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Saccharum

Saccharum is a genus of grasses that includes several species of sugarcane, a valuable crop cultivated worldwide for its sugar-rich stems.
These tall, perennial grasses are characterized by their thick, juicy stalks and distinctive inflorescences.
Saccharum species are widely used for the production of sucrose, biofuels, and other industrial products.
This genus is of great economic importance, particularly in tropical and subtropical regions where sugarcane is a major agricultural commodity.
Researchers can optimize their Saccharum studies by leveraging PubCompare.ai's AI-powered platform, which enhances reproducibility by helping identify the best protocols and products from literature, preprints, and patents.
This innovative tool can streamline the research process and improve results.

Most cited protocols related to «Saccharum»

Optimized DNA Extraction from Recalcitrant Plants

Cited 27 times

Since the advent of the CTAB-based extraction method from plant leaves by Doyle and Doyle in 1987, many different iterations have been published, each with modifications to contend with the co-extractives of polyphenolics and polysaccharides present in the leaves of many plant species [3 ,5 (link)-8 (link),15 (link)]. While having demonstrated their effectiveness for isolating DNA that is suitable for PCR amplification or restriction digests, all methods currently published in the literature require long incubations, and multiple precipitation steps and ethanol washes to produce RNA-free genomic DNA of high purity. As next-generation sequencing requires large amounts of high quality DNA, each additional precipitation and wash increases handling time and lowers overall yield. Commercial column based extraction kits, such as DNeasy (Qiagen, Australia) or Wizard (Promega, Australia), are effective for isolating contaminant free DNA from recalcitrant plant species, including eucalypts [4 (link),16 (link)]. However, commercial kits can be expensive and carry the risk of losing DNA on the column, which in turn necessitates several extractions followed by pooling of DNA.
To test the modifications made to the extraction method (NGS protocol) against the well-established original CTAB method (used routinely in our laboratory to reliably extract high quality DNA from rice, sugarcane, barley and wheat for sequencing [17 ,18 (link)]), six grams of frozen Corymbia citriodora subsp. variegata leaf tissue was ground and aliquoted evenly into the extractions described below. The quality of DNA from each extraction was verified spectrophotometrically using a NanoDrop instrument and agarose gel electrophoresis. The NanoDrop absorbance profile is useful for detecting contamination such as protein, salts or polysaccharides, all of which can inhibit NGS library preparation. High quality DNA is characterized as having a 260/280 nm absorbance ratio of approximately 1.8, with a single absorbance peak at 260 nm. The spectrophotometric profile is also useful for detecting phenolic oxidation, as the aromatic structure will absorb at 230 and 270 nm [1 ]. If oxidation is suspected to have occurred, endonuclease digestion can be used to further assess DNA quality before library preparation as phenolics, which inhibit polymerases, also inhibit restriction enzymes [8 (link),9 ].
Visualization of DNA on an agarose gel provides evidence of band shearing and RNA and polysaccharide contamination. Mechanical disruption, such as vortexing, causes DNA strands to shred apart, indicated by a wide DNA band with poor resolution. NGS library submission requires intact, high molecular weight genomic DNA, so all solution mixing steps were done by gentle inversion. Gel electrophoresis is also beneficial for visualizing RNA and polysaccharides, both of which contaminate sequencing reactions. RNA is evident as a distinct banding pattern at various sizes throughout the gel, whereas polysaccharides will migrate quickly and conglomerate at the bottom of the gel as a non-distinct fluorescent structure. Yield was determined through relative band intensity approximation with 100 and 200 ng λ DNA standards, as the NanoDrop concentration readings can inflate yield of genomic DNA.

Healey A., Furtado A., Cooper T, & Henry R.J. (2014). Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods, 10, 21.

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Publication 2014

Cardiac Arrest Cetrimonium Bromide Digestion DNA Library DNA Restriction Enzymes Electrophoresis Electrophoresis, Agar Gel Endonuclease Ethanol Freezing Genome Hordeum vulgare Inversion, Chromosome Plant Leaves Plants Polysaccharides Promega Proteins Rice Saccharum Salts Sepharose Spectrophotometry Tissues Triticum aestivum

Quantifying Lignin in Cell Walls

Cited 25 times

Protein-free cell wall sample (20 mg) was placed into a screw-cap centrifuge tube containing 0.5 ml of 25% acetyl bromide (v/v in glacial acetic acid) and incubated at 70°C for 30 min. After complete digestion, the sample was quickly cooled in an ice bath, and then mixed with 0.9 ml of 2 M NaOH, 0.1 ml of 5 M hydroxylamine-HCl, and a volume of glacial acetic acid sufficient for complete solubilization of the lignin extract (4 ml for soybean tissues or 6 ml for sugarcane bagasse). After centrifugation (1,400×g, 5 min), the absorbance of the supernatant was measured at 280 nm [21] (link). A standard curve was generated with alkali lignin (Aldrich 37, 096-7) and the absorptivity (ε) value obtained was 22.9 g⁻¹L cm⁻¹. The results were expressed as mg lignin g⁻¹ cell wall.

