and available resources

Sweet sorghum is a promising target for biofuel production. It is a C4 crop with low input requirements and accumulates high levels of sugars in its stalks. However, large-scale planting on marginal lands would require improved varieties with optimized biofuel-related traits and tolerance to biotic and abiotic stresses. Considering this, many studies have been carried out to generate genetic and genomic resources for sweet sorghum. In this review, we discuss various attributes of sweet sorghum that make it an ideal candidate for biofuel feedstock, and provide an overview of genetic diversity, tools, and resources available for engineering and/or marker-assisting breeding of sweet sorghum. Finally, the progress made so far, in identification of genes/quantitative trait loci (QTLs) important for agronomic traits and ongoing molecular breeding efforts to generate improved varieties, has been discussed.

Silencing CHALCONE SYNTHASE in Maize Impedes the Incorporation of Tricin into Lignin and Increases Lignin Content

Lignin is a phenolic heteropolymer that is deposited in secondary-thickened cell walls, where it provides mechanical strength. A recent structural characterization of cell walls from monocot species showed that the flavone tricin is part of the native lignin polymer, where it is hypothesized to initiate lignin chains. In this study, we investigated the consequences of altered tricin levels on lignin structure and cell wall recalcitrance by phenolic profiling, nuclear magnetic resonance, and saccharification assays of the naturally silenced maize (Zea mays) C2-Idf (inhibitor diffuse) mutant, defective in the CHALCONE SYNTHASE Colorless2 (C2) gene. We show that the C2-Idf mutant produces highly reduced levels of apigenin- and tricin-related flavonoids, resulting in a strongly reduced incorporation of tricin into the lignin polymer. Moreover, the lignin was enriched in β-β and β-5 units, lending support to the contention that tricin acts to initiate lignin chains and that, in the absence of tricin, more monolignol dimerization reactions occur. In addition, the C2-Idf mutation resulted in strikingly higher Klason lignin levels in the leaves. As a consequence, the leaves of C2-Idf mutants had significantly reduced saccharification efficiencies compared with those of control plants. These findings are instructive for lignin engineering strategies to improve biomass processing and biochemical production.

Hybrid photosynthesis-powering biocatalysts with solar energy captured by inorganic devices

The biological reduction of CO₂ driven by sunlight via photosynthesis is a crucial process for life on earth. However, the conversion efficiency of solar energy to biomass by natural photosynthesis is low. This translates in bioproduction processes relying on natural photosynthesis that are inefficient energetically. Recently, hybrid photosynthetic technologies with the potential of significantly increasing the efficiency of solar energy conversion to products have been developed. In these systems, the reduction of CO₂ into biofuels or other chemicals of interest by biocatalysts is driven by solar energy captured with inorganic devices such as photovoltaic cells or photoelectrodes. Here, we explore hybrid photosynthesis and examine the strategies being deployed to improve this biotechnology.

Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode "proteins of unknown function," and determining their role in lignocellulose degradation presents opportunities and challenges for future research.

IMPORTANCE

This study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.

SorghumFDB: sorghum functional genomics database with multidimensional network analysis

Sorghum (Sorghum bicolor [L.] Moench) has excellent agronomic traits and biological properties, such as heat and drought-tolerance. It is a C₄ grass and potential bioenergy-producing plant, which makes it an important crop worldwide. With the sorghum genome sequence released, it is essential to establish a sorghum functional genomics data mining platform. We collected genomic data and some functional annotations to construct a sorghum functional genomics database (SorghumFDB). SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis related enzymes, R-genes and organelle-genes), detailed gene annotations, miRNA and target gene information, orthologous pairs in the model plants Arabidopsis, rice and maize, gene loci conversions and a genome browser. We further constructed a dynamic network of multidimensional biological relationships, comprised of the co-expression data, protein–protein interactions and miRNA-target pairs. We took effective measures to combine the network, gene set enrichment and motif analyses to determine the key regulators that participate in related metabolic pathways, such as the lignin pathway, which is a major biological process in bioenergy-producing plants.

Database URL:http://structuralbiology.cau.edu.cn/sorghum/index.html.

