Wild Sugarcane Research Articles

Collection, Characterization and Diversity Analysis of New Wild Sugarcane Germplasm Collected from Western Ghats: A Rich Biodiversity Spot in India

Western Ghats in India with diverse climatic condition and different types of vegetation covering the states of Tamil Nadu, Kerala, Karnataka, Goa and Maharashtra, is a biodiversity hot spot. This important area was not explored earlier for sugarcane wild genetic resources. Targeted explorations in these areas resulted in the collection of 39 Saccharum spontaneum (3 in Tamil Nadu, 5 in Kerala, 9 in Karnataka, 4 in Goa and 18 in Maharashtra), 11 Erianthus arundinaceus (3 in Tamil Nadu, 6 in Kerala, 1 in Goa and 1 in Maharashtra), 3 Erianthus bengalense (1 in Tamil Nadu and 2 in Goa) and 2 Saccharum officinarum (one each in Tamil Nadu and Karnataka). S. spontaneum was distributed throughout the regions, while Erianthus species were abundant in Kerala, Goa and Tamil Nadu. S. spontaneum exhibited wide variation for different traits like plant height (312 to 45 cm), leaf length (102 to 21 cm), leaf width (1.3 to 0.2 cm), peduncle length (59 to 16 cm), arrow length (46 to 14 cm), internode length (15.3 to 4.5) and cane diameter (0.8 to 0.3 cm). E. arundinaceus also showed wide range for plant height (631 to 192 cm), leaf width (5.7 to 3.8 cm) and internode length (8.5 to 17 cm). Cluster analysis grouped the germplasm into four clusters, and 97% of the S. spontaneum grouped into Cluster IV. Cluster III had three accessions and all were E. bengalense, while most of the E. arundinaceus accessions were grouped into Cluster I. Genetic diversity of the new germplasm collected and their utilization in sugarcane genetic improvement programme are discussed.

Detection of a major QTL related to smut disease resistance inherited from a Japanese wild sugarcane using GRAS-Di technology.

Smut disease of sugarcane causes considerable yield losses and the use of resistant varieties is the best control practice. Our group identified a Japanese wild sugarcane with highly smut disease resistance named ‘Iriomote8’. In this study, we conducted QTL analysis for smut disease resistance using a mapping population derived from a resistant variety ‘Yaenoushie’, in which resistance is inherited from ‘Iriomote8’. We identified 4813 non-redundant markers using GRAS-Di technology and developed a linkage map of mapping parents. We evaluated smut disease resistance of the mapping population by the inoculation test. Consequently, a large number of clones did not show the disease symptoms and the distribution of smut disease incidence tended to be “L shaped”. Composite interval mapping detected an identical QTL for indices of smut disease incidence with a markedly high LOD score (26.6~45.6) at the end of linkage group 8 of ‘Yaenoushie’. This QTL explained approximately 50% of the cases of smut disease incidence. In the mapping population, there were no correlations between the indices of smut disease incidence and other agronomic traits. In conclusion, this QTL could be used for marker-assisted selection to significantly improve smut disease resistance without negative effects on other agronomic traits.

“Kans Is King and the Cultivator Is His Subject”: Environmental History and Agrarian Development in Modern India

Abstract Throughout the nineteenth and twentieth centuries, cultivators and administrators in India contended with the ravages of kans grass (Saccharum spontaneum), a deeply rooted wild sugarcane capable of rendering productive land wholly barren. Difficult to eliminate and endemic throughout India, kans disrupted agricultural efforts in north and central India, particularly in the regions of Jhansi, Bundelkhand, and the Himalayan Terai. Yet the fight against this ecological antagonist was bound up in broader political transformations. As India’s colonial agriculture grew increasingly tied to global markets in the late nineteenth century, and dry regions offered new possible spaces for settled agriculture, imperial administrators grew certain that mechanical tractors held the solution to its eradication. Likewise, postcolonial Indian agronomists cast the production of abundant food as central to their political legitimacy, and they made the eradication of kans a national aim, enlisting the World Bank as a partner. British administrators, nationalist Indians and their postcolonial successors, as well as the World Bank all found a mechanized approach to the eradication of kans politically expedient, at the expense of heeding local ecological and social conditions. The remarkable resilience of kans defied efforts at mechanical removal, and the project foundered until the political economy of Indian agriculture shifted to emphasize chemical pesticides and decentralized control.

Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum

Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.

Physicochemical Characterization of Native and Steam Explosion Pretreated Wild Sugarcane (Saccharum spontaneum)

The technology of biomass conversion to bioethanol primarily based on pretreatment, enzymatic hydrolysis, and fermentation. This study was to investigate the effectiveness of the steam explosion pretreatment of Saccharum spontaneum L., which accomplishes the greater efficacy of physicochemical and structural properties. The collected plant material was processed and analyzed for ash, moisture, Carbon content, and other elements. The cellulose content of pretreated biomass was increased to 54.31% when compared to native wild sugarcane 41.23% due to the removal of lignin. SEM and FTIR results identified the changes in structural and functional groups also the BET analysis confirmed the increased surface area of Pretreated biomass is 55.541m²/g whereas the surface area of native biomass is 17.939 m²/g, this is due to the increase in pore volume and pore diameter of pretreated wild sugarcane which is 0.260 cc/g and 9.712 nm when compared to pore volume and Pore Diameter Dv(d) of raw material is 0.040 cc/g and 3.650 nm. XRD crystallinity pattern of pretreated wild sugarcane showed an increase in the crystallinity index due to the breakage of lignin during pretreatment. This comparative study has been carried out to know the effect of steam explosion pretreatment over the physicochemical composition and structural changes of wild sugarcane for sustainable bioethanol production.

Bioethanol production from agro-industrial Saccharum spp. residues: using Trametes versicolor (L.: Fr.) Quél in simple fermentation and saccharification processes

Objective: To quantify the production of total and reducing sugars, as well as bioethanol from sugarcane bagasse (Saccharum spp.) pretreated with Trametes versicolor and 20 % (P/V) NaOH solution. Design/methodology/approach: An experimental 2K design was used to determine the effect of the volume of inoculant added to wild sugarcane bagasse samples (Factor A; 8 and 10 mL), its incubation period (Factor B; 18 and 24 d), and the bagasse weight/ volume of 20% (P/V) NaOH solution (Factor C; 5 and 20%(P/V), on the production of total and reducing sugars during simple saccharification. ANOVA analysis was used to evaluate the significance of these factors. The production of bioethanol was achieved via simple fermentation using a commercial strain of Saccharomyces cerevisiae. Results: It was found that the highest yields of reducing and total sugars were obtained with the use of 10 mL of inoculant solution and with an 18 d incubation period during biological pretreatments. The ANOVA analysis suggests that Factors A and B influence the release of sugars, while Factor C was irrelevant. The bioethanol production registered concentrations of up to 7.3 mg mL-1 for every 5 g of sugarcane bagasse. Limitations/implications: This study focused on how treatments using T. versicolor and NaOH affected the release of sugars. Optimization of bioethanol production needs to be considered subsequently in another study. Findings/conclusions: The results have implications for the use of pretreatments for the production of bioethanol from agro-industrial residues.

Estimating the Heating Values of Napier Grass (Pennisetum purpureum Schumach) and Wild Sugarcane (Sacharrum spontaneum L.) Biomass using Proximate Composition

The study aimed to determine the heating values (HV) and proximate composition of the four varieties of Napier Grass (Pennisetum purpureum Schumach) and native wild sugarcane (Sacharrum spontaneum L.) to generate a mathematical model for predicting HV of Napier Grass varieties and wild sugarcane biomass. The four varieties of Napier Grass namely King, Florida, Dwarf, and Princess Caroline as well as the wild sugarcane were used in this study. The proximate composition such as moisture, ash, organic matter (OM), carbon (C), nitrogen (N), C/N ratio, and heating value (HV) were determined to generate mathematical models. Only ash, nitrogen, organic matter (OM) and carbon (C) have statistically significant r values toward the heating value. Positive correlation was obtained in OM and C whereas negative correlations were obtained in ash and N. Linear regression using Waikato Environment for Knowledge Analysis (WEKA) machine learning generated mathematical models for group variables for predicting the heating value (HV). The organic matter (OM) content showed the most accurate model among the group variables used with adjusted R2 value of 0.900, Pearson’s r value of 0.915 and root mean square error (RMSE) value of 481.64 MJ/kg. Among the proximate composition parameters tested, OM is the most accurate predictor of the HV of the Napier Grass varieties and wild sugarcane biomass.