Moreira-Vilar F.C., Siqueira-Soares R.D., Finger-Teixeira A., de Oliveira D.M., Ferro A.P., da Rocha G.J., Ferrarese M.D., dos Santos W.D, & Ferrarese-Filho O. (2014). The Acetyl Bromide Method Is Faster, Simpler and Presents Best Recovery of Lignin in Different Herbaceous Tissues than Klason and Thioglycolic Acid Methods. PLoS ONE, 9(10), e110000.

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Publication 2014

Acetic Acid acetyl bromide Alkalies bagasse Bath Cell Wall Centrifugation Digestion Gastrin-Secreting Cells Hydroxylamine Lignin Proteins Saccharum Soybeans Tissues

qRT-PCR of Sugarcane Reference Genes

Cited 17 times

An ABI 7500 Real Time PCR machine (Applied Biosystems, Foster City, CA, USA) and its default program (2 min at 50°C and 10 min at 95°C followed by 40 cycles at 94°C for 15 s, and at 60°C for 60 s.) were employed for qRT-PCR with a reaction mixture volume of 20 µL in an optical 96-well plate. 10 µL of SYBR Green Master Mix (Roche), 10 pM of each primer, 10 ng of final cDNA and 6.4 µL of RNase-free water were added to the reaction mixture. A control was also included in each plate with 2.0 µL of RNase-free water as a template. Three technical replicates were contained in each plate. Specificity verification of the PCR amplification dissociation and the PCR efficiency curves were determined for each candidate reference gene prior to the qRT-PCR evaluation of these genes in sugarcane.

Ling H., Wu Q., Guo J., Xu L, & Que Y. (2014). Comprehensive Selection of Reference Genes for Gene Expression Normalization in Sugarcane by Real Time Quantitative RT-PCR. PLoS ONE, 9(5), e97469.

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Publication 2014

2-5A-dependent ribonuclease DNA, Complementary Genes Oligonucleotide Primers Real-Time Polymerase Chain Reaction RNase 2 Saccharum SYBR Green I

Comprehensive Sugarcane Genome Annotation

Cited 15 times

Structural annotation was performed using EuGene 4.2a (http://eugene.toulouse.inra.fr), which combines evidence from alternative splice site detection, sequence model training, genome masking, transcript mapping, and protein homology to define confident gene models. The R570 cultivar RNA transcripts, together with transcripts from six sugarcane genotypes produced by Cardoso-Silva et al.^{65 (link)}, were aligned on the sugarcane STP using GMAP (https://github.com/juliangehring/GMAP-GSNAP/) and best-scoring hits were kept. The resulting alignments were integrated as sugarcane transcript evidence in the prediction process. Protein sequences from the reference sorghum proteome (Phytozome, release 3.1.1) were aligned with the sugarcane STP using BLASTX to obtain protein homology evidence.
Gene function annotation was assigned based on sequence and domain conservation. Protein sequences were aligned with SwissProt, TrEMBL, and sorghum datasets by BLASTP using an E-value threshold of 1e-10. Best-hit BLAST results were then used to define the gene functions. Moreover, InterProScan =(https://www.ebi.ac.uk/interpro/search/sequence-search) was performed to annotate protein domains, extending the annotation to Gene Ontology terms associated with these protein domains. The predicted gene models were finally screened to remove models that could correspond to TEs using CENSOR (https://www.girinst.org/censor/)^{66 (link)} resulting in a total of 25,316 sugarcane genes annotated on the STP.

Garsmeur O., Droc G., Antonise R., Grimwood J., Potier B., Aitken K., Jenkins J., Martin G., Charron C., Hervouet C., Costet L., Yahiaoui N., Healey A., Sims D., Cherukuri Y., Sreedasyam A., Kilian A., Chan A., Van Sluys M.A., Swaminathan K., Town C., Bergès H., Simmons B., Glaszmann J.C., van der Vossen E., Henry R., Schmutz J, & D’Hont A. (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9, 2638.

