Identification of resistance to Sugarcane mosaic virus, Sugarcane streak mosaic virus, and Sugarcane bacilliform virus in new elite sugarcane accessions in India

Sugarcane mosaic and leaf fleck diseases are significant viral diseases affecting sugarcane crops in India. The use of resistant sugarcane varieties is considered the most economical and effective approach to manage viral diseases, especially in vegetatively propagated crops such as sugarcane. Sugarcane mosaic virus (SCMV) and Sugarcane streak mosaic virus (SCSMV) are the primary pathogens responsible for mosaic disease in sugarcane-growing regions of India. Sugarcane bacilliform virus (SCBV), causing leaf fleck disease, is also often found in mixed infections with mosaic symptoms. The study aimed to identify new sources of resistance by screening sugarcane germplasm for resistance to SCMV, SCSMV, and SCBV. The screening was carried out under high inoculum using the infector row method in both plant and ratoon crops. Out of 129 genotypes tested, only 8 were found to be free of mosaic viruses, indicating a rare occurrence of resistant sources. The study revealed that mosaic disease is widespread, with nearly 95% of tested varieties/genotypes being infected with mosaic viruses. SCMV, SCSMV, and SCBV were detected in 121 out of 129 genotypes using the RT-PCR and PCR assays. Based on their response to the viruses, the tested genotypes were categorized into different resistance grades: highly resistant (grade 1), resistant (grade 2), moderately resistant (grade 3), susceptible (grade 4), and highly susceptible (grade 5). The results of the study provide valuable information about elite resistance resources that can be used for the prevention and control of mosaic disease. These resistant genotypes could also serve as potential donors for mosaic and leaf fleck disease resistance in breeding programs.

Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum

Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.

Silicon mitigates iron deficiency in two energy cane cultivars by modulating physiological and nutritional mechanisms

Introduction

Alkaline soils with iron (Fe) deficiency are found in many regions of the world, and the use of silicon (Si) can mitigate the damages caused by such deficiency. The aim of this study was to evaluate the effect of Si in mitigating a moderate deficiency of Fe in two energy cane cultivars.

Methods

Two experiments were performed, one with the VX2 cultivar and the other with the VX3 cultivar of energy cane, which were cultivated in pots with sand and a nutrient solution. In both experiments, treatments followed a factorial scheme 2x2, designed based on the sufficiency and deficiency of Fe, being combined with the absence or presence of Si (2.5 mmol L^-1), disposed in a randomized blocks design with six replicates. In the condition of Fe sufficiency, plants were cultivated in a solution containing 368 µmol L^-1 of Fe, while plants cultivated under deficiency were initially submitted to cultivation with a 54 µmol L^-1 concentration of Fe for 30 days, and later, with Fe complete omission for 60 days. The supply of Si was carried out by applying 15 fertirrigations with Si (via root and leaf) during the initial stage of seedling development, and after transplanting, the nutrient solution was added daily (via root).

Results and discussion

Both cultivars of energy cane were sensitive to Fe deficiency in the absence of Si, impairing its growth by causing stress and pigment degradation, thus reducing the photosynthesis efficiency. The supply of Si mitigated the damages caused by Fe deficiency in both cultivars, by increasing Fe accumulation in new and intermediate leaves, stem, and roots in the VX2 cultivar, and in new, intermediate, and old leaves and stem in the VX3 cultivar, which in turn reduced stress and favored both the nutritional and photosynthesis efficiency, while increasing the dry matter production. Si by modulating physiological and nutritional mechanisms, mitigates Fe deficiency in two energy cane cultivars. It was concluded that Si can be used as a strategy to improve growth and nutrition of energy cane in environments that are susceptible to Fe deficiency.

Metabolic engineering of energycane to hyperaccumulate lipids in vegetative biomass

Background

The metabolic engineering of high-biomass crops for lipid production in their vegetative biomass has recently been proposed as a strategy to elevate energy density and lipid yields for biodiesel production. Energycane and sugarcane are highly polyploid, interspecific hybrids between Saccharum officinarum and Saccharum spontaneum that differ in the amount of ancestral contribution to their genomes. This results in greater biomass yield and persistence in energycane, which makes it the preferred target crop for biofuel production.