Lovastatin Production by Aspergillus sclerotiorum Using Agricultural Waste.

SUMMARYResearch backgroundLovastatin is a well-known drug used to reduce hypercholesterolaemia. However, the cost of lovastatin production is still high. Therefore, alternative low-cost carbon sources for the production of lovastatin are desirable.Experimental approachFour different agricultural wastes, namely corn trunks, rice husks, wild sugarcane, and soya bean sludge, were tested separately as substrates to produce lovastatin using a new fungal strain, Aspergillus sclerotiorum PSU-RSPG 178, under both submerged and solid-state fermentation (SSF).Results and conclusionsOf these substrates and cultivation systems, soya bean sludge gave the highest lovastatin yield on dry mass basis of 0.04 mg/g after 14 days of SSF at 25 °C. Therefore, the soya bean sludge was separately supplemented with glucose, wheat flour, trace elements, palm oil, urea and molasses. The addition of the palm oil enhanced the lovastatin yield to 0.99 mg/g. In addition, the optimum conditions, which gave a lovastatin yield of (20±2) mg/g after 18 days of SSF, were soya bean sludge containing 80% moisture (dry basis) at a ratio of soya bean sludge (g) to mycelial agar plugs of 1:4, and a ratio of soya bean sludge (g) to palm oil (mL) of 1:2. Besides, the lovastatin yields obtained from SSF using fresh or dry soya bean sludge were not significantly different.Novelty and scientific contributionWe conclude that A. sclerotiorum PSU-RSPG 178 has a good potential as an alternative strain for producing lovastatin using soya bean sludge supplemented with palm oil as a carbon source.

種子島と沖縄本島におけるサトウキビ国内野生種「西表8」後代集団の評価

種子島と沖縄本島におけるサトウキビ国内野生種「西表8」後代集団の評価

Root transcriptome analysis of Saccharum spontaneum uncovers key genes and pathways in response to low-temperature stress

Low-temperature (LT) stress is known to restrain sugarcane productivity in sub-tropical regions significantly. Many researchers have prioritized their work towards developing climate-resilient sugarcane varieties incorporating genome of stress-tolerant sugarcane related wild-type species in the pre-breeding programs. However, the lack of genomic resources for wild-type sugarcane limits the identification and utilization of stress-related genes in molecular breeding. In this study, for the first time, we generated ∼182 million RNA-seq paired-end reads for Saccharum spontaneum roots grown under low temperature (10 °C) at different time intervals (0 h, 3 h, 6 h, 12 h, 24 h, and 48 h), to identify LT stress responsive genes and pathways. These data were assembled into 141,409 unigenes and subsequently used to identify 2715 upregulated and 1710 downregulated transcripts under LT stress. Combining evidences from GO enrichment, KEGG pathways, histological studies, biochemical assays, and physiological analysis, our results revealed several key genes and pathways involved in cold acclimatization in the S. spontaneum roots. Transcription profiling of roots during LT stress revealed cold stress sensors (i.e., proline, MDA, calcium-dependent kinase, G-coupled proteins, and histidine kinase) that trigger and activate signal transduction through transcription factors (i.e., MYB, ERF, ARF2, DREB, CAMTA, and C2H2) resulting in upregulation of LT stress responsive genes (i.e, annexin, LEA, germins, LT dehydrins, osmotins, and COR) thereby enhancing cold tolerance. Also, transcriptomic analysis envisaged cold responsive metabolic pathways such as phenylpropanoid and sugar metabolism stimulate the synthesis of flavonoid, sucrose, galactose, raffinose, and fructose, antioxidants, phytohormones, and secondary metabolites, and thus trigger cold-responsive transcriptional regulation. Together, this study provides insights into cold tolerance of wild sugarcane roots to LT stress, thus providing a foundation for developing climate-resilient sugarcane varieties.