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Publication 2018

Alternative Splice Sites Amino Acid Sequence Gene Annotation Genes Genome Genotype Operator, Genetic Protein Domain Proteins Proteome Saccharum Self Confidence Sorghum

Sugarcane Biotic and Abiotic Stress Protocols

Cited 14 times

Smut whips were collected in the most popular cultivar “ROC”22 in the Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture (Fuzhou, China), and stored at 4°C. Sugarcane varieties of Yacheng05–179 (smut resistant) and Liucheng03–182 (smut susceptible) were cultivated in the Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture (Fuzhou, China). All of the treatments were repeated independently three times.
For tissue distribution studies, six healthy 10 month old plants were selected. For each plant, the youngest fully expanded leaf viz +1 leaf with a visible dewlap (the collar between the leaf blade and sheath), all the buds, stem epidermis and the stem pith were taken for RNA extraction.
During biotic treatments, two-bud sets of both sugarcane genotypes, Yacheng05–179 and Liucheng03–182, were inoculated with 0.5 µL suspension containing 5×10⁶ spores·mL⁻¹ in 0.01% (v/v) Tween-20, while controls were mock inoculated with 0.01% (v/v) Tween-20 in sterile distilled water instead of spores [25] , [26] (link). All the inoculated sets were grown at 28°C in condition of 12 h light/12 h dark. Five buds from each of both genotypes were collected at each of the time point of 0 h, 6 h, 12 h, 24 h, 48 h, 72 h and 96 h. Samples were frozen in liquid nitrogen, and stored at −80°C.
During abiotic treatments, uniform four-month-old sugarcane tissue cultured plantlets of Yacheng05–179 were grown in water for one week and then transferred to the following seven different treatments in conical tubes at 28°C with 16 h light/8 h dark. The plantlets were treated with 5 mM SA solution, 25 µM MeJA (methyl jasmonate) in 0.1% (v/v) ethanol and 0.05% (v/v) Tween-20, 100 µM ABA, and 25% PEG (polyethylene glycol), and the plantlets were set to different periods of time (0 h, 6 h, 12 h and 24 h), respectively. In addition, plantlets were separately treated with 250 mM NaCl and 100 µM CuCl₂ (copper chloride) for 0 h, 12 h, 24 h and 48 h [27] , [28]
_. For H₂O₂ stress, the leaves were sprayed with 10 mM H₂O₂, and the sampling time points were 0 h, 6 h, 12 h and 24 h, respectively. After treatments, three sugarcane plantlets per time point were collected and immediately fixed in liquid nitrogen, and then kept at −80°C until used for analysis.

Su Y., Guo J., Ling H., Chen S., Wang S., Xu L., Allan A.C, & Que Y. (2014). Isolation of a Novel Peroxisomal Catalase Gene from Sugarcane, Which Is Responsive to Biotic and Abiotic Stresses. PLoS ONE, 9(1), e84426.

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Publication 2014

Aftercare Chlorides Copper cupric chloride Epidermis Ethanol Freezing Genotype Hartnup Disease Light methyl jasmonate Nitrogen Peroxide, Hydrogen Plants Polyethylene Glycols Saccharum Sodium Chloride Spores Stem, Plant Sterility, Reproductive Tissues Tween 20 Ustilaginales

Most recents protocols related to «Saccharum»

Diverse Agroecosystem Soil Sampling

Cited 1 time

A total of 90 soil samples were used for this research. Soils were collected in five different plots under different land uses in the Everglades Agricultural Area (EAA) including an unmanaged native plot (plot 1), a sugarcane-spinach-fallow-sugarcane rotation plot (plot 2), a sugarcane-sweetcorn-rice-sugarcane rotation plot (plot 3), a sugarcane-sweetcorn-fallow-sugarcane rotation plot (plot 4), and a year-round sugar cane plantation plot (plot 5). Plots 2–5 had been historically cultivated with sugar cane for 2 (plot 5) or 3 (plot 2–4) years. Starting from January 2017, plot 2 was planted with spinach till May 2017, followed by a 28-week fallow period before sugar cane plantation in December 2017. Plot 3 was planted with sweet corn from January to May 2017, followed by rice cultivation from May to October 2017 and an 8-week fallow period before sugar cane plantation in December 2017. Plot 4 was planted with sweet corn from January to May 2017, also followed by a 28-week fallow before sugar cane plantation in December 2017. Plot 5 was cultivated with sugar cane for a third consecutive year. Soils were collected during May 2017 to April 2018 at 2–3-month intervals. The area of each plot is ~20,000 m² (~100 × 200 m square). Biological triplicates were sampled in each plot, each containing 9 random cores of 10-cm topsoil within a subplot of ~10 × 10 m square, and the samples were immediately transported to the laboratory on ice. Part of the soil samples were stored in –20°C before DNA extraction.

Zhao J., Rodriguez J, & Martens-Habbena W. (2023). Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils. Frontiers in Microbiology, 14, 1140487.

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Publication 2023

Biopharmaceuticals Oryza sativa Saccharum Spinach

Sampling Protocol of Western Kenya Sites

The sites of isolation that represented Western Kenya were selected based on centric random systematic sampling from respective counties and subcounties (Figure 1). They were Lurambi (N 0° 0.29“; E 34° 69.71′) in Kakamega County, Emuhaya (N 0° 5.42′; E 34° 34.65′) in Vihiga County, Teso South (N 0° 33.729′; E 34° 16.21′) in Busia County, and Chaptais (N 0° 48.36′; E 34° 28.26′) in Bungoma County. Samples were collected during mid of June 2021. The main source of income of Western Kenya inhabitants is mixed agricultural farming [22 (link)]. Sugarcane, maize, beans, finger millets, bananas, and sweet potatoes are among the main food and cash crops grown in the region [23 ]. Western Kenya is typically hot and humid, with year-round rainfall. According to the World Bank Climate Change Knowledge Portal, it is indicated that it received average temperature of 21.28°C and an average rainfall of 2233.59 mm in the year 2021.

Kiprotich K., Muoma J., Omayio D.O., Ndombi T.S, & Wekesa C. (2023). Molecular Characterization and Mineralizing Potential of Phosphorus Solubilizing Bacteria Colonizing Common Bean (Phaseolus vulgaris L.) Rhizosphere in Western Kenya. International Journal of Microbiology, 2023, 6668097.

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Publication 2023

Agricultural Crops Banana Climate Change Eleusine coracana Food isolation Maize Potato, Sweet Saccharum

Malaria Epidemiology in Lake Victoria Region

The study was carried out in the Nyakach and Muhoroni Sub-County of Kisumu County in western Kenya near the shores of Lake Victoria at latitude 0.333333°S and longitude 34.99100°E. Based on malaria prevalence and incidence, malaria vector densities and topographical features [4 (link), 7 (link), 17 (link), 18 (link)], the study area was divided into three eco-epidemiological zones: Kano Plains, Lowland Lakeshore and Highland Plateau. The Kano Plains is characterized by a shallow inland plain with an elevation of about 1150 m to 1200 m, frequented by flooding during the rainy season, with rice irrigation and sugarcane plantation as the main cash crops. The Lowland Lakeshore and Highland Plateau eco-epidemiological zones have previously been described [7 (link)]. Each ecological zone was further randomly selected with 24 clusters for study. Based on the administrative village or natural boundary, such as a river or major road, a cluster was delineated with approximately 1 km2 area. Each study area had around 150 households, with an average of about 400 residents under the management of a CHV. Malaria prevalence in the study area is estimated to be around 18% [7 (link)], with the common vectors of malaria transmission being Anopheles funestus and Anopheles gambiae [18 (link)].

Otambo W.O., Ochwedo K.O., Omondi C.J., Lee M.C., Wang C., Atieli H., Githeko A.K., Zhou G., Kazura J., Githure J, & Yan G. (2023). Community case management of malaria in Western Kenya: performance of community health volunteers in active malaria case surveillance. Malaria Journal, 22, 83.

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Publication 2023

Anopheles Anopheles gambiae Cloning Vectors Crop, Avian Households Malaria Oryza sativa Rain Rivers Saccharum Transmission, Communicable Disease

Nitrogen Inputs in Agricultural Systems

Total N input to agricultural systems was calculated by summing N inputs in the form of SNF, ANM, atmospheric N deposition, and BNF.
We collected historical data on SNF use on cropland for each EAC state from 1961 to 2018 from the FAOstat and the IFAstat databases (FAOSTAT 2018 ; IFASTAT 2018 ). Historical data on ANM applied to cropland from 1961 to 2018 for each EAC state were accessed from the FAOstat database. We estimated atmospheric N deposition (deposition of oxidized and reduced N compounds) for each EAC state by multiplying the regional estimate of atmospheric N deposition onto cropland reported in Dentener et al. (2006 ) by the annual cropland area from 1961 to 2018. N input from BNF in agricultural land by N-fixing crops included in the FAOstat database (FAOSTAT 2018 ) was calculated using a yield-based model, assuming that crop yield is the best aggregator of crop-related variables associated with soil and climatic conditions, such as N availability, soil moisture, stand vigor, and other management factors affecting N₂ fixation, as shown in equation (1) (Lassaletta et al. 2014 ).

N Fixed = % N d f a \times \frac{Crop yield}{NHI} \times BGN

Where %Ndfa is the percentage of N uptake resulting from N fixation, Crop yield is the crop harvest (kg N ha^-1yr^-1), NHI is the N harvest index (ratio of N stored in grain over the total amount of grain and straw), BGN is a multiplicative factor that accounts for the proportion of underground N₂ fixation to total N₂ fixation. For N fixing in soybeans, we used a regional %Ndfa. The values of %Ndfa, NHI and BGN used in this study are presented in Table S3. A constant rate of BNF per hectare was also used for sugarcane and rice paddy, as suggested by Herridge et al. (2008 (link)).

Harerimana B., Zhou M., Zhu B, & Xu P. (2023). Regional estimates of nitrogen budgets for agricultural systems in the East African Community over the last five decades. Agronomy for Sustainable Development, 43(2), 27.

Publication 2023

Agricultural Crops Cereals Climate Crop, Avian Nitrogen Fixation Oryza sativa Saccharum Soybeans

Identification of Conserved NBS-LRR Genes

The MCScanX installed in Tbtools (Wang et al., 2012 (link)) was used for rapid identification of intraspecies collinearity NBS-LRR genes with E-value of 10^-5 in the four closely related monocotyledonous species, S. bicolor, M. sinensis, S. spontaneum and S. officinarum. The allelic loss of NBS-LRR gene in S. spontaneum and S.officinarum was calculated based on their genome annotations (http://sugarcane.zhangjisenlab.cn/sgd/html/download.html). Orthofinder-2.5.4 was used to identify homologous genes between the four species, which were conserved NBS-LRR genes, and the comparison software was Blast (E-value=10^-3) (Emms and Kelly, 2015 (link)).

Jiang Z., Zhao M., Qin H., Li S, & Yang X. (2023). Genome-wide analysis of NBS-LRR genes revealed contribution of disease resistance from Saccharum spontaneum to modern sugarcane cultivar. Frontiers in Plant Science, 14, 1091567.

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Publication 2023

Genes Genome Loss of Heterozygosity Saccharum

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What are the different species of Saccharum, and how do they vary in their applications?

The Saccharum genus includes several species of sugarcane, each with its own unique characteristics and applications. The most commonly cultivated species is Saccharum officinarum, which is prized for its high sugar content and is a major source of sucrose worldwide. Other species like Saccharum spontaneum and Saccharum robustum have lower sugar levels but are more hardy and disease-resistant, making them useful for biofuel production and as genetic resources for breeding. Saccharum sinense and Saccharum barberi are ancient cultivars grown in Asia and are valued for their distinct flavors and cultural significance.

What are the key economic and industrial uses of Saccharum?

Saccharum, particularly sugarcane, is of immense economic importance globally. The primary use is for the production of sucrose, which is extracted from the sugar-rich stems and used in a wide range of food and beverage products. Saccharum is also a valuable source of biofuels, with the fibrous biomass being processed into ethanol and other biofuel feedstocks. Additionally, Saccharum has industrial applications, such as the production of paper, textiles, and building materials from its fibers. The versatility of this genus makes it a crucial crop for both food security and renewable energy production.

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More about "Saccharum"

Saccharum, a genus of grasses, includes several species of sugarcane, a valuable crop cultivated worldwide for its sugar-rich stems.
These tall, perennial grasses are characterized by their thick, juicy stalks and distinctive inflorescences.
Saccharum species are widely used for the production of sucrose, biofuels, and other industrial products, making this genus of great economic importance, particularly in tropical and subtropical regions where sugarcane is a major agricultural commodity.
Researchers studying Saccharum can optimize their research by leveraging PubCompare.ai's AI-powered platform, which enhances reproducibility by helping identify the best protocols and products from literature, preprints, and patents.
This innovative tool can streamline the research process and improve results.
To extract high-quality RNA from Saccharum samples, researchers may utilize TRIzol reagent or the RNeasy Plant Mini Kit.
The Agilent 2100 Bioanalyzer or NanoDrop spectrophotometer can be used to assess RNA quality and concentration.
For reverse transcription, the PrimeScript RT reagent kit may be employed.
Saccharum research may also involve the use of Cellic® CTec2, an enzyme cocktail effective in hydrolyzing cellulose and hemicellulose, including the sugar xylose, which is an important constituent of sugarcane biomass.
By incorporating these techniques and tools, along with the AI-powered insights from PubCompare.ai, researchers can streamline their Saccharum studies, enhance reproducibility, and improve the overall quality and efficiency of their research.