Overexpression of GA20-OXIDASE1 impacts plant height, biomass allocation and saccharification efficiency in maize

Increased biomass yield and quality are of great importance for the improvement of feedstock for the biorefinery. For the production of bioethanol, both stem biomass yield and the conversion efficiency of the polysaccharides in the cell wall to fermentable sugars are of relevance. Increasing the endogenous levels of gibberellic acid (GA) by ectopic expression of GA20-OXIDASE1 (GA20-OX1), the rate-limiting step in GA biosynthesis, is known to affect cell division and cell expansion, resulting in larger plants and organs in several plant species. In this study, we examined biomass yield and quality traits of maize plants overexpressing GA20-OX1 (GA20-OX1). GA20-OX1 plants accumulated more vegetative biomass than control plants in greenhouse experiments, but not consistently over two years of field trials. The stems of these plants were longer but also more slender. Investigation of GA20-OX1 biomass quality using biochemical analyses showed the presence of more cellulose, lignin and cell wall residue. Cell wall analysis as well as expression analysis of lignin biosynthetic genes in developing stems revealed that cellulose and lignin were deposited earlier in development. Pretreatment of GA20-OX1 biomass with NaOH resulted in a higher saccharification efficiency per unit of dry weight, in agreement with the higher cellulose content. On the other hand, the cellulose-to-glucose conversion was slower upon HCl or hot-water pretreatment, presumably due to the higher lignin content. This study showed that biomass yield and quality traits can be interconnected, which is important for the development of future breeding strategies to improve lignocellulosic feedstock for bioethanol production.

The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling

BACKGROUND

SWEET is a newly identified family of sugar transporters. Although SWEET transporters have been characterized by using Arabidopsis and rice, very little knowledge of sucrose accumulation in the stem region is available, as these model plants accumulate little sucrose in their stems. To elucidate the expression of key SWEET genes involved in sucrose accumulation of sorghum, we performed transcriptome profiling by RNA-seq, categorization using phylogenetic trees, analysis of chromosomal synteny, and comparison of amino acid sequences between SIL-05 (a sweet sorghum) and BTx623 (a grain sorghum).

RESULTS

We identified 23 SWEET genes in the sorghum genome. In the leaf, SbSWEET8-1 was highly expressed and was grouped in the same clade as AtSWEET11 and AtSWEET12 that play a role in the efflux of photosynthesized sucrose. The key genes in sucrose synthesis (SPS3) and that in another step of sugar transport (SbSUT1 and SbSUT2) were also highly expressed, suggesting that sucrose is newly synthesized and actively exported from the leaf. In the stem, SbSWEET4-3 was uniquely highly expressed. SbSWEET4-1, SbSWEET4-2, and SbSWEET4-3 were categorized into the same clade, but their tissue specificities were different, suggesting that SbSWEET4-3 is a sugar transporter with specific roles in the stem. We found a putative SWEET4-3 ortholog in the corresponding region of the maize chromosome, but not the rice chromosome, suggesting that SbSWEET4-3 was copied after the branching of sorghum and maize from rice. In the panicle from the heading through to 36 days afterward, SbSWEET2-1 and SbSWEET7-1 were expressed and grouped in the same clade as rice OsSWEET11/Xa13 that is essential for seed development. SbSWEET9-3 was highly expressed in the panicle only just after heading and was grouped into the same clade as AtSWEET8/RPG1 that is essential for pollen viability. Five of 23 SWEET genes had SNPs that caused nonsynonymous amino acid substitutions between SIL-05 and BTx623.

CONCLUSIONS

We determined the key SWEET genes for technological improvement of sorghum in the production of biofuels: SbSWEET8-1 for efflux of sucrose from the leaf; SbSWEET4-3 for unloading sucrose from the phloem in the stem; SbSWEET2-1 and SbSWEET7-1 for seed development; SbSWEET9-3 for pollen nutrition.

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change. Database URL: http://webapp.cabgrid.res.in/sbmdb/.

Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land

Understanding the genetic basis of water use efficiency (WUE) and its roles in plant adaptation to a drought environment is essential for the production of second-generation energy crops in water-deficit marginal land. In this study, RNA-Seq and WUE measurements were performed for 78 individuals of Miscanthus lutarioriparius grown in two common gardens, one located in warm and wet Central China near the native habitats of the species and the other located in the semiarid Loess Plateau, the domestication site of the energy crop. The field measurements showed that WUE of M. lutarioriparius in the semiarid location was significantly higher than that in the wet location. A matrix correlation analysis was conducted between gene expression levels and WUE to identify candidate genes involved in the improvement of WUE from the native to the domestication site. A total of 48 candidate genes were identified and assigned to functional categories, including photosynthesis, stomatal regulation, protein metabolism, and abiotic stress responses. Of these genes, nearly 73% were up-regulated in the semiarid site. It was also found that the relatively high expression variation of the WUE-related genes was affected to a larger extent by environment than by genetic variation. The study demonstrates that transcriptome-wide correlation between physiological phenotypes and expression levels offers an effective means for identifying candidate genes involved in the adaptation to environmental changes.

Preventing lodging in bioenergy crops: a biomechanical analysis of maize stalks suggests a new approach

The hypothetical ideal for maize (Zea mays) bioenergy production would be a no-waste plant: high-yielding, with silage that is easily digestible for conversion to biofuel. However, increased digestibility is typically associated with low structural strength and a propensity for lodging. The solution to this dilemma may lie in our ability to optimize maize morphology using tools from structural engineering. To investigate how material (tissue) and geometric (morphological) factors influence stalk strength, detailed structural models of the maize stalk were created using finite-element software. Model geometry was obtained from high-resolution x-ray computed tomography (CT) scans, and scan intensity information was integrated into the models to infer inhomogeneous material properties. A sensitivity analysis was performed by systematically varying material properties over broad ranges, and by modifying stalk geometry. Computational models exhibited realistic stress and deformation patterns. In agreement with natural failure patterns, maximum stresses were predicted near the node. Maximum stresses were observed to be much more sensitive to changes in dimensions of the stalk cross section than they were to changes in material properties of stalk components. The average sensitivity to geometry was found to be more than 10-fold higher than the average sensitivity to material properties. These results suggest a new strategy for the breeding and development of bioenergy maize varieties in which tissue weaknesses are counterbalanced by relatively small increases (e.g. 5%) in stalk diameter that reduce structural stresses.

Combining Next Generation Sequencing with Bulked Segregant Analysis to Fine Map a Stem Moisture Locus in Sorghum (Sorghum bicolor L. Moench)

Sorghum is one of the most promising bioenergy crops. Stem juice yield, together with stem sugar concentration, determines sugar yield in sweet sorghum. Bulked segregant analysis (BSA) is a gene mapping technique for identifying genomic regions containing genetic loci affecting a trait of interest that when combined with deep sequencing could effectively accelerate the gene mapping process. In this study, a dry stem sorghum landrace was characterized and the stem water controlling locus, qSW6, was fine mapped using QTL analysis and the combined BSA and deep sequencing technologies. Results showed that: (i) In sorghum variety Jiliang 2, stem water content was around 80% before flowering stage. It dropped to 75% during grain filling with little difference between different internodes. In landrace G21, stem water content keeps dropping after the flag leaf stage. The drop from 71% at flowering time progressed to 60% at grain filling time. Large differences exist between different internodes with the lowest (51%) at the 7^th and 8^th internodes at dough stage. (ii) A quantitative trait locus (QTL) controlling stem water content mapped on chromosome 6 between SSR markers Ch6-2 and gpsb069 explained about 34.7-56.9% of the phenotypic variation for the 5^th to 10^th internodes, respectively. (iii) BSA and deep sequencing analysis narrowed the associated region to 339 kb containing 38 putative genes. The results could help reveal molecular mechanisms underlying juice yield of sorghum and thus to improve total sugar yield.

Genotype, development and tissue-derived variation of cell-wall properties in the lignocellulosic energy crop Miscanthus

BACKGROUND AND AIMS

Species and hybrids of the genus Miscanthus contain attributes that make them front-runners among current selections of dedicated bioenergy crops. A key trait for plant biomass conversion to biofuels and biomaterials is cell-wall quality; however, knowledge of cell-wall composition and biology in Miscanthus species is limited. This study presents data on cell-wall compositional changes as a function of development and tissue type across selected genotypes, and considers implications for the development of miscanthus as a sustainable and renewable bioenergy feedstock.

METHODS

Cell-wall biomass was analysed for 25 genotypes, considering different developmental stages and stem vs. leaf compositional variability, by Fourier transform mid-infrared spectroscopy and lignin determination. In addition, a Clostridium phytofermentans bioassay was used to assess cell-wall digestibility and conversion to ethanol.