Results

Here, we report on the hyperaccumulation of triacylglycerol (TAG) in energycane following the overexpression of the lipogenic factors Diacylglycerol acyltransferase1-2 (DGAT1-2) and Oleosin1 (OLE1) in combination with RNAi suppression of SUGAR-DEPENDENT1 (SDP1) and Trigalactosyl diacylglycerol1 (TGD1). TAG accumulated up to 1.52% of leaf dry weight (DW,) a rate that was 30-fold that of non-modified energycane, in addition to almost doubling the total fatty acid content in leaves to 4.42% of its DW. Pearson’s correlation analysis showed that the accumulation of TAG had the highest correlation with the expression level of ZmDGAT1-2, followed by the level of RNAi suppression for SDP1.

Conclusions

This is the first report on the metabolic engineering of energycane and demonstrates that this resilient, high-biomass crop is an excellent target for the further optimization of the production of lipids from vegetative tissues.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-022-00753-7.

Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids

Energy cane is a dedicated crop to high biomass production and selected during Saccharum breeding programs to fit specific industrial needs for 2G bioethanol production. Internode elongation is one of the most important characteristics in Saccharum hybrids due to its relationship with crop yield. In this study, we selected the third internode elongation of the energy cane. To characterize this process, we divided the internode into five sections and performed a detailed transcriptome analysis (RNA-Seq) and cell wall characterization. The histological analyses revealed a remarkable gradient that spans from cell division and protoxylem lignification to the internode maturation and complete vascular bundle lignification. RNA-Seq analysis revealed more than 11,000 differentially expressed genes between the sections internal. Gene ontology analyzes showed enriched categories in each section, as well as the most expressed genes in each section, presented different biological processes. We found that the internode elongation and division zones have a large number of unique genes. Evaluated the specific profile of genes related to primary and secondary cell wall formation, cellulose synthesis, hemicellulose, lignin, and growth-related genes. For each section these genes presented different profiles along the internode in elongation in energy cane. The results of this study provide an overview of the regulation of gene expression of an internode elongation in energy cane. Gene expression analysis revealed promising candidates for transcriptional regulation of energy cane lignification and evidence key genes for the regulation of internode development, which can serve as a basis for understanding the molecular regulatory mechanisms that support the growth and development of plants in the Saccahrum complex.

Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane

Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER (TFL)-like genes. As expected, these genes all show very high homology to their corresponding genes in Sorghum, and also to FT-like, MFT-like, and TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot. High expression levels of ScFT3 in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that ScFT3 is likely to play a role in floral induction in sugarcane; however, other sugarcane FT-like genes may also be involved in the flowering process.

Silicon as a Sustainable Option to Increase Biomass With Less Water by Inducing Carbon:Nitrogen:Phosphorus Stoichiometric Homeostasis in Sugarcane and Energy Cane

Climate change has prolonged periods of water deficit in sugarcane and energy cane crops. This condition induces an imbalance of the carbon (C): nitrogen (N): phosphorus (P) stoichiometric homeostasis, impairing accumulated nutrients from being converted into biomass. Silicon (Si) supplementation can mitigate the damage caused by water deficit in plants by improving the C:N:P balance, increasing C, N, and P use efficiencies and the biomass conversion, and reducing climate change effects on crops. This study assesses the beneficial effects of Si applied through fertigation associated with foliar spraying on the alleviation of damage caused by severe water deficit in sugarcane and energy cane for intermediate and long periods. In addition, the effects in maintenance of nutritional homeostasis we assessed and C, N, and P use efficiencies on sugarcane and energy cane under those conditions were increased. Four experiments were conducted during the first growth cycle of each species. The effect of fertigation associated with Si foliar spraying was evaluated by applying Si only during the seedling formation phase in sugarcane and energy cane grown under severe water deficit for 60 days after transplanting (intermediate period). Then, the effect of Si applied during seedling formation and supplemented after transplanting was evaluated in sugarcane and energy cane grown under severe water deficit for 160 days after transplanting (long period). The Si supply decreased C contents, modified the C:N:P ratio, and increased C, N, and P use efficiencies in plants of both species under water deficit at the intermediate and long periods after transplanting. The effects of applying Si through fertigation associated with foliar spraying during seedling formation mitigated the damage caused by severe water deficit in the intermediate period, which was mainly observed in sugarcane. When supplemented with Si after transplanting, the mitigating effects occurred in both species under severe long period water deficit. Therefore, the Si supply through fertigation associated with foliar spraying is a viable alternative to provide Si to the plant. It also comes with beneficial effects that partially reverse the damage to nutritional homeostasis and increase nutritional efficiency in plants under severe water deficit.