Marginal Agricultural Land Low-Input Systems for Biomass Production

This study deals with approaches for a social-ecological friendly European bioeconomy based on biomass from industrial crops cultivated on marginal agricultural land. The selected crops to be investigated are: Biomass sorghum, camelina, cardoon, castor, crambe, Ethiopian mustard, giant reed, hemp, lupin, miscanthus, pennycress, poplar, reed canary grass, safflower, Siberian elm, switchgrass, tall wheatgrass, wild sugarcane, and willow. The research question focused on the overall crop growth suitability under low-input management. The study assessed: (i) How the growth suitability of industrial crops can be defined under the given natural constraints of European marginal agricultural lands; and (ii) which agricultural practices are required for marginal agricultural land low-input systems (MALLIS). For the growth-suitability analysis, available thresholds and growth requirements of the selected industrial crops were defined. The marginal agricultural land was categorized according to the agro-ecological zone (AEZ) concept in combination with the marginality constraints, so-called ‘marginal agro-ecological zones’ (M-AEZ). It was found that both large marginal agricultural areas and numerous agricultural practices are available for industrial crop cultivation on European marginal agricultural lands. These results help to further describe the suitability of industrial crops for the development of social-ecologically friendly MALLIS in Europe.

Isolation, characterization and expression of transcription factor ScDREB2 from wild, commercial and interspecific hybrid sugarcane in salinity condition

Dehydration Responsive Element Binding (DREB) gene is one of the essential transcription factors plants use for responding to stress conditions including salinity, drought, and cold stress. The purpose of this study was to isolate the full length and characterize the DREB gene from three different genotypes of sugarcane, wild, commercial cultivar, and interspecific hybrid sugarcane. The length of the gene, designated ScDREB was 789 bp, and coding for a putative polypeptide of 262 amino acid residues. Sequences of the gene were submitted to the GenBank database with accession numbers of KX280722.1, KX280721.1, and KX280719.1 for wild sugarcane, commercial cultivar (KPS94-13), and interspecific hybrid (Biotec2), respectively. In silico characterization indicated that the deduced polypeptide contains a putative nuclear localization signal (NLS) sequence, and a conserved AP2/ERF domain of the DREB family, at 82-140 amino residues. Based on multiple sequence alignment, sequences of the gene from the three sugarcane genotypes were classified in the DREB2 group. Gene expression analysis indicated, that ScDREB2 expression pattern in tested sugarcane was up-regulated by salt stress. When the plants were under 100 mM NaCl stress, relative expressions of the gene in leaves was higher than those in roots. In contrast, under 200 mM NaCl stress, relative expressions of the gene in roots was higher than those in leaves. This is the first report on cloning the full length and characterization, of ScDREB2 gene of sugarcane. Results indicate that ScDREB2 is highly responsive to salt stress.

Genetic analysis of sugarcane brown rust resistance genes in wild sugarcane germplasm Erianthus rockii ‘Yundian 95-19’ and Erianthus rockii ‘Yundian 95-20’

AbstractWe assessed inheritance of resistance to sugarcane brown rust (Puccinia melanocephala) in selfing F1 populations of wild sugarcane germplasm Erianthus rockii ‘Yundian 95-19’ and E. rockii ‘Yundian 95-20’. We tested parent and selfing F1 individuals for the brown rust resistance gene, Bru1, that has been shown to confer resistance to brown rust in sugarcane. The Bru1 gene was not detected in E. rockii ‘Yundian 95-19’, E. rockii ‘Yundian 95-20’ or their selfing F1 individuals, and we found there was segregation of resistance in the two selfing F1 populations (segregation ratio: 3:1). The results confirmed resistance in E. rockii ‘Yundian 95-19’ and E. rockii ‘Yundian 95-20’ to sugarcane brown rust is controlled by a novel, single dominant gene.