KEY RESULTS

Important cell-wall compositional differences between miscanthus stem and leaf samples were found to be predominantly associated with structural carbohydrates. Lignin content increased as plants matured and was higher in stem tissues. Although stem lignin concentration correlated inversely with ethanol production, no such correlation was observed for leaves. Leaf tissue contributed significantly to total above-ground biomass at all stages, although the extent of this contribution was genotype-dependent.

CONCLUSIONS

It is hypothesized that divergent carbohydrate compositions and modifications in stem and leaf tissues are major determinants for observed differences in cell-wall quality. The findings indicate that improvement of lignocellulosic feedstocks should encompass tissue-dependent variation as it affects amenability to biological conversion. For gene-trait associations relating to cell-wall quality, the data support the separate examination of leaf and stem composition, as tissue-specific traits may be masked by considering only total above-ground biomass samples, and sample variability could be mostly due to varying tissue contributions to total biomass.

Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis

• Increasing demands for food and energy require a step change in the effectiveness, speed and flexibility of crop breeding. Therefore, the aim of this study was to assess the potential of genome-wide association studies (GWASs) and genomic selection (i.e. phenotype prediction from a genome-wide set of markers) to guide fundamental plant science and to accelerate breeding in the energy grass Miscanthus. • We generated over 100,000 single-nucleotide variants (SNVs) by sequencing restriction site-associated DNA (RAD) tags in 138 Micanthus sinensis genotypes, and related SNVs to phenotypic data for 17 traits measured in a field trial. • Confounding by population structure and relatedness was severe in naïve GWAS analyses, but mixed-linear models robustly controlled for these effects and allowed us to detect multiple associations that reached genome-wide significance. Genome-wide prediction accuracies tended to be moderate to high (average of 0.57), but varied dramatically across traits. As expected, predictive abilities increased linearly with the size of the mapping population, but reached a plateau when the number of markers used for prediction exceeded 10,000-20,000, and tended to decline, but remain significant, when cross-validations were performed across subpopulations. • Our results suggest that the immediate implementation of genomic selection in Miscanthus breeding programs may be feasible.

Physiological and growth responses to water deficit in the bioenergy crop Miscanthus x giganteus

High yielding perennial biomass crops of the species Miscanthus are widely recognized as one of the most promising lignocellulosic feedstocks for the production of bioenergy and bioproducts. Miscanthus is a C4 grass and thus has relatively high water use efficiency. Cultivated Miscanthus comprises primarily of a single clone, Miscanthus x giganteus, a sterile hybrid between M. sacchariflorus and M. sinensis. M. x giganteus is high yielding and expresses desirable combinations of many traits present in the two parental species types; however, it responds poorly to low water availability. To identify the physiological basis of the response to water stress in M. x giganteus and to identify potential targets for breeding improvements we characterized the physiological responses to water-deficit stress in a pot experiment. The experiment has provided valuable insights into the temporal aspects of drought-induced responses of M. x giganteus. Withholding water resulted in marked changes in plant physiology with growth-associated traits among the first affected, the most rapid response being a decline in the rate of stem elongation. A reduction in photosynthetic performance was among the second set of changes observed; indicated by a decrease in stomatal conductance followed by decreases in chlorophyll fluorescence and chlorophyll content. Measures reflecting the plant water status were among the last affected by the drought treatment. Metabolite analysis indicated that proline was a drought stress marker in M. x giganteus, metabolites in the proline synthesis pathway were more abundant when stomatal conductance decreased and dry weight accumulation ceased. The outcomes of this study in terms of drought-induced physiological changes, accompanied by a proof-of-concept metabolomics investigation, provide a platform for identifying targets for improved drought-tolerance of the Miscanthus bioenergy crop.