Silage Quality of two energy-cane cultivars produced with different additives

ABSTRACT This study examined the quality of silage from two cultivars of energy cane (Saccharum spontaneum) produced with different additives. The experiment was laid out in a completely randomized design with a 2×5 factorial arrangement of treatments consisting of two cultivars (VG3, VG1126) and four additives (1% urea; 1% NaOH; 1% CaO; and 1.0 × 1011 CFU g-1 of Lactobacillus plantarum- LP) + control, with eight replicates. Experimental mini-silos were used, which were opened 72 days after ensiling. The dry matter (DM), crude protein (CP), organic matter (OM), mineral matter (MM), ether extract (EE), neutral detergent fiber (NDF) and acid detergent fiber (ADF) contents, and silage degradability were. We identified significant interactions effect between cultivar and type of additive for DM, CP, EE, NDF. ADF. Organic and mineral matter percentage were similar between the two cultivars. LP was the least beneficial additive for DM degradation.After 72 h of fermentation, in vitro NDF degradation of cultivar VG3 increased due to urea, NaOH, and CaO, whereas degradation cultivar VG1126 decreased when inoculated with LP or CaO. The NaOH and CaO improved silage degradability thus improving its quality. The use of LP in the present study did not benefit silage for energy-cane cultivars. The use of NaOH and CaO improves the quality of the silage, two varieties of sugarcane energy VG3 and VG1126, enabling its use with better efficiency for animal feed.

Metabolite profiles of energy cane and sugarcane reveal different strategies during the axillary bud outgrowth

Commercial cultivation of sugarcane is usually carried out by planting culm segments (sett) carrying buds in their internodes. However, this is an inefficient practice due to high sprouting irregularity. In this work, we inspect the first stages of the physiological preparation of the culm for sprouting, trying to identify compounds that actively participate in this process. We compared, during the first 48 h, the metabolic profile of sugarcane against energy cane, a cultivar known to have higher sprouting speed and consistency. In fact, during this short period it was possible to observe that energy cane already had a higher physiological activity than sugarcane, with significant changes in the catabolism of amino acids, increased levels of reducing sugars, lipids and metabolic activity in the phenylpropanoid pathway. On the other hand, sugarcane samples had just begun their activity during this same period, with an increase in the level of glutamate as the most significant change, which may be linked to the strategy of these cultivars to develop their roots before leaves, opposite of what is seen for energy cane. These results contribute to the development of strategies for increasing the efficiency of sprouting in sugarcane.

Genomic Selection in Sugarcane: Current Status and Future Prospects

Sugarcane is a C4 and agro-industry-based crop with a high potential for biomass production. It serves as raw material for the production of sugar, ethanol, and electricity. Modern sugarcane varieties are derived from the interspecific and intergeneric hybridization between Saccharum officinarum, Saccharum spontaneum, and other wild relatives. Sugarcane breeding programmes are broadly categorized into germplasm collection and characterization, pre-breeding and genetic base-broadening, and varietal development programmes. The varietal identification through the classic breeding programme requires a minimum of 12-14 years. The precise phenotyping in sugarcane is extremely tedious due to the high propensity of lodging and suckering owing to the influence of environmental factors and crop management practices. This kind of phenotyping requires data from both plant crop and ratoon experiments conducted over locations and seasons. In this review, we explored the feasibility of genomic selection schemes for various breeding programmes in sugarcane. The genetic diversity analysis using genome-wide markers helps in the formation of core set germplasm representing the total genomic diversity present in the Saccharum gene bank. The genome-wide association studies and genomic prediction in the Saccharum gene bank are helpful to identify the complete genomic resources for cane yield, commercial cane sugar, tolerances to biotic and abiotic stresses, and other agronomic traits. The implementation of genomic selection in pre-breeding, genetic base-broadening programmes assist in precise introgression of specific genes and recurrent selection schemes enhance the higher frequency of favorable alleles in the population with a considerable reduction in breeding cycles and population size. The integration of environmental covariates and genomic prediction in multi-environment trials assists in the prediction of varietal performance for different agro-climatic zones. This review also directed its focus on enhancing the genetic gain over time, cost, and resource allocation at various stages of breeding programmes.

