Genetic engineering approaches to improve bioethanol production from maize

Breeding for improved digestibility and processing of lignocellulosic biomass in Zea mays

Forage maize is a versatile crop extensively utilized for animal nutrition in agriculture and holds promise as a valuable resource for the production of fermentable sugars in the biorefinery sector. Within this context, the carbohydrate fraction of the lignocellulosic biomass undergoes deconstruction during ruminal digestion and the saccharification process. However, the cell wall's natural resistance towards enzymatic degradation poses a significant challenge during both processes. This so-called biomass recalcitrance is primarily attributed to the presence of lignin and ferulates in the cell walls. Consequently, maize varieties with a reduced lignin or ferulate content or an altered lignin composition can have important beneficial effects on cell wall digestibility. Considerable efforts in genetic improvement have been dedicated towards enhancing cell wall digestibility, benefiting agriculture, the biorefinery sector and the environment. In part I of this paper, we review conventional and advanced breeding methods used in the genetic improvement of maize germplasm. In part II, we zoom in on maize mutants with altered lignin for improved digestibility and biomass processing.

An unconventional proanthocyanidin pathway in maize

Proanthocyanidins (PAs), flavonoid polymers involved in plant defense, are also beneficial to human health and ruminant nutrition. To date, there is little evidence for accumulation of PAs in maize (Zea mays), although maize makes anthocyanins and possesses the key enzyme of the PA pathway, anthocyanidin reductase (ANR). Here, we explore whether there is a functional PA biosynthesis pathway in maize using a combination of analytical chemistry and genetic approaches. The endogenous PA biosynthetic machinery in maize preferentially produces the unusual PA precursor (+)-epicatechin, as well as 4β-(S-cysteinyl)-catechin, as potential PA starter and extension units. Uncommon procyanidin dimers with (+)-epicatechin as starter unit are also found. Expression of soybean (Glycine max) anthocyanidin reductase 1 (ANR1) in maize seeds increases the levels of 4β-(S-cysteinyl)-epicatechin and procyanidin dimers mainly using (-)-epicatechin as starter units. Introducing a Sorghum bicolor transcription factor (SbTT2) specifically regulating PA biosynthesis into a maize inbred deficient in anthocyanin biosynthesis activates both anthocyanin and PA biosynthesis pathways, suggesting conservation of the PA regulatory machinery across species. Our data support the divergence of PA biosynthesis across plant species and offer perspectives for future agricultrural applications in maize.

Genetic Engineering of Starch Biosynthesis in Maize Seeds for Efficient Enzymatic Digestion of Starch during Bioethanol Production

Maize accumulates large amounts of starch in seeds which have been used as food for human and animals. Maize starch is an importantly industrial raw material for bioethanol production. One critical step in bioethanol production is degrading starch to oligosaccharides and glucose by α-amylase and glucoamylase. This step usually requires high temperature and additional equipment, leading to an increased production cost. Currently, there remains a lack of specially designed maize cultivars with optimized starch (amylose and amylopectin) compositions for bioethanol production. We discussed the features of starch granules suitable for efficient enzymatic digestion. Thus far, great advances have been made in molecular characterization of the key proteins involved in starch metabolism in maize seeds. The review explores how these proteins affect starch metabolism pathway, especially in controlling the composition, size and features of starch. We highlight the roles of key enzymes in controlling amylose/amylopectin ratio and granules architecture. Based on current technological process of bioethanol production using maize starch, we propose that several key enzymes can be modified in abundance or activities via genetic engineering to synthesize easily degraded starch granules in maize seeds. The review provides a clue for developing special maize cultivars as raw material in the bioethanol industry.

Identifying Factors that Determine Effectiveness of Delivery Agents in Biolistic Delivery Using a Library of Amine-Containing Molecules

Biolistic transfection is a popular and versatile tool for plant transformation. A key step in the biolistic process is the binding of DNA to the heavy microprojectile using a delivery agent, usually a positively charged molecule containing amine groups. Currently, the choice of the commercial delivery agent is mostly limited to spermidine. In addition, the detailed delivery mechanism has not been reported. To help broaden the selection of the delivery agent and reveal the fundamental mechanisms that lead to high delivery performance, a library of amine-containing molecules was investigated. A double-barrel biolistic delivery device was utilized for testing hundreds of samples with much-improved consistency. The performance was evaluated on onion epidermis. The binding and release of DNA were measured via direct high-performance liquid chromatography analysis. This study shows that the overwhelming majority of the amine library performed at the same level as spermidine. To further interpret these results, correlations were performed with thousands of molecular descriptors generated by chemical modeling. It was discovered that the overall charge is most likely the key factor to a successful binding and delivery. Furthermore, even after increasing the amount of the DNA concentration 50-fold to stress the binding capacity of the molecules, the amines in the library continued to deliver at a near identical level while binding all the DNA. The increased DNA was also demonstrated with a Cas9 editing test that required a large amount of DNA to be delivered, and the result was consistent with the previously determined amine performance. This study greatly expands the delivery agent selection for biolistic delivery, allowing alternatives to a commercial reagent that are more shelf-stable and cheaper. The library also offers an approach to investigate more challenging delivery of protein and CRISPR-Cas via the biolistic process in the future.

The transcription factor ZmMYB69 represses lignin biosynthesis by activating ZmMYB31/42 expression in maize

A MYB family transcription factor ZmMYB69 is a transcriptional activator at the upper level of ZmMYB31 and ZmMYB42 in the hierarchical network that controls lignin biosynthesis in maize.