Thermostabilization of extremophilic Dictyoglomus thermophilum GH11 xylanase by an N-terminal disulfide bridge and the effect of ionic liquid [emim]OAc on the enzymatic performance

In the present study, an extremophilic GH11 xylanase was stabilized by an engineered N-terminal disulphide bridge. The effect of the stabilization was then tested against high temperatures and in the presence of a biomass-dissolving ionic liquid, 1-ethyl-3-methylimidazolium acetate ([emim]OAc). The N-terminal disulfide bridge increased the half-life of a GH11 xylanase (XYNB) from the hyperthermophilic bacterium Dictyoglomus thermophilum by 10-fold at 100°C. The apparent temperature optimum increased only by ∼5°C, which is less than the corresponding increase in mesophilic (∼15°C) and moderately thermophilic (∼10°C) xylanases. The performance of the enzyme was increased significantly at 100-110°C. The increasing concentration of [emim]OAc almost linearly increased the inactivation level of the enzyme activity and 25% [emim]OAc inactivated the enzyme almost fully. On the contrary, the apparent temperature optimum did not decrease to a similar extent, and the degree of denaturation of the enzyme was also much lower according to the residual activity assays. Also, 5% [emim]OAc largely counteracted the benefit obtained by the stabilizing disulfide bridge in the temperature-dependent activity assays, but not in the stability assays. Km was increased in the presence of [emim]OAc, indicating that [emim]OAc interfered the substrate-enzyme interactions. These results indicate that the effect of [emim]OAc is targeted more to the functioning of the enzyme than the basic stability of the hyperthermophilic GH11 xylanase.

Identification of bioconversion quantitative trait loci in the interspecific cross Sorghum bicolor × Sorghum propinquum

For lignocellulosic bioenergy to be economically viable, genetic improvements must be made in feedstock quality including both biomass total yield and conversion efficiency. Toward this goal, multiple studies have considered candidate genes and discovered quantitative trait loci (QTL) associated with total biomass accumulation and/or grain production in bioenergy grass species including maize and sorghum. However, very little research has been focused on genes associated with increased biomass conversion efficiency. In this study, Trichoderma viride fungal cellulase hydrolysis activity was measured for lignocellulosic biomass (leaf and stem tissue) obtained from individuals in a F5 recombinant inbred Sorghum bicolor × Sorghum propinquum mapping population. A total of 49 QTLs (20 leaf, 29 stem) were associated with enzymatic conversion efficiency. Interestingly, six high-density QTL regions were identified in which four or more QTLs overlapped. In addition to enzymatic conversion efficiency QTLs, two QTLs were identified for biomass crystallinity index, a trait which has been shown to be inversely correlated with conversion efficiency in bioenergy grasses. The identification of these QTLs provides an important step toward identifying specific genes relevant to increasing conversion efficiency of bioenergy feedstocks. DNA markers linked to these QTLs could be useful in marker-assisted breeding programs aimed at increasing overall bioenergy yields concomitant with selection of high total biomass genotypes.

Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus

Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we present a summary of recent and on-going biochemical studies, including prospects and limitations for the development of powerful phenotyping approaches. Second, we review current knowledge about genetic variation for cell wall characteristics of Miscanthus and illustrate how phenotypic data, combined with high-density arrays of single-nucleotide polymorphisms, are being used in genome-wide association studies to generate testable hypotheses and guide biological discovery. Finally, we provide an overview of the current knowledge about the molecular biology of cell wall biosynthesis in Miscanthus and closely related grasses, discuss the key conceptual and technological bottlenecks, and outline the short-term prospects for progress in this field.

Biomass for thermochemical conversion: targets and challenges

Bioenergy will be one component of a suite of alternatives to fossil fuels. Effective conversion of biomass to energy will require the careful pairing of advanced conversion technologies with biomass feedstocks optimized for the purpose. Lignocellulosic biomass can be converted to useful energy products via two distinct pathways: enzymatic or thermochemical conversion. The thermochemical pathways are reviewed and potential biotechnology or breeding targets to improve feedstocks for pyrolysis, gasification, and combustion are identified. Biomass traits influencing the effectiveness of the thermochemical process (cell wall composition, mineral and moisture content) differ from those important for enzymatic conversion and so properties are discussed in the language of biologists (biochemical analysis) as well as that of engineers (proximate and ultimate analysis). We discuss the genetic control, potential environmental influence, and consequences of modification of these traits. Improving feedstocks for thermochemical conversion can be accomplished by the optimization of lignin levels, and the reduction of ash and moisture content. We suggest that ultimate analysis and associated properties such as H:C, O:C, and heating value might be more amenable than traditional biochemical analysis to the high-throughput necessary for the phenotyping of large plant populations. Expanding our knowledge of these biomass traits will play a critical role in the utilization of biomass for energy production globally, and add to our understanding of how plants tailor their composition with their environment.