Effects of Energy Cane (Saccharum spp.) Juice on Corn Ethanol (Zea mays) Fermentation Efficiency: Integration towards a More Sustainable Production

Despite being considered renewable, corn (Zea mays) ethanol still generates much debate over the use of fossil fuels in its production and is considered less sustainable than sugarcane (Saccharum spp.) ethanol. In Brazil, corn ethanol is starting to be produced in the Center-West and is expected to increase with the RenovaBio, a promising policy for biofuels adoption. In this context, energy cane (Saccharum spp.) is a biomass crop with high yields that can provide bagasse to supply the energy demand of the corn ethanol industry and provide juice with about 10% sugar content. However, the effects of introducing its juice in the production process are unknown. For these reasons, the objective of this study was to assess the effects of adding energy cane juice in corn ethanol production. Energy cane juice brings several advantages: (i) It provides sugars that can reduce by almost 50% the amount of corn and enzymes used, (ii) reduces the amount of water needed for ethanol production, and (iii) increases significantly the fermentation efficiency from 86.4% to 90.8% by providing minerals that support yeast growth. Therefore, energy cane can be integrated into the corn ethanol production process, making the fermentation more efficient and the production systems more sustainable.

Balancing sugar recovery and inhibitor generation during energycane processing: Coupling cryogenic grinding with hydrothermal pretreatment at low temperatures

Pretreatment of lignocellulosic biomass at high temperatures or with oxidizing chemicals generate various inhibitors that restrict the efficient bioconversion of sugars in subsequent steps. The present study systematically investigates individual and combinatorial effects of pretreatment parameters on the generation of inhibitors. A plot between pretreatment temperature and inhibitor revealed optimum pretreatment temperature for energycane bagasse i.e., 170 °C beyond which total inhibitor production increased exponentially. No inhibitor production was observed on mechanical processing i.e., disk milling/cryogenic grinding of biomass. Evaluation of response surface regression exhibited that biomass solids loading has a significant effect on inhibitor generation at higher temperatures. The concentrations of certain inhibitors such as acetic acid, furfurals, and HMF increased more than 3-folds on doubling the solids loading. Furthermore, a novel low-severity approach of low-temperature hydrothermal pretreatment coupled with cryogenic grinding for lignocellulosic biomasses has been introduced which improved sugar yields while maintaining a low inhibitor concentration.

Chemical Free Two-Step Hydrothermal Pretreatment to Improve Sugar Yields from Energy Cane

Energy cane is an attractive lignocellulosic feedstock for processing into biofuels and bioproducts. A low-severity two-step hydrothermal pretreatment was investigated on energy cane for the production of monomeric sugar. Pretreatment temperature and time, in addition to the effect of disk milling, were observed for the glucose and xylose yields during hydrolysis. At residence times above 5 min in case of pretreatment at 200 °C, all of the hemicellulose was observed to be solubilized. The pretreatment condition of 200 °C for 10 min with disk milling was observed to provide the highest glucose concentration of 5.4%, and 200 °C for 5 min with disk milling provided the highest xylose concentration of 2.15%. The effect of disk milling in improving the sugar concentrations during hydrolysis was significant, especially at lower pretreatment temperatures and times. Low xylose yields at higher temperatures were attributed to the formation of degradation products at increased severity.