The maize low-lignin brown midrib3 mutant shows pleiotropic effects on photosynthetic and cell wall metabolisms in response to chilling

Maize (Zea mays L.) is one of the major cereal crops in the world and is highly sensitive to low temperature. Here, changes in photosynthetic and cell wall metabolisms were investigated during a long chilling exposure in inbred line F2 and a low-lignin near-isogenic brown midrib3 mutant (F2bm3), which has a mutation in the caffeic acid O-methyltransferase (COMT) gene. Results revealed that the plant biomass was reduced, and this was more pronounced in F2bm3. Photosynthesis was altered in both lines with distinct changes in photosynthetic pigment content between F2bm3 and F2, indicating an alternative photoprotection mechanism between lines under chilling. Starch remobilization was observed in F2bm3 while concentrations of sucrose, fructose and starch increased in F2, suggesting a reduced sugar partitioning in F2. The cell wall was altered upon chilling, resulting in changes in the composition of glucuronorabinoxylan and a reduced cellulose level in F2. Chilling shifted lignin subunit composition in F2bm3 mutant to a higher proportion of p-hydroxyphenyl (H) units, whereas it resulted in lignin with a higher proportion of syringyl (S) residues in F2. On average, the total cell wall ferulic acid (FA) content increased in both genotypes, with an increase in ether-linked FA in F2bm3, suggesting a greater degree of cross-linking to lignin. The reinforcement of the cell wall with lignin enriched in H-units and a higher concentration in cell-wall-bound FA observed in F2bm3 as a response to chilling, could be a strategy to protect the photosystems.

Degree of Biomass Conversion in the Integrated Production of Bioethanol and Biogas

The integrated production of bioethanol and biogas makes it possible to optimise the production of carriers from renewable raw materials. The installation analysed in this experimental paper was a hybrid system, in which waste from the production of bioethanol was used in a biogas plant with a capacity of 1 MWe. The main objective of this study was to determine the energy potential of biomass used for the production of bioethanol and biogas. Based on the results obtained, the conversion rate of the biomass—maize, in this case—into bioethanol was determined as the efficiency of the process of bioethanol production. A biomass conversion study was conducted for 12 months, during which both maize grains and stillage were sampled once per quarter (QU-I, QU-II, QU-III, QU-IV; QU—quarter) for testing. Between 342 L (QU-II) and 370 L (QU-I) of ethanol was obtained from the organic matter subjected to alcoholic fermentation. The mass that did not undergo conversion to bioethanol ranged from 269.04 kg to 309.50 kg, which represented 32.07% to 36.95% of the organic matter that was subjected to the process of bioethanol production. On that basis, it was concluded that only two-thirds of the organic matter was converted into bioethanol. The remaining part—post-production waste in the form of stillage—became a valuable raw material for the production of biogas, containing one-third of the biodegradable fraction. Under laboratory conditions, between 30.5 m3 (QU-I) and 35.6 m3 (QU-II) of biogas per 1 Mg of FM (FM—fresh matter) was obtained, while under operating conditions, between 29.2 m3 (QU-I) and 33.2 m3 (QU-II) of biogas was acquired from 1 Mg of FM. The Biochemical Methane Potential Correction Coefficient (BMPCC), which was calculated based on the authors’ formula, ranged from 3.2% to 7.4% in the analysed biogas installation.

Understanding Maize Response to Nitrogen Limitation in Different Light Conditions for the Improvement of Photosynthesis

The photosynthetic capacity of leaves is determined by their content of nitrogen (N). Nitrogen involved in photosynthesis is divided between soluble proteins and thylakoid membrane proteins. In C4 plants, the photosynthetic apparatus is partitioned between two cell types: mesophyll cells and bundle sheath. The enzymes involved in the C4 carbon cycle and assimilation of nitrogen are localized in a cell-specific manner. Although intracellular distribution of enzymes of N and carbon assimilation is variable, little is known about the physiological consequences of this distribution caused by light changes. Light intensity and nitrogen concentration influence content of nitrates in leaves and can induce activity of the main enzymes involved in N metabolism, and changes that reduce the photosynthesis rate also reduce photosynthetic N use efficiency. In this review, we wish to highlight and discuss how/whether light intensity can improve photosynthesis in maize during nitrogen limitation. We described the general regulation of changes in the main photosynthetic and nitrogen metabolism enzymes, their quantity and localization, thylakoid protein abundance, intracellular transport of organic acids as well as specific features connected with C4 photosynthesis, and addressed the major open questions related to N metabolism and effects of light on photosynthesis in C4 plants.

Effect of dietary-aged maize on growth performance, nutrient utilization, and serum metabolites in broilers

In China, most maize used for animal diets is stored for long periods. We examined the effects of dietary aged maize on growth performance, nutrients utilization, and serum metabolites in broilers. A total of 270 healthy 1-day-old male Cobb broilers were assigned randomly into three treatments groups and fed maize stored for different times (24 days, M0; 18 months, M18; 36 months, M36). Growth performance was examined at 21 and 42 days of age. Nutrient digestibility was studied on days 18-21 and 38-41. At day 42, blood samples were collected for serum metabolite analysis. Dietary aged maize significantly affected the feed to gain ratio, total starch digestibility, and apparent metabolizable energy (p < 0.05). Compared with the M0 group, 39 and 144 differential metabolites were observed in the M18 and M36 groups, respectively, whereas 56 differential metabolites were identified between the M18 and M36 groups. Pathway analysis indicated that the main altered pathways were clustered into lipid metabolism in M18, and lipid and glucose metabolism in M0 and M36, respectively. In conclusion, negative effects were observed for both new harvested maize and maize stored for 36 months; maize stored for 18 months may improve broiler performance.

Development of stable transgenic maize plants tolerant for drought by manipulating ABA signaling through Agrobacterium-mediated transformation

BACKGROUND

In crop plants, to cope up with the demand of food for rising population, revolutionary crop improvement programmes are being implemented for higher and higher yields. Abiotic stress, especially at flowering stage, causes drastic effect on yield in plants. Deforestation and urbanization made the water table very low and changed the climate which led to untimely and unforeseen rains which affect the yield of a crop through stress, both by lack of water as well as water logging (abiotic stress). Development of tolerant plants through breeding is a time-consuming programme and does not perform well in normal conditions. Development of stress-tolerant plants through transgenic technology is the better solution. Maize is a major crop used as food and fodder and has the commercial value in ethanol production. Hence, the genes viz., nced (9-cis-epoxycarotenoid dioxygenase) and rpk (receptor-like protein kinase), which play the key roles in the abscisic acid pathway and upstream component in ABA signaling have been transferred into maize plants through Agrobacterium-mediated transformation by optimizing several parameters to obtain maximum frequency of transformation.

