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Sugarcane is the most important sugar and bioenergy crop. Sugarcane ratoon crop chlorosis, caused by deficiencies of Fe, Ca and Mg because of low soil pH and excessive absorption of Mn, is a major crop production constraint in China and reduces cane yield as much as 40%. The molecular basis of the ratoon crop chlorosis is little understood. In this study, we employed TMT-labeling quantitative proteomics approach to study the proteins associated with sugarcane ratoon crop chlorosis using chlorotic leaves collected from the field. An in-house transcriptome database for sugarcane leaf was also constructed. From the proteome database, 7480 sugarcane proteins were identified; among them, 199 and 80 were found to be up- and down-regulated by the chlorosis. By functional characterization and protein–protein interaction studies, we were able to identify the components and pathways that might play a role in sugarcane chlorosis response. In addition to genes associated with photosynthesis, drought-responsive and jasmonic acid biosynthesis genes were also found to be associated with ratoon crop chlorosis in sugarcane. Data obtained in the presented study provide the molecular details of sugarcane ratoon crop proteome response during chlorosis.

Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

Internode elongation determines plant height, which in turn affects the cane yield in sugarcane. This study aimed to explore the mechanisms of sugarcane internode elongation regulation by plant growth regulators, gibberellic acid (GA3) and its inhibitor 1, 1-dimethylpiperidinium chloride (DPC, also called mepiquat chloride). We sprayed GA3 or DPC on the leaves at the early shoot elongation stage with water as the control. The contents of endogenous hormones and the expression of GA20 ox1, GID1, and GAI in sugarcane leaves were measured at days 3, 6, 12, and 24 after treatment. It was found that the height of sugarcane plants treated with GA3 showed a significant increase compared to the control, whereas an opposite trend was observed in the DPC-treated plants. Compared to the control, the content of gibberellins (GAs) in leaves was increased significantly, while the indole acetic acid (IAA) content showed an initial increase, then a decline, and eventually remained stable in the GA3-treated plants. The contents of cytokinins (CTK), abscisic acid (ABA), and ethylene (ETH) in leaves exhibited a significant downward trend in the GA3-treated plants compared to the control. In the DCP-treated plants, however, the levels of ABA and ETH in leaves were significantly increased, IAA and GAs significantly decreased, and CTK showed a trend of an initial decline followed by an increase. After GA3 treatment, the gene expression levels of GA20 ox1 and GID1 in sugarcane increased first then decreased, whereas the gene expression level of GAI first decreased and then stabilized. After DPC treatment, the expression of GA20 ox1 in sugarcane showed an initial decrease followed by an increase, while the expression of GID1 decreased gradually and then stabilized, and the expression of GAI showed a trend of an initial increase followed by stabilization. The results of the present study indicate that exogenous GA3 treatment stimulated the internode elongation in sugarcane mainly by increasing the endogenous levels of GAs, decreasing the levels of ABA and ETH, and regulating the expression of GA20 ox1, GID1 and GAI genes; the DPC treatment mainly increased the contents of ABA and ETH and reduced the contents of GAs and IAA, thereby inhibiting the expression of GID1, promoting the expression of GAI, and ultimately inhibiting the internode elongation in sugarcane.

Background Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. Results In the present study, we first obtained high-quality long transcripts from the internodes of sugarcane using the PacBio Sequel System. A total of 72,671 isoforms, with N50 at 3073, were generated. These long isoforms were used as a reference for the subsequent RNA-seq. Afterwards, short reads generated from the Illumina HiSeq 4000 platform were used to compare the differentially expressed genes in both the DPC and the control groups. Transcriptome profiling showed that most significant gene changes occurred after six days post DPC treatment. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating that DPC affected multiple pathways, in addition to suppressing gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the 36 constructed modules, the top positive correlated module, at the stage of six days post spraying DPC, was sienna3. Notably, Stf0 sulfotransferase, cyclin-like F-box, and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. Furthermore, the qPCR validated the high accuracy of the RNA-seq results. Conclusion Taken together, we have demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.

Sugarcane is the most important sugar crop in China, which mainly focuses on the upper stem of the harvested land. The proper regulation of the proportion of internode elongation is the key to determine the yield and sugar. Therefore, it is of great significance to study the mechanism of the dynamic change of elongation between cane joints in order to improve the yield of sugar cane and sucrose. To investigate the biochemical mechanism of stem elongation in sugarcane, stem samples were collected at the pre-elongation stage (9-10 leaves) (Ls1), early elongation stage (12-13 leaves) (Ls2) and rapid elongation stage (15-16 leaves) (Ls3). The change trends in the activities of NAD kinase (NADK), calcium-dependent protein kinase (CDPKs), α-mannosidase, α-galactosidase, β-glucosidase, cellulase, xyloglucan endo-transglycosylase/hydrolase (XTH) and catalase (CAT) were completely consistent, showing rapid elongation stage > early elongation stage > pre-elongation stage, while the activities of β-glucosidase, peroxidase (POD) and α-glucosidase were in opposite, and the activities of calmodulin and β-mannosidase showed the same single-peak trend, and the peak was at early elongation stage. The enzyme activities of β-galactosidase and pectinase did not show significant difference at different stages. The results indicate that the elongation of internodes was closely related to the complex physiological metabolism of sugarcane, and the key enzymes play roles at different time but β-galactosidase and pectinase have little effect on internodes elongation in sugarcane.

Mesoporous silica (MS) and amino-functionalized mesoporous silica (NH(2)-FMS) were prepared and characterized using the techniques of transmission electron microscopy (TEM) and nitrogen adsorption-desorption. Voltammetry was used to investigate the electrochemical behavior of capsaicin at the amino-functionalized mesoporous silica, which was modified through carbon paste electrode (NH(2)-FMS/CPE). NH(2)-FMS/CPE showed better performance for the electrochemical oxidation of capsaicin, when compared with bare carbon paste electrode (CPE) and mesoporous silica modified carbon paste electrode (MS/CPE). We optimized the experimental conditions influencing the determination of capsaicin. Under optimal conditions, the oxidation peak current was proportional to capsaicin concentration in the range of 0.040-0.40 μmol L(-1)and 0.40-4.0 μmol L(-1), when the detection limit was 0.020 μmol L(-1) (S/N=3). The above method was successfully applied to determine capsaicin in hot pepper samples, yielding satisfactory results. The spiked recoveries were in the range of 93.1-100.7%.