Comprehensive transcriptome analysis reveals genes in response to water deficit in the leaves of Saccharum narenga (Nees ex Steud.) hack

BackgroundSugarcane is an important sugar and energy crop that is widely planted in the world. Among the environmental stresses, the water-deficit stress is the most limiting to plant productivity. Some groups have used PCR-based and microarray technologies to investigate the gene expression changes of multiple sugarcane cultivars under water stress. Our knowledge about sugarcane genes in response to water deficit is still poor.ResultsA wild sugarcane type, Saccharum narenga, was selected and treated with drought stress for 22 days. Leaves from drought treated (DTS) and control (CK) plants were obtained for deep sequencing. Paired-end sequencing enabled us to assemble 104,644 genes (N50 = 1605 bp), of which 38,721 were aligned to other databases, such as UniProt, NR, GO, KEGG and Pfam. Single-end and paired-end sequencing identified 30,297 genes (> 5 TPM) in all samples. Compared to CK, 3389 differentially expressed genes (DEGs) were identified in DTS samples, comprising 1772 up-regulated and 1617 down-regulated genes. Functional analysis showed that the DEGs were involved in biological pathways like response to blue light, metabolic pathways and plant hormone signal transduction. We further observed the expression patterns of several important gene families, including aquaporins, late embryogenesis abundant proteins, auxin related proteins, transcription factors (TFs), heat shock proteins, light harvesting chlorophyll a-b binding proteins, disease resistance proteins, and ribosomal proteins. Interestingly, the regulation of genes varied among different subfamilies of aquaporin and ribosomal proteins. In addition, DIVARICATA and heat stress TFs were first reported in sugarcane leaves in response to water deficit. Further, we showed potential miRNAs that might be involved in the regulation of gene changes in sugarcane leaves under the water-deficit stress.ConclusionsThis is the first transcriptome study of Saccharum narenga and the assembled genes are a valuable resource for future research. Our findings will improve the understanding of the mechanism of gene regulation in sugarcane leaves under the water-deficit stress. The output of this study will also contribute to the sugarcane breeding program.

Evaluation of the juice brix of wild sugarcanes (Saccharum spontaneum) indigenous to Japan

Modern sugarcane cultivars are derived from the interspecific crossing between Saccharum officinarum and wild sugarcane, Saccharum spontaneum. The introgression of valuable characteristics from wild sugarcane is recognized as extremely important, but this process typically requires long-term effort over multiple generations of backcrosses owing to the low sugar content of the initial interspecific hybrids. In this study, we aimed to identify Japanese wild sugarcanes with high juice brix in order to promote effective interspecific crossing of sugarcane. Sixty-four accessions from the Nansei Islands and 70 accessions from the Honshu were evaluated for juice brix. Wild sugarcanes with high juice brix were demonstrated to exist among wild sugarcanes indigenous to the Honshu. A significant difference was observed between the median juice brix values of wild sugarcanes of the Nansei Islands and those of the Honshu. The relationship between juice brix and stem traits was then examined in 20 wild sugarcanes, 10 each from the Nansei Islands and the Honshu. The reproducibility of juice brix value in both experiments was confirmed. In contrast to juice brix, stem traits, such as length, diameter, and volume, were typically smaller in wild sugarcanes from the Honshu. Moreover, a negative correlation was observed between the index of stem volume and juice brix. In this study, we identified outstanding wild sugarcanes with high juice brix. Using germplasms from the identified wild sugarcanes in interspecific crossing could contribute to the increases in both yield and sugar content.

Truncated Ubiquitin 5' Regulatory Region from Erianthus arundinaceus Drives Enhanced Transgene Expression in Heterologous Systems.

Characterization of novel plant gene promoters underpins the development of transgenic crop plants. Here, we report a novel 5' regulatory sequence (Eriubi D7) of the ubiquitin gene from Erianthus arundinaceus, a wild relative of sugarcane resistant to many biotic and abiotic stresses. A 3.2-kb regulatory sequence of ubiquitin gene was isolated through random amplification of genomic ends technique and characterized in rice, tobacco, and sugarcane. In silico analysis revealed that the regulatory sequence contained a promoter region of 1600bp upstream to the transcription start site. Between the promoter and the coding region, two putative introns of 584 and 583bp and two putative non-coding exons of 459 and 37bp were spaced alternatively. To identify the active domains required for gene regulation, 12 truncations/recombinants were made in the regulatory sequence and characterized in heterologous systems. Transformation studies with the recombinant constructs revealed that Eriubi D7, a truncated fragment containing 830bp promoter and the intron I, conferred enhanced GUS reporter gene expression in both monocots and dicots compared to other routinely used promoters such as maize ubi1 and Cauliflower Mosaic Virus 35S. Further analysis confirms that this regulatory sequence is quite distinct from the other reported ubiquitin promoters and was also found to enhance expression of the reporter gene upon wounding. This is the first report on the isolation and characterization of a promoter from a wild sugarcane germplasm and is expected to be useful for development of transgenic crop plants.