RESULTS

Cultures raised from immature embryos of 2-mm size isolated from maize cobs, 12-15 days after pollination, were used for transformation. rpk and nced genes under the control of leaP and salT promoters respectively, cloned using gateway technology, have been introduced into elite maize inbred lines. Maximum frequency of transformation was observed with the callus infected after 20 days of inoculation by using 100 μM acetosyringone, 10 min infection time, and 2 days incubation period after co-cultivation resulted in maximum frequency of transformation (6%) in the NM5884 inbred line. Integration of the genes has been confirmed with molecular characterization by performing PCRs with marker as well as gene-specific primers and through southern hybridization. Physiological and biochemical characterization was done in vitro (artificial stress) and in vivo (pot experiments).

CONCLUSIONS

Changes in the parameters which affect the transformation frequency yielded maximum frequency of transformation with 20-day-old callus in the NM5884 inbred line. Introducing two or more genes using gateway technology is useful for developing stable transgenic plants with desired characters, abiotic stress tolerance in this study.

Potential applications of algae in biochemical and bioenergy sector

Algae have gained substantial importance as the most promising potential green fuel source across the globe and is on growing demand due to their antioxidant, anticancer, antiviral, antihypertensive, cholesterol reducing and thickening properties. Therefore, it has vast range of application in medicines, pharmaceutical, cosmetics, paper and nutraceutical industries. In this work, the remarkable ability of algae to convert CO₂ and other toxic compounds in atmosphere to potential biofuels, foods, feeds and high-value bioactive compounds is reviewed. Algae produce approximately 50% of the earth's oxygen using its photosynthetic activity, thus acting as a potent tool to mitigate the effects of air pollution. Further, the applicability of algae as a desirable energy source has also been discussed, as they have the potential to serve as an effective alternative to intermittent renewable energy; and also, to combustion-based fossil fuel energy, making them effective for advanced biofuel conversions. This work also evaluates the current applications of algae and the implications of it as a potential substrate for bioplastic, natural alternative to inks and for making paper besides high-value products. In addition, the scope for integrated biorefinery approach is also briefly explored in terms of economic aspects at the industrial scale, as such energy conversion mechanisms are directly linked with sustainability, thus providing a positive overall energy outlook.

The effects of deletion of cellobiohydrolase genes on carbon source-dependent growth and enzymatic lignocellulose hydrolysis in Trichoderma reesei

The saprophytic fungus Trichoderma reesei has long been used as a model to study microbial degradation of lignocellulosic biomass. The major cellulolytic enzymes of T. reesei are the cellobiohydrolases CBH1 and CBH2, which constitute more than 70% of total proteins secreted by the fungus. However, their physiological functions and effects on enzymatic hydrolysis of cellulose substrates are not sufficiently elucidated. Here, the cellobiohydrolase-encoding genes cbh1 and cbh2 were deleted, individually or combinatively, by using an auxotrophic marker-recycling technique in T. reesei. When cultured on media with different soluble carbon sources, all three deletion strains (Δcbh1, Δcbh2, and Δcbh1Δcbh2) exhibited no dramatic variation in morphological phenotypes, but their growth rates increased apparently when cultured on soluble cellulase-inducing carbon sources. In addition, Δcbh1 showed dramatically reduced growth and Δcbh1Δcbh2 could hardly grew on microcrystalline cellulose (MCC), whereas all strains grew equally on sodium carboxymethyl cellulose (CMC-Na), suggesting that the influence of the CBHs on growth was carbon source-dependent. Moreover, five representative cellulose substrates were used to analyse the influence of the absence of CBHs on saccharification efficiency. CBH1 deficiency significantly affected the enzymatic hydrolysis rates of various cellulose substrates, where acid pre-treated corn stover (PCS) was influenced the least. CBH2 deficiency reduced the hydrolysis of MCC, PCS, and acid pre-treated and delignified corncob but improved the hydrolysis ability of filter paper. These results demonstrate the specific contributions of CBHs to the hydrolysis of different types of biomass, which could facilitate the development of tailor-made strains with highly efficient hydrolysis enzymes for certain biomass types in the biofuel industry.

An Overview of the Sociological and Environmental Factors Influencing Eating Food Behavior in Canada

This review extensively discusses various socio environmental factors affecting eating behavior of the general public within Canada including the development and implementation of national policies. A framework representing the determinants of healthy eating can be grouped into four categories i.e., the individual determinants, the economic environment, the social environment and the physical environment. This framework allowed for addressing food insecurity and social economic ecosystem of Canadians. Lastly, we investigate the role in which biotechnology plays in improving food security and addresses the significant impact biotechnology has contributed toward on agriculture and the food market. Overall, this review using such sources as Web of Science, Pub Med and Scopus provides significant contribution toward understanding the social economic environment and eating behavior of people living in Canada. In conclusion, this has led to identify a research gap as there is a significant need to address the development and implementation of policies in the food and nutrition environment.

Dietary resistant starch modifies the composition and function of caecal microbiota of broilers

BACKGROUND

Diet plays an important role in shaping the composition of gut microbiota. Starch is the main source of carbohydrates in diets of broilers. This study investigated the effects of dietary corn starch and resistant starch on composition and function of caecal microbiota of broilers. A total of 320, 1-day-old male Arbor Acres broiler chicks were randomly assigned into five groups including normal corn-soybean (NC) diet, corn starch (CS) diet group, 4%, 8% and 12% resistant starch (RS) diet groups. The caecal contents of 42-day old broilers were sampled and microbiota community was analysed with 16S rRNA gene sequences.