Techno-Economic and Environmental Assessment of Biomass Gasification and Fischer–Tropsch Synthesis Integrated to Sugarcane Biorefineries

Large-scale deployment of both biochemical and thermochemical routes for advanced biofuels production is seen as a key climate change mitigation option. This study addresses techno-economic and environmental aspects of advanced liquid biofuels production alternatives via biomass gasification and Fischer–Tropsch synthesis integrated to a typical sugarcane distillery. The thermochemical route comprises the conversion of the residual lignocellulosic fraction of conventional sugarcane (bagasse and straw), together with eucalyptus and energy-cane as emerging lignocellulosic biomass options. This work promotes an integrated framework to simulate the mass and energy balances of process alternatives and incorporates techno-economic analyses and sustainability assessment methods based on a life-cycle perspective. Results show that integrated biorefineries provide greenhouse gas emission reduction between 85–95% compared to the fossil equivalent, higher than that expected from a typical sugarcane biorefinery. When considering avoided emissions by cultivated area, biorefinery scenarios processing energy-cane are favored, however at lower economic performance. Thermochemical processes may take advantage of the integration with the typical sugarcane mills and novel biofuels policies (e.g., RenovaBio) to mitigate some of the risks linked to the implementation of new biofuel technologies.

High-Level Production of Recombinant Snowdrop Lectin in Sugarcane and Energy Cane

Sugarcane and energy cane (Saccharum spp. hybrids) are ideal for plant-based production of recombinant proteins because their high resource-use efficiency, rapid growth and efficient photosynthesis enable extensive biomass production and protein accumulation at a cost-effective scale. Here, we aimed to develop these species as efficient platforms to produce recombinant Galanthus nivalis L. (snowdrop) agglutinin (GNA), a monocot-bulb mannose-specific lectin with potent antiviral, antifungal and antitumor activities. Initially, GNA levels of 0.04% and 0.3% total soluble protein (TSP) (0.3 and 3.8 mg kg^–1 tissue) were recovered from the culms and leaves, respectively, of sugarcane lines expressing recombinant GNA under the control of the constitutive maize ubiquitin 1 (Ubi) promoter. Co-expression of recombinant GNA from stacked multiple promoters (pUbi and culm-regulated promoters from sugarcane dirigent5-1 and Sugarcane bacilliform virus) on separate expression vectors increased GNA yields up to 42.3-fold (1.8% TSP or 12.7 mg kg^–1 tissue) and 7.7-fold (2.3% TSP or 29.3 mg kg^–1 tissue) in sugarcane and energy cane lines, respectively. Moreover, inducing promoter activity in the leaves of GNA transgenic lines with stress-regulated hormones increased GNA accumulation to 2.7% TSP (37.2 mg kg^–1 tissue). Purification by mannose-agarose affinity chromatography yielded a functional sugarcane recombinant GNA with binding substrate specificity similar to that of native snowdrop-bulb GNA, as shown by enzyme-linked lectin and mannose-binding inhibition assays. The size and molecular weight of recombinant GNA were identical to those of native GNA, as determined by size-exclusion chromatography and MALDI-TOF mass spectrometry. This work demonstrates the feasibility of producing recombinant GNA at high levels in Saccharum species, with the long-term goal of using it as a broad-spectrum antiviral carrier molecule for hemopurifiers and in related therapeutic applications.

Role of NGS and SNP genotyping methods in sugarcane improvement programs

Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.

Metabolic Regulation and Development of Energy Cane Setts upon Auxin Stimulus

Energy cane is a bioenergy crop with an outstanding ability to bud sprouting and increasing yield in ratoon cycles even in marginal lands. Bud fate control is key to biomass production and crop profits due to vegetative propagation and tiller dependency, as well as phenotype plasticity to withstand harsh environmental conditions. During the establishment stage (plant cane cycle), energy cane has a tendency for low root:shoot ratio, which might hamper the ability to cope with stress. Auxin is known to modulate bud sprouting and stimulate rooting in sugarcane. Hence, we treated a slow and a fast bud sprouting energy cane cultivars with auxin or controls (with and without water soaking) for 6 h prior to planting and evaluate plant growth parameters and metabolic profiling using two techniques (gas chromatography with time-of-flight mass spectrometer and nuclear magnetic resonance) to characterize the effect and identify metabolite markers associated with bud inhibition and outgrowth. Auxin inhibited bud burst and promote rooting in setts changing the root:shoot ratio of plantlets. Metabolome allowed the identification of lactate, succinate and aspartate family amino acids as involved in bud fate control through the potential modulation of oxygen and energy status. Investigating environmental and biochemical factors that regulate bud fate can be incremental to other monocot species. Our study provides new insights into bud quiescence and outgrowth in cane hybrids, with the potential to leverage our understanding of yield-related traits, crop establishment and adaptation to global climate change.

