Integrated transcriptomic and proteomic analyses of two sugarcane (Saccharum officinarum Linn.) varieties differing in their lodging tolerance
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SUBMITTER: Li X
PROVIDER: S-EPMC10685470 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.
| S-EPMC10598656 | biostudies-literature
Project description:Sugarcane bacilliform virus (SCBV) is considered one of the most economically damaging pathogens for sugarcane production worldwide. Three open reading frames (ORFs) are characterized in the circular, ds-DNA genome of the SCBV; these encode for a hypothetical protein (ORF1), a DNA binding protein (ORF2), and a polyprotein (ORF3). A comprehensive evaluation of sugarcane (Saccharum officinarum L.) miRNAs for the silencing of the SCBV genome using in silico algorithms were carried out in the present study using mature sugarcane miRNAs. miRNAs of sugarcane are retrieved from the miRBase database and assessed in terms of hybridization with the SCBV genome. A total of 14 potential candidate miRNAs from sugarcane were screened out by all used algorithms used for the silencing of SCBV. The consensus of three algorithms predicted the hybridization site of sof-miR159e at common locus 5534. miRNA-mRNA interactions were estimated by computing the free-energy of the miRNA-mRNA duplex using the RNAcofold algorithm. A regulatory network of predicted candidate miRNAs of sugarcane with SCBV-ORFs, generated using Circos-is used to identify novel targets. The predicted data provide useful information for the development of SCBV-resistant sugarcane plants.
| S-EPMC8775236 | biostudies-literature
Project description:Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum.
| S-EPMC5381655 | biostudies-literature
Project description:The finite nature, regional availability, and environmental problems associated with the use of fossil fuels have forced all countries of the world to look for renewable eco-friendly alternatives. Agricultural waste biomasses, generated through the cultivation of cereal and noncereal crops, are being considered renewable and viable alternatives to fossil fuels. In view of this, there has been a global spurt in research efforts for using abundantly available agricultural wastes as feedstocks for obtaining energy and value-added products through biochemical and thermal conversion routes. In the present work, the thermochemical characteristics and thermal degradation behavior of sugarcane leaves (SCL) and tops were studied. The batch pyrolysis was carried out in a fixed-bed tubular reactor to obtain biochar, bio-oil, and pyrolytic gas. Effects of bed height (4-16 cm), particle size (0.180-0.710 mm), heating rate (15-30 °C/min), and temperature (350-650 °C) were investigated. The maximum yields of bio-oil (44.7%), biogas (36.67%), and biochar (36.82%) were obtained at 550, 650, and 350 °C, respectively, for a 16 cm deep bed of particles of size 0.18-0.30 mm at the heating rate of 25 °C/min. The composition of bio-oil was analyzed using Fourier transform infrared spectroscopy (FTIR), proton nuclear magnetic resonance (1H NMR), and gas chromatography-mass spectrometry (GC-MS) techniques. Several aliphatic, aromatic, phenolic, ketonic, and other acidic compounds were found in the bio-oil. The biochar had a highly porous structure and several micronutrients, making it useful as a soil conditioner. In the middle temperature ranges, biogas had more methane and CO and less hydrogen, but at higher temperatures, hydrogen was predominant.
| S-EPMC9386804 | biostudies-literature
Project description:BackgroundSugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane.ResultsTo improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like "plant hormone signal transduction" and "plant-pathogen interaction", which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane.ConclusionsWe not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs.
| S-EPMC5613641 | biostudies-literature
Project description:The natural occurrence of entomopathogenic fungal endophytes in sugarcane (Saccharum officinarum) and in soil samples from sugarcane fields was evaluated in Chikwawa District, southern Malawi. Fungi from soil were isolated by baiting using Galleria mellonella larva. Fungal endophytes were isolated from surface-sterilized plant tissue sections. Forty-seven isolates resembled the genus Beauveria, 9 isolates were Metarhizium, and 20 isolates were Isaria. There was no significant difference in the number and type of fungal isolates collected from soil and from plant tissue. There was, however, a significant difference in the part of the plant where fungal species were isolated, which fungal species were isolated, and the number of fungal species isolated at each location. Phylogenetic analysis of 47 Beauveria isolates based on DNA sequencing of the Bloc intergenic region indicated that these isolates all belonged to B. bassiana and aligned with sequences of B. bassiana isolates of African and Neotropical origin. The Malawian B. bassiana isolates formed a distinct clade. No larvae died from infestation by multiple fungi. To the best of our knowledge, this is the first report of B. bassiana and Isaria spp. occurring naturally as endophytes in sugarcane. Further, it is the first report of B. bassiana, Isaria spp., and Metarhizium spp. in the soil of sugarcane fields in Africa.
| S-EPMC7917985 | biostudies-literature
Project description:Sugarcane (Saccharum officinarum L.), a globally cultivated carbohydrate producing crop of industrial importance is being challenged by soil salinity due to its glycophytic nature. Water stress coupled with cellular and metabolic alterations resulting from excess sodium (Na+) ion accumulation is irreversibly damaging during early crop developmental stages that often results in complete crop failure. This study therefore aimed to explore the potential of salicylic acid as a sett priming material to mitigate the negative effects of salt stress on sugarcane during germination and early growth stages. Five doses of salicylic acid (0 [hydropriming] [control], 0.5 mM, 1 mM, 1.5 mM and 2 mM) were tested against three levels of salinity (0.5 dS m-1 [control], 4 dS m-1, and 8 dS m-1) within a polyhouse environment. Results revealed 11.2%, 18.5%, 25.4%, and 38.6%, average increase in final germination, germination energy, seedling length and seedling vigor index respectively with a subsequent reduction of 21% mean germination time. Investigations during early seedling growth revealed 21.6%, 17.5%, 27.0%, 39.9%, 10.7%, 11.5%, 17.5%, 47.9%, 35.3% and 20.5% overall increase in plant height, total leaf area, shoot dry matter, root dry matter, leaf greenness, relative water content, membrane stability index, proline content, total antioxidant activity and potassium (K+) ion accumulation respectively with a subsequent reduction of 24.9% Na+ ion accumulation and 35.8% Na+/K+ ratio due to salicylic acid priming. Germination, seedling growth and recovery of physiochemical traits were highly satisfactory in primed setts than non-primed ones even under 8 dS m-1 salinity level. This study should provide useful information for strategizing salinity management approaches for better productivity of sugarcane.
| S-EPMC10192769 | biostudies-literature
Project description:Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. Its highly polyploid, complex genome has hindered progress in understanding its molecular structure. Flow cytometric sorting and analysis has been used in other important crops with large genomes to dissect the genome into component chromosomes. Here we present for the first time a method to prepare suspensions of intact sugarcane chromosomes for flow cytometric analysis and sorting. Flow karyotypes were generated for two S. officinarum and three hybrid cultivars. Five main peaks were identified and each genotype had a distinct flow karyotype profile. The flow karyotypes of S. officinarum were sharper and with more discrete peaks than the hybrids, this difference is probably due to the double genome structure of the hybrids. Simple Sequence Repeat (SSR) markers were used to determine that at least one allelic copy of each of the 10 basic chromosomes could be found in each peak for every genotype, except R570, suggesting that the peaks may represent ancestral Saccharum sub genomes. The ability to flow sort Saccharum chromosomes will allow us to isolate and analyse chromosomes of interest and further examine the structure and evolution of the sugarcane genome.
| S-EPMC6920420 | biostudies-literature
Project description:In plants, both abscisic acid (ABA) dependent and independent pathways form the basis for the response to environmental stresses. Sucrose non-fermenting 1-related protein kinase 2 (SnRK2) plays a central role in plant stress signal transduction. However, complete annotation and specific expression patterns of SnRK2s in sugarcane remain unclear. For the present study, we performed a full-length cDNA library survey of sugarcane, thus identifying ten SoSnRK2 genes via phylogenetic, local BLAST methods, and various bioinformatics analyses. Phylogenetic analysis indicated division of SoSnRK2 genes into three subgroups, similar to other plant species. Gene structure comparison with Arabidopsis suggested a unique evolutionary imprint of the SnRK2 gene family in sugarcane. Both sequence alignment and structural annotation provided an overview of the conserved N-terminal and variations of the C-terminal, suggesting functional divergence. Transcript and transient expression assays revealed SoSnRK2s to be involved in the responses to diverse stress signals, and strong ABA induction of SoSnRK2s in subgroup III. Co-expression network analyses indicated the existence of both conserved and variable biological functions among different SoSnRK2s members. In summary, this comprehensive analysis will facilitate further studies of the SoSnRK2 family and provide useful information for the functional validation of SoSnRK2s.
| S-EPMC5732291 | biostudies-literature
Project description:BackgroundSugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest.ResultsTo determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants.ConclusionOur results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane.
| S-EPMC4779555 | biostudies-literature