RESULTS

The CS group increased the abundances of Bilophila, Eggerthella, Olsenella and Sellimonas and decreased proportion of Akkermansia, Eisenbergiella, Oscillospira, Ruminococcaceae NK4A214 group and Synergistes in the caecum of birds compared to the NC group. However, the birds from RS groups had higher abundances of Anaerofilum, Bacteroides, Desulfovibrio and Parasutterella and lower abundances of Alistipes, Bilophila, Christensenellaceae R-7 group, Eggerthella and Ruminiclostridium 1 than the CS group. Functional prediction of these changes in microbiota revealed that the CS diet drove caecal microbiota that were more inclined to utilize carbohydrates through glycolysis/gluconeogenesis metabolism, while the 8%RS and 12%RS diets depleted microbial glycolysis/gluconeogenesis and amino acids metabolism.

CONCLUSION

Dietary CS and RS alter the microbial composition and diversity, and modulate the metabolic pathways of microbial metabolism in caecum of broilers, which may further affect nutrient utilization and hindgut health of the host. © 2019 Society of Chemical Industry.

Bioethanol Production From High Sugary Corn Genotypes by Decreasing Enzyme Consumption

This is a PhD proposal defended in a 2012-2013 session at the Institute of Biological Sciences, Faculty of Science, University of Malaya, Malaysia. The proposal has been written in accordance with the requirements of the university under the sub-headings: background, problem statement, rationale, hypothesis and research questions, research objectives, literature review, methodology, scope, expected outcomes and concluding remarks, work schedule, and references. This proposal provides a comprehensive study on bioethanol production from corn. First, it discusses development and field experiments of high sugary genotypes (HSGs). Secondly, it provides a comparative evaluation of enzyme consumptions and ethanol production between normal and HSG corn genotypes. Finally, this proposal provides evaluation of the co-product quality for both groups of genotypes. The readers who are interested to conduct any further study on corn-based bioethanol would be benefited from this proposal.

Effects of carbon-based nanomaterials on seed germination, biomass accumulation and salt stress response of bioenergy crops

Bioenergy crops are an attractive option for use in energy production. A good plant candidate for bioenergy applications should produce a high amount of biomass and resist harsh environmental conditions. Carbon-based nanomaterials (CBNs) have been described as promising seed germination and plant growth regulators. In this paper, we tested the impact of two CBNs: graphene and multi-walled carbon nanotubes (CNTs) on germination and biomass production of two major bioenergy crops (sorghum and switchgrass). The application of graphene and CNTs increased the germination rate of switchgrass seeds and led to an early germination of sorghum seeds. The exposure of switchgrass to graphene (200 mg/l) resulted in a 28% increase of total biomass produced compared to untreated plants. We tested the impact of CBNs on bioenergy crops under salt stress conditions and discovered that CBNs can significantly reduce symptoms of salt stress imposed by the addition of NaCl into the growth medium. Using an ion selective electrode, we demonstrated that the concentration of Na⁺ ions in NaCl solution can be significantly decreased by the addition of CNTs to the salt solution. Our data confirmed the potential of CBNs as plant growth regulators for non-food crops and demonstrated the role of CBNs in the protection of plants against salt stress by desalination of saline growth medium.

Structural insight into industrially relevant glucoamylases: flexible positions of starch-binding domains

Glucoamylases are one of the most important classes of enzymes in the industrial degradation of starch biomass. They consist of a catalytic domain and a carbohydrate-binding domain (CBM), with the latter being important for the interaction with the polymeric substrate. Whereas the catalytic mechanisms and structures of the individual domains are well known, the spatial arrangement of the domains with respect to each other and its influence on activity are not fully understood. Here, the structures of three industrially used fungal glucoamylases, two of which are full length, have been crystallized and determined. It is shown for the first time that the relative orientation between the CBM and the catalytic domain is flexible, as they can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The flexibility in the orientations of the two domains presented a considerable challenge for the crystallization of the enzymes.

Application of phase correction to improve the characterization of photooxidation products of lignin using 7 Tesla Fourier-transform ion cyclotron resonance mass spectrometry

Lignin is the second most abundant natural biopolymer and potentially a valuable alternative energy source for conventional fossil fuels. In this study, Fourier-transform ion cyclotron resonance-mass spectrometry (FTICR-MS) in conjunction with phase correction was applied to study photooxidation products of lignin using a 7 Tesla (T) mass spectrometer. The application of 7 T FTICR-MS has often been inadequate for the analysis of complex natural organic matter because of insufficient resolving power as compared with high-field FTICR, which led to incorrect assignments of elemental formulae and discontinuous plots in graphical and statistical analyses. Here, the application of phase correction to the FTICR mass spectra of lignin oxidation products greatly improved the spectral quality, and thus, readily permitted characterization of photooxidation processes of lignin compounds under simulated solar radiation conditions.

Overexpression of MusaMYB31, a R2R3 type MYB transcription factor gene indicate its role as a negative regulator of lignin biosynthesis in banana

Lignin and polyphenols are important cellular components biosynthesized through phenylpropanoid pathway. Phenylpropanoid pathway in plants is regulated by some important transcription factors including R2R3 MYB transcription factors. In this study, we report the cloning and functional characterization of a banana R2R3-MYB transcription factor (MusaMYB31) by overexpression in transgenic banana plants and evaluated its potential role in regulating biosynthesis of lignin and polyphenols. Sequence analysis of MusaMYB31 indicated its clustering with members of subgroup 4 (Sg4) of R2R3MYB family which are well known for their role as repressors of lignin biosynthesis. Expression analysis indicated higher expression of MusaMYB31 in corm and root tissue, known for presence of highly lignified tissue than other organs of banana. Overexpression of MusaMYB31 in banana cultivar Rasthali was carried out and four transgenic lines were confirmed by GUS histochemical staining, PCR analysis and Southern blot. Histological and biochemical analysis suggested reduction of cell wall lignin in vascular elements of banana. Transgenic lines showed alteration in transcript levels of general phenylpropanoid pathway genes including lignin biosynthesis pathway genes. Reduction of total polyphenols content in transgenic lines was in line with the observation related to repression of general phenylpropanoid pathway genes. This study suggested the potential role of MusaMYB31 as repressor of lignin and polyphenols biosynthesis in banana.

Advances in Maize Transformation Technologies and Development of Transgenic Maize

Maize is the principal grain crop of the world. It is also the crop where genetic engineering has been employed to a great extent to improve its various traits. The ability to transform maize is a crucial step for application of gene technology in maize improvement. There have been constant improvements in the maize transformation technologies over past several years. The choice of genotype and the explant material to initiate transformation and the different types of media to be used in various stages of tissue culture can have significant impact on the outcomes of the transformation efforts. Various methods of gene transfer, like the particle bombardment, protoplast transformation, Agrobacterium-mediated, in planta transformation, etc., have been tried and improved over years. Similarly, various selection systems for retrieval of the transformants have been attempted. The commercial success of maize transformation and transgenic development is unmatched by any other crop so far. Maize transformation with newer gene editing technologies is opening up a fresh dimension in transformation protocols and work-flows. This review captures the various past and recent facets in improvement in maize transformation technologies and attempts to present a comprehensive updated picture of the current state of the art in this area.

An AGAMOUS intron-driven cytotoxin leads to flowerless tobacco and produces no detrimental effects on vegetative growth of either tobacco or poplar

Flowerless trait is highly desirable for poplar because it can prevent pollen- and seed-mediated transgene flow. We have isolated the second intron of PTAG2, an AGAMOUS (AG) orthologue from Populus trichocarpa. By fusing this intron sequence to a minimal 35S promoter sequence, we created two artificial promoters, fPTAG2I (forward orientation of the PTAG2 intron sequence) and rPTAG2I (reverse orientation of the PTAG2 intron sequence). In tobacco, expression of the β-glucuronidase gene (uidA) demonstrates that the fPTAG2I promoter is non-floral-specific, while the rPTAG2I promoter is active in floral buds but with no detectable vegetative activity. Under glasshouse conditions, transgenic tobacco plants expressing the Diphtheria toxin A (DT-A) gene driven by the rPTAG2I promoter produced three floral ablation phenotypes: flowerless, neuter (stamenless and carpel-less) and carpel-less. Further, the vegetative growth of these transgenic lines was similar to that of the wild-type plants. In field trials during 2014 and 2015, the flowerless transgenic tobacco stably maintained its flowerless phenotype, and also produced more shoot and root biomass when compared to wild-type plants. In poplar, the rPTAG2I::GUS gene exhibited no detectable activity in vegetative organs. Under field conditions over two growing seasons (2014 to the end of 2015), vegetative growth of the rPTAG2I::DT-A transgenic poplar plants was similar to that of the wild-type plants. Our results demonstrate that the rPTAG2I artificial promoter has no detectable activities in vegetative tissues and organs, and the rPTAG2I::DT-A gene may be useful for producing flowerless poplar that retains normal vegetative growth.

A Novel FC116/BC10 Mutation Distinctively Causes Alteration in the Expression of the Genes for Cell Wall Polymer Synthesis in Rice

We report isolation and characterization of a fragile culm mutant fc116 that displays reduced mechanical strength caused by decreased cellulose content and altered cell wall structure in rice. Map-based cloning revealed that fc116 was a base substitution mutant (G to A) in a putative beta-1,6-N-acetylglucosaminyltransferase (C2GnT) gene (LOC_Os05g07790, allelic to BC10). This mutation resulted in one amino acid missing within a newly-identified protein motif "R, RXG, RA." The FC116/BC10 gene was lowly but ubiquitously expressed in the all tissues examined across the whole life cycle of rice, and slightly down-regulated during secondary growth. This mutant also exhibited a significant increase in the content of hemicelluloses and lignins, as well as the content of pentoses (xylose and arabinose). But the content of hexoses (glucose, mannose, and galactose) was decreased in both cellulosic and non-cellulosic (pectins and hemicelluloses) fractions of the mutant. Transcriptomic analysis indicated that the typical genes in the fc116 mutant were up-regulated corresponding to xylan biosynthesis, as well as lignin biosynthesis including p-hydroxyphenyl (H), syringyl (S), and guaiacyl (G). Our results indicate that FC116 has universal function in regulation of the cell wall polymers in rice.

Two-dimensional mass defect matrix plots for mapping genealogical links in mixtures of lignin depolymerisation products

Lignin is the second most abundant natural biopolymer, and lignin wastes are therefore potentially significant sources for renewable chemicals such as fuel compounds, as alternatives to fossil fuels. Waste valorisation of lignin is currently limited to a few applications such as in the pulp industry, however, because of the lack of effective extraction and characterisation methods for the chemically highly complex mixtures after decomposition. Here, we have implemented high resolution mass spectrometry and developed two-dimensional mass defect matrix plots as a data visualisation tool, similar to the Kendrick mass defect plots implemented in fields such as petroleomics. These 2D matrix plots greatly simplified the highly convoluted lignin mass spectral data acquired from Fourier transform ion cyclotron resonance (FTICR)–mass spectrometry, and the derived metrics provided confident peak assignments and strongly improved structural mapping of lignin decomposition product series from the various linkages within the lignin polymer after electrochemical decomposition.

Graphical Abstract

Ammonium oxalate-extractable uronic acids positively affect biomass enzymatic digestibility by reducing lignocellulose crystallinity in Miscanthus

Based on systems biology analyses of total 179 representative Miscanthus accessions, ammonium oxalate (AO)-extractable uronic acids could either positively affect biomass digestibility or negatively alter lignocellulose crystallinity at p<0.01 or 0.05. Comparative analysis of four typical pairs of Miscanthus samples indicated that the AO-extractable uronic acids, other than hexoses and pentoses, play a predominant role in biomass enzymatic saccharification upon various chemical pretreatments, consistent with observations of strong cell tissue destruction in situ and rough biomass residue surface in vitro in the unique Msa24 sample rich in uronic acids. Notably, AO-extraction of uronic acids could significantly increase lignocellulose CrI at p<0.05, indicating that uronic acids-rich polymers may have the interactions with β-1,4-glucan chains that reduce cellulose crystallinity. It has also suggested that increasing of uronic acids should be a useful approach for enhancing biomass enzymatic digestibility in Miscanthus and beyond.

Accumulation of Hydrocarbons by Maize (Zea mays L.) in Remediation of Soils Contaminated with Crude Oil

This study has investigated the use of screened maize for remediation of soil contaminated with crude oil. Pots experiment was carried out for 60 days by transplanting maize seedlings into spiked soils. The results showed that certain amount of crude oil in soil (≤2 147 mg·kg(-1)) could enhance the production of shoot biomass of maize. Higher concentration (6 373 mg·kg(-1)) did not significantly inhibit the growth of plant maize (including shoot and root). Analysis of plant shoot by GC-MS showed that low molecular weight polycyclic aromatic hydrocarbons (PAHs) were detected in maize tissues, but PAHs concentration in the plant did not increase with higher concentration of crude oil in soil. The reduction of total petroleum hydrocarbon in planted soil was up to 52.21-72.84%, while that of the corresponding controls was only 25.85-34.22% in two months. In addition, data from physiological and biochemical indexes demonstrated a favorable adaptability of maize to crude oil pollution stress. This study suggested that the use of maize (Zea mays L.) was a good choice for remediation of soil contaminated with petroleum within a certain range of concentrations.

An integrated genomic and metabolomic framework for cell wall biology in rice

Background

Plant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synthesis and maintenance. However, functional association for the majority of these gene products remains obscure. One useful approach to infer biological associations is via transcriptional coordination, or co-expression of genes. This approach has proved useful for several biological processes. Nevertheless, combining co-expression with other large-scale measurements may improve the biological inferences.

Results

In this study, we used a combined approach of co-expression and cell wall metabolomics to obtain new insight into cell wall synthesis in rice. We initially created a weighted gene co-expression network from publicly available datasets, and then established a comprehensive cell wall dataset by determining cell wall compositions from 29 tissues that almost cover the whole life cycle of rice. We subsequently combined the datasets through the conversion of co-expressed gene modules into eigen-vectors, representing expression profiles for the genes in the modules, and performed comparative analyses against the cell wall contents. Here, we made three major discoveries. First, we confirmed our approach by finding primary and secondary wall cellulose biosynthesis modules, respectively. Second, we found co-expressed modules that strongly correlated with re-organization of the secondary cell walls and with modifications and degradation of hemicellulosic structures. Third, we inferred that at least one module is likely to play a regulatory role in the production of G-rich lignification.

Conclusions

Here, we integrated transcriptomic associations and cell wall metabolism and found that certain co-expressed gene modules are positively correlated with distinct cell wall characteristics. We propose that combining multiple data-types, such as coordinated transcription and cell wall analyses, may be a useful approach to glean new insight into biological processes. The combination of multiple datasets, as illustrated here, can further improve the functional inferences that typically are generated via a single type of datasets. In addition, our data extend the typical co-expression approach to allow deeper insight into cell wall biology in rice.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-596) contains supplementary material, which is available to authorized users.

Enhancing the productivity of grasses under high-density planting by engineering light responses: from model systems to feedstocks

The successful commercialization of bioenergy grasses as lignocellulosic feedstocks requires that they be produced, processed, and transported efficiently. Intensive breeding for higher yields in food crops has resulted in varieties that perform optimally under high-density planting but often with high input costs. This is particularly true of maize, where most yield gains in the past have come through increased planting densities and an abundance of fertilizer. For lignocellulosic feedstocks, biomass rather than grain yield and digestibility of cell walls are two of the major targets for improvement. Breeding for high-density performance of lignocellulosic crops has been much less intense and thus provides an opportunity for improving the feedstock potential of these grasses. In this review, we discuss the role of vegetative shade on growth and development and suggest targets for manipulating this response to increase harvestable biomass under high-density planting. To engineer grass architecture and modify biomass properties at increasing planting densities, we argue that new model systems are needed and recommend Setaria viridis, a panicoid grass, closely related to major fuel and bioenergy grasses as a model genetic system.

Carbon dioxide bio-fixation and wastewater treatment via algae photochemical synthesis for biofuels production

Utilizing the energy, nutrients and CO₂held within residual waste materials to provide all necessary inputs except for sunlight, the cultivation of algae becomes a closed-loop engineered ecosystem. Developing this green biotechnology is a tangible step towards a waste-free sustainable society.

Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiae identifies mutants with improved heterologous exocellulase activity and host secretion

Background

As a strong fermentator, Saccharomyces cerevisiae has the potential to be an excellent host for ethanol production by consolidated bioprocessing. For this purpose, it is necessary to transform cellulose genes into the yeast genome because it contains no cellulose genes. However, heterologous protein expression in S. cerevisiae often suffers from hyper-glycosylation and/or poor secretion. Thus, there is a need to genetically engineer the yeast to reduce its glycosylation strength and to increase its secretion ability.

Results

Saccharomyces cerevisiae gene-knockout strains were screened for improved extracellular activity of a recombinant exocellulase (PCX) from the cellulose digesting fungus Phanerochaete chrysosporium. Knockout mutants of 47 glycosylation-related genes and 10 protein-trafficking-related genes were transformed with a PCX expression construct and screened for extracellular cellulase activity. Twelve of the screened mutants were found to have a more than 2-fold increase in extracellular PCX activity in comparison with the wild type. The extracellular PCX activities in the glycosylation-related mnn10 and pmt5 null mutants were, respectively, 6 and 4 times higher than that of the wild type; and the extracellular PCX activities in 9 protein-trafficking-related mutants, especially in the chc1, clc1 and vps21 null mutants, were at least 1.5 times higher than the parental strains. Site-directed mutagenesis studies further revealed that the degree of N-glycosylation also plays an important role in heterologous cellulase activity in S. cerevisiae.

Conclusions

Systematic screening of knockout mutants of glycosylation- and protein trafficking-associated genes in S. cerevisiae revealed that: (1) blocking Golgi-to-endosome transport may force S. cerevisiae to export cellulases; and (2) both over- and under-glycosylation may alter the enzyme activity of cellulases. This systematic gene-knockout screening approach may serve as a convenient means for increasing the extracellular activities of recombinant proteins expressed in S. cerevisiae.

Biofuels as a sustainable energy source: an update of the applications of proteomics in bioenergy crops and algae

Sustainable energy is the need of the 21st century, not because of the numerous environmental and political reasons but because it is necessary to human civilization's energy future. Sustainable energy is loosely grouped into renewable energy, energy conservation, and sustainable transport disciplines. In this review, we deal with the renewable energy aspect focusing on the biomass from bioenergy crops to microalgae to produce biofuels to the utilization of high-throughput omics technologies, in particular proteomics in advancing our understanding and increasing biofuel production. We look at biofuel production by plant- and algal-based sources, and the role proteomics has played therein. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Maize source leaf adaptation to nitrogen deficiency affects not only nitrogen and carbon metabolism but also control of phosphate homeostasis

Crop plant development is strongly dependent on the availability of nitrogen (N) in the soil and the efficiency of N utilization for biomass production and yield. However, knowledge about molecular responses to N deprivation derives mainly from the study of model species. In this article, the metabolic adaptation of source leaves to low N was analyzed in maize (Zea mays) seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under sufficient (15 mM) or limiting (0.15 mM) nitrate supply for up to 30 d. Limited availability of N caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the N stress but showed strong genotype- and age-dependent patterns. N starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation-related transcripts, on the other hand, were not influenced. Carbon assimilation-related transcripts were characterized by high transcriptional coordination and general down-regulation under low-N conditions. N deprivation caused a slight accumulation of starch but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions.

Rhizobia species: A Boon for "Plant Genetic Engineering"

Since past three decades new discoveries in plant genetic engineering have shown remarkable potentials for crop improvement. Agrobacterium Ti plasmid based DNA transfer is no longer the only efficient way of introducing agronomically important genes into plants. Recent studies have explored a novel plant genetic engineering tool, Rhizobia sp., as an alternative to Agrobacterium, thereby expanding the choice of bacterial species in agricultural plant biotechnology. Rhizobia sp. serve as an open license source with no major restrictions in plant biotechnology and help broaden the spectrum for plant biotechnologists with respect to the use of gene transfer vehicles in plants. New efficient transgenic plants can be produced by transferring genes of interest using binary vector carrying Rhizobia sp. Studies focusing on the interactions of Rhizobia sp. with their hosts, for stable and transient transformation and expression of genes, could help in the development of an adequate gene transfer vehicle. Along with being biologically beneficial, it may also bring a new means for fast economic development of transgenic plants, thus giving rise to a new era in plant biotechnology, viz. "Rhizobia mediated transformation technology."

Analysis of soluble lignin in sugarcane by ultrahigh performance liquid chromatography-tandem mass spectrometry with a do-it-yourself oligomer database

Lignin is a polymer found in the cell wall of plants and is one of the main obstacles to the implementation of second-generation ethanol production because it confers the recalcitrance of the lignocellulosic material. The recalcitrance of biomass is affected by the amount of lignin, by its monomer composition, and the way the monomers are arranged in the plant cell wall. Analysis of lignin structure demands mass spectrometry analysis, and identification of oligomers is usually based on libraries produced by laborious protocols. A robust method to build a do-it-yourself lignin oligomer library was tested. This library can be built using commercially available enzymes, standards, and reagents and is relatively easy to accomplish. An ultrahigh performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the separation and characterization of monomers and oligomers was developed and was equally applicable to the synthetic lignin and to soluble lignin extracted from a sample of sugar cane.

Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies

The organized lignocellulosic assemblies of cell walls provide the structural integrity required for the large statures of terrestrial plants. Silencing two CINNAMYL ALCOHOL DEHYDROGENASE (CAD) genes in Nicotiana attenuata produced plants (ir-CAD) with thin, red-pigmented stems, low CAD and sinapyl alcohol dehydrogenase activity, low lignin contents, and rubbery, structurally unstable stems when grown in the glasshouse (GH). However, when planted into their native desert habitat, ir-CAD plants produced robust stems that survived wind storms as well as the wild-type plants. Despite efficient silencing of NaCAD transcripts and enzymatic activity, field-grown ir-CAD plants had delayed and restricted spread of red stem pigmentation, a color change reflecting blocked lignification by CAD silencing, and attained wild-type-comparable total lignin contents. The rubbery GH phenotype was largely restored when field-grown ir-CAD plants were protected from wind, herbivore attack, and ultraviolet B exposure and grown in restricted rooting volumes; conversely, it was lost when ir-CAD plants were experimentally exposed to wind, ultraviolet B, and grown in large pots in growth chambers. Transcript and liquid chromatography-electrospray ionization-time-of-flight analysis revealed that these environmental stresses enhanced the accumulation of various phenylpropanoids in stems of field-grown plants; gas chromatography-mass spectrometry and nuclear magnetic resonance analysis revealed that the lignin of field-grown ir-CAD plants had GH-grown comparable levels of sinapaldehyde and syringaldehyde cross-linked into their lignins. Additionally, field-grown ir-CAD plants had short, thick stems with normal xylem element traits, which collectively enabled field-grown ir-CAD plants to compensate for the structural deficiencies associated with CAD silencing. Environmental stresses play an essential role in regulating lignin biosynthesis in lignin-deficient plants.

Altered lignin biosynthesis improves cellulosic bioethanol production in transgenic maize plants down-regulated for cinnamyl alcohol dehydrogenase

Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme involved in the last step of monolignol biosynthesis. The effect of CAD down-regulation on lignin production was investigated through a transgenic approach in maize. Transgenic CAD-RNAi plants show a different degree of enzymatic reduction depending on the analyzed tissue and show alterations in cell wall composition. Cell walls of CAD-RNAi stems contain a lignin polymer with a slight reduction in the S-to-G ratio without affecting the total lignin content. In addition, these cell walls accumulate higher levels of cellulose and arabinoxylans. In contrast, cell walls of CAD-RNAi midribs present a reduction in the total lignin content and of cell wall polysaccharides. In vitro degradability assays showed that, although to a different extent, the changes induced by the repression of CAD activity produced midribs and stems more degradable than wild-type plants. CAD-RNAi plants grown in the field presented a wild-type phenotype and produced higher amounts of dry biomass. Cellulosic bioethanol assays revealed that CAD-RNAi biomass produced higher levels of ethanol compared to wild-type, making CAD a good target to improve both the nutritional and energetic values of maize lignocellulosic biomass.

Controlling lipid accumulation in cereal grains

Plant oils have so far been mostly directed toward food and feed production. Nowadays however, these oils are more and more used as competitive alternatives to mineral hydrocarbon-based products. This increasing demand for vegetable oils has led to a renewed interest in elucidating the metabolism of storage lipids and its regulation in various plant systems. Cereal grains store carbon in the form of starch in a large endosperm and as oil in an embryo of limited size. Complementary studies on kernel development and metabolism have paved the way for breeding or engineering new varieties with higher grain oil content. This could be achieved either by increasing the relative proportion of the oil-rich embryo within the grain, or by enhancing oil synthesis and accumulation in embryonic structures. For instance, diacylglycerol acyltransferase (DGAT) that catalyses the ultimate reaction in the biosynthesis of triacylglycerol appears to be a promising target for increasing oil content in maize embryos. Similarly, over-expression of the maize transcriptional regulators ZmLEAFY COTYLEDON1 and ZmWRINKLED1 efficiently stimulates oil accumulation in the kernels of transgenic lines. Redirecting carbon from starch to oil in the endosperm, though not yet realized, is discussed.

Development of SCAR marker for simultaneous identification of Miscanthus sacchariflorus, M. sinensis and M. x giganteus

The sequence-characterized amplified region (SCAR) marker for simultaneous identification of Miscanthus sacchariflorus, Miscanthus sinensis, and Miscanthus x giganteus was developed. In this study, it was attempted for the first time to develop the SCAR marker for detecting the molecular phenotypes among Miscanthus species. Randomly amplified polymorphic DNA technique was applied for this study and one fragment which is unique to M. sacchariflorus was identified and then sequenced. Based on the specific fragment, one SCAR primer pair designated as MS62-5F and MS62-5R was designed to amplify an approximately 1,000 bp DNA fragment within the sequenced region. Diagnostic PCR was performed using the primer pair. Using this SCAR marker, approximately 1,000 bp and 1,200 bp DNA fragments were obtained in M. sacchariflorus and M. sinensis, respectively. Moreover, M. x giganteus was obtained both bands at the same time. The result showed that this SCAR marker can clearly distinguish the M. sacchariflorus, M. sinensis, and M. x giganteus, respectively.

Amylolytic microorganism from são paulo zoo composting: isolation, identification, and amylase production

Composting is a way of transforming the organic waste into fertilizer, minimizing the use of inorganic compounds that may contaminate the environment. This transformation is the result of the microorganism action, converting complex carbon sources into energy. Enzymes that are exported by the microorganisms to the surrounding environment mediate this process. The aiming of the present work is to prospect the compost produced by the organic composting unit (OCU) of the Fundação Parque Zoológico de São Paulo (FPZSP) to find novel starch hydrolyzing organisms (SHO) that secrete large amounts of amylases under harsh conditions, such as high temperature. We found five bacterial isolates that have amylolytic activity induced by soluble starch and 39°C temperature of growth. These bacterial strains were identified by MALDI-TOF (Matrix-assisted laser desorption/ionization-Time of Flight) analysis, a rapid and efficient methodology for microbe identification in large scale. Our results present amylolytic strains that belong to diverse taxonomic groups (Solibacillus silvestris, Arthrobacter arilaitensis, Isoptericola variabilis, and Acinetobacter calcoaceticus); some of them have never been associated with this kind of hydrolytic activity before. The information regarding enzyme induction will be important to optimize the production by the bacterial isolates, which may be a great value for biotechnological applications.

Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Background

Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar.

Results

Here, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome.

Conclusions

Sequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time.

Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species.

Genetic engineering of energy crops: a strategy for biofuel production in China

Biomass utilization is increasingly considered as a practical way for sustainable energy supply and long-term environment care around the world. In concerns with food security in China, starch or sugar-based bioethanol and edible-oil-derived biodiesel are harshly restricted for large scale production. However, conversion of lignocellulosic residues from food crops is a potential alternative. Because of its recalcitrance, current biomass process is unacceptably expensive, but genetic breeding of energy crops is a promising solution. To meet the need, energy crops are defined with a high yield for both food and biofuel purposes. In this review, main grasses (rice, wheat, maize, sorghum and miscanthus) are evaluated for high biomass production, the principles are discussed on modification of plant cell walls that lead to efficient biomass degradation and conversion, and the related biotechnologies are proposed in terms of energy crop selection.