Genomic resources for energy cane breeding in the post genomics era

Sugarcane is one of the most sustainable energy crops among cultivated crops presenting the highest tonnage of cultivated plants. Its high productivity of sugar, bioethanol and bioelectricity make it a promising green alternative to petroleum. Furthermore, the myriad of products that can be derived from sugarcane biomass has been driving breeding programs towards varieties with a higher yield of fiber and a more vigorous and sustainable performance: the energy cane. Here we provide an overview of the energy cane including plant description, breeding efforts, types, and end-uses. In addition, we describe recently published genomic resources for the development of this crop, discuss current knowledge of cell wall metabolism, bioinformatic tools and databases available for the community.

Relationship between sugarcane culm and leaf biomass composition and saccharification efficiency

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations

Traditional sugarcane cultivars (Saccharum officinarum) proved highly susceptible to diseases, and this led breeders to progress to interspecific crosses resulting in disease resistance. A backcrossing program to S. officinarum was then required to boost sucrose content. Clonal selection across generations and incorporation of other germplasm into cultivated backgrounds established the (narrow) genetic base of modern cultivars (Saccharum spp.), which have a man-made genome. The genome complexity has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution, architecture, and cytogenetics. However, there is a critical shortage of information on chromosome behavior throughout meiosis in modern cultivars. In this study, we examined the microsporogenesis of a contemporary variety, providing a detailed analysis of the meiotic process and chromosome association at diakinesis, using FISH with centromeric probes. Chromosomal abnormalities were documented by examining high quality preparations of pollen mother cells (700 in total). Approximately 70% of the cells showed abnormalities, such as metaphase chromosomes not lined up at the plate, lagging chromosomes and chromosomal bridges, and tetrad cells with micronuclei. Some dyads with asynchronous behavior were also observed. Due to the hybrid composition of the sugarcane genome, we suggest that bivalent incomplete pairing may occur in the first prophase leading to univalency. The presence of rod bivalents showing the lagging tendency is consistent with a reduction in chiasma frequency. Finally, the presence of chromatin bridges indicates the indirect occurrence of chromosomal inversions, although chromosome fragments were not clearly recognized. Possible reasons for such meiotic abnormalities and the large prevalence of bivalent formation are discussed.

Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers

The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: Φ^ST = 0.211 and S. spontaneum: Φ^ST = 0.216, P<0.001), and significant contribution of the latter in the genetic variability of commercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny.

Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement

Lignocellulosic biomass has become an emerging feedstock for second-generation bioethanol production. Sugarcane (Saccharum spp. hybrids), a very efficient perennial C4 plant with a high polyploid level and complex genome, is considered a top-notch candidate for biomass production due to its salient features viz. fast growth rate and abilities for high tillering, ratooning, and photosynthesis. Energy cane, an ideal type of sugarcane, has been bred specifically as a biomass crop. In this review, we described (1) biomass potentials of sugarcane and its underlying genetics, (2) challenges associated with biomass improvement such as large and complex genome, narrow gene pool in existing commercial cultivars, long breeding cycle, and non-synchronous flowering, (3) available genetic resources such as germplasm resources, and genomic and cell wall-related databases that facilitate biomass improvement, and (4) mining candidate genes controlling biomass in genomic databases. We extensively reviewed databases for biomass-related genes and their usefulness in biofuel generation. This review provides valuable resources for sugarcane breeders, geneticists, and broad scientific communities involved in bioenergy production.

The Challenge of Analyzing the Sugarcane Genome

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.