Efficiency of Different Antimitotics in Cytological Preparations of Sugarcane

Commercial sugarcane cultivars and wild species have a high ploidy level allied to a complex genome and usual chromosomal instability. There are few studies related to the standardization of cytogenetic techniques in sugarcane. This work tested the efficiency of three antimitotics (colchicine, 8-hydroxyquinoline, and trifuralin) at different concentrations on the quality of metaphases spreads from a commercial sugarcane cultivar (IAC911099-Saccharum spp.) and a wild sugarcane accession (Krakatau-S. spontaneum). Although all three antimitotics were efficient for obtaining metaphases, 8-hydroxyquinoline was the most efficient for both IAC911099 and Krakatau. The chromosome number of these two genotypes was inferred. The variation in chromosome number was 2n = 90–112 for IAC911099, with a statistical modal of 2n = 112 chromosomes while the variation in chromosome number was 2n = 90–129 chromosome with a statistical modal of 2n = 128 chromosomes for Krakatau (S. spontaneum).

Cloning and allelic variation of two novel catalase genes (SoCAT-1 and SsCAT-1) in Saccharum officinarum L. and Saccharum spontaneum L.

Catalases (CAT) play important roles in plant defence mechanisms, stress response, cellular redox balance and aging delay. In order to clone CAT genes in cultivated (Saccharum officinarum L.) and wild (S. spontaneum L.) sugarcane, we designed two pairs of specific primers using a full length cDNA sequence of sorghum CAT gene (XM 002437586.1) as the probe. Two novel full-length sequences of CAT genes (SoCAT-1 in S. officinarum and SsCAT-1 in S. spontaneum) were cloned by nested polymerase chain reaction. Two allelic variants were found at SoCAT-1 (SoCAT-1a and SoCAT-1b, GenBank accession nos. KF864224-25) and SsCAT-1 (SsCAT-1a and SsCAT-1b, GenBank accession nos. KF864226-27) loci. The full lengths of SoCAT-1a, SoCAT-1b, SsCAT-1a and SsCAT-1b were 3816 bp, 3814 bp, 3777 bp and 3812 bp, respectively, and all contained eight exons and seven introns, with a similar gene structure. The length of cDNA for all four genes was 1532 bp, containing 10 bp 5'-untranslated region (UTR) and 43 bp 3'-UTR, and an open reading frame of 1479 bp encoding a polypeptide of 492 amino acids. High homology of DNA (99.0% for SoCAT-1, 98.2% for SsCAT-1) and cDNA (99.3% for SoCAT-1, 99.4% for SsCAT-1) were found. Eleven single nucleotide polymorphisms were found in cDNA SoCAT-1 and nine ones in SsCAT-1, and nine and five amino-acid mutation sites in the predicted proteins, respectively. The predicted proteins encoded by SoCAT-1 and SsCAT-1 showed high homology with CAT in sorghum, rice, corn and other species.

Screening Sugarcane Wild Accessions for Resistance to Sugarcane Mosaic Virus (SCMV)

In order to identify new sources of resistance for future introgression crosses, wild sugarcane germplasm was screened for resistance to Sugarcane mosaic virus (SCMV) under high inoculum pressure. Evaluation of symptoms by a grade scale associated with serological diagnostic by plate-trapped antigen-enzyme-linked immunosorbent assay (PTA-ELISA) with a specific antiserum were performed in 43 accessions, encompassing Saccharum officinarum, S. barberi, S. spontaneum and S. robustum species and hybrids. Differential patterns of resistance and susceptibility were observed among the Saccharum species, with S. officinarum followed by S. robustum accessions showing higher susceptibility, whereas S. barberi and S. spontaneum had the most resistant accessions. The results indicate that accessions IS76-155, IJ76-418 red, NG57-50, Ceram red, Badilla, Sac.off 8276, Fiji19, IJ76-313, US57-141-5, Krakatau, IN84-58, IN84-88, IN84-82, Gandacheni, and Chin, possibly consist in good sources of resistance to mosaic.

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.

Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.