Visualizing chemical functionality in plant cell walls

Understanding plant cell wall cross-linking chemistry and polymeric architecture is key to the efficient utilization of biomass in all prospects from rational genetic modification to downstream chemical and biological conversion to produce fuels and value chemicals. In fact, the bulk properties of cell wall recalcitrance are collectively determined by its chemical features over a wide range of length scales from tissue, cellular to polymeric architectures. Microscopic visualization of cell walls from the nanometer to the micrometer scale offers an in situ approach to study their chemical functionality considering its spatial and chemical complexity, particularly the capabilities of characterizing biomass non-destructively and in real-time during conversion processes. Microscopic characterization has revealed heterogeneity in the distribution of chemical features, which would otherwise be hidden in bulk analysis. Key microscopic features include cell wall type, wall layering, and wall composition-especially cellulose and lignin distributions. Microscopic tools, such as atomic force microscopy, stimulated Raman scattering microscopy, and fluorescence microscopy, have been applied to investigations of cell wall structure and chemistry from the native wall to wall treated by thermal chemical pretreatment and enzymatic hydrolysis. While advancing our current understanding of plant cell wall recalcitrance and deconstruction, microscopic tools with improved spatial resolution will steadily enhance our fundamental understanding of cell wall function.

Allometric Models for Predicting Aboveground Biomass and Carbon Stock of Tropical Perennial C4 Grasses in Hawaii

Biomass is a promising renewable energy option that provides a more environmentally sustainable alternative to fossil resources by reducing the net flux of greenhouse gasses to the atmosphere. Yet, allometric models that allow the prediction of aboveground biomass (AGB), biomass carbon (C) stock non-destructively have not yet been developed for tropical perennial C₄ grasses currently under consideration as potential bioenergy feedstock in Hawaii and other subtropical and tropical locations. The objectives of this study were to develop optimal allometric relationships and site-specific models to predict AGB, biomass C stock of napiergrass, energycane, and sugarcane under cultivation practices for renewable energy and validate these site-specific models against independent data sets generated from sites with widely different environments. Several allometric models were developed for each species from data at a low elevation field on the island of Maui, Hawaii. A simple power model with stalk diameter (D) was best related to AGB and biomass C stock for napiergrass, energycane, and sugarcane, (R² = 0.98, 0.96, and 0.97, respectively). The models were then tested against data collected from independent fields across an environmental gradient. For all crops, the models over-predicted AGB in plants with lower stalk D, but AGB was under-predicted in plants with higher stalk D. The models using stalk D were better for biomass prediction compared to dewlap H (Height from the base cut to most recently exposed leaf dewlap) models, which showed weak validation performance. Although stalk D model performed better, however, the mean square error (MSE)-systematic was ranged from 23 to 43 % of MSE for all crops. A strong relationship between model coefficient and rainfall was existed, although these were irrigated systems; suggesting a simple site-specific coefficient modulator for rainfall to reduce systematic errors in water-limited areas. These allometric equations provide a tool for farmers in the tropics to estimate perennial C₄ grass biomass and C stock during decision-making for land management and as an environmental sustainability indicator within a renewable energy system.

Kinetics of SO2-ethanol-water (AVAP®) fractionation of sugarcane straw

Kinetics of SO2-ethanol-water (AVAP®) fractionation was determined for sugarcane (SC) straw in terms of pulp composition (non-carbohydrate components, cellulose, hemicelluloses) and properties (kappa number, pulp intrinsic viscosity in CED and cellulose degree of polymerization). Effect of temperature (135-165°C) and time (18-118min) was studied at fixed liquor composition (SO2/ethanol/water=12:22.5:65.5, w/w) and a liquor-to-solid ratio (4Lkg(-1)). Interpretation is given in terms of major fractionation reactions, removal of non-carbohydrate components and xylan, as well as acid hydrolysis of cellulose, and is compared to other lignocellulosic substrates (beech, spruce and wheat straw). Overall, SO2-ethanol-water process efficiently fractionates SC straw by separating cellulose from both non-carbohydrate components and xylan while reducing cellulose DP.

Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane

Sugarcane is the main source of the world's sugar and is becoming increasingly important as a source of biofuel. The highly polyploid and heterozygous nature of the sugarcane genome has meant that characterization of the genome has lagged behind that of other important crops. Here we developed a method using a combination of quantitative PCR with a transposable marker system to score the relative number of alleles with a transposable element (TE) present at a particular locus. We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes. We showed how this method could be used in various ways. First, we showed that the method could be extended to be used as part of a genotyping system. Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex. Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum.