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In order to understand the genetic diversity and structure within and between the genera of Saccharum and Erianthus , 79 accessions from five species ( S. officinarum , S. spontaneum , S. robustum , S. barberi , S. sinense ), six accessions of E. arundinaceus , and 30 Saccharum spp. hybrids were analyzed using 21 pairs of fluorescence-labeled highly poloymorphic SSR primers and a capillary electrophoresis (CE) detection system. A total of 167 polymorphic SSR alleles were identified by CE with a mean value of polymorphic information content (PIC) of 0.92. Genetic diversity parameters among these 115 accessions revealed that Saccharum spp. hybrids were more diverse than those of Saccharum and Erianthus species. Based on the SSR data, the 115 accessions were classified into seven main phylogenetic groups, which corresponded to the Saccharum and Erianthus genera through phylogenetic analysis and principle component analysis (PCA). We propose that seven core SSR primer pairs, namely, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, SMC24DUQ, mSSCIR3, and mSSCIR43, may have a wide appicability in genotype identification of Saccharum species and Saccharum spp. hybrids. Thus, the information from this study contibites to manage sugarcane genetic resources.

Summary Sugarcane (Saccharum spp.) is a highly energy‐efficient crop primarily for sugar and bio‐ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high‐quality genome‐wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in‐depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide 1 . While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued 2 . The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species ( Saccharum officinarum ) and the wild species ( Saccharum spontaneum ). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions. We build a polyploid reference genome for hybrid sugarcane cultivar R570, improving on its current ‘mosaic monoploid’ representation, enabling fine-grain description of genome architecture and the exploration of candidate genes underlying the Bru1 brown rust resistance locus.

Plant growth-promoting rhizobacteria (PGPR) are promising candidates that enhance plant growth under stressful conditions. In this study, 10 bacterial isolates were screened for their IAA production, among them JTB1 and MT22 isolates were selected which produced high IAA levels under 10% PEG and 2% NaCl stress. The isolates showed a high capacity for phosphate solubilization and ACC deaminase activity. Phytogenic analysis showed that the isolate belonged to Bacillus megaterium species JTB1 and MT22. Application of JTB1, MT22, and their consortia as PGPR significantly promoted root development and sugarcane growth under moderate and severe drought stress. Sugarcane growth promotion resulted from the retardation of reactive oxygen species (ROS) synthesis, malondialdehyde (MDA), electrolyte leakage, and cell damage by increasing antioxidant scavenging systems, such as catalase (CAT) and ascorbate peroxidase (APX), owing to PGPR inoculation under drought stress. Inoculation with PGPR resulted in increased auxin transporter expression, which modulated the increase in photosynthetic gene expression of RBC-L , PEPC , SPS in sugarcane under drought stress. The application of JTB1, MT22, or their consortia seemed to have similar effects on all observed parameters. Collectively, these results indicated that inoculation with PGPR enhanced root development and increased the antioxidant system and photosynthetic activity, which promoted sugarcane growth under drought stress.

The SnRK1, hexokinase, and TORC1 (TOR, LST8, RAPTOR) are three pivotal kinases at the core of sugar level sensing, significantly impacting plant metabolism and development. We retrieved and analyzed protein sequences of these three kinase pathways from seven sugarcane transcriptome and genome datasets, identifying protein domains, phylogenetic relationships, sequence ancestry, and in silico expression levels. Additionally, we predicted HXK subcellular localization and assessed its enzymatic activity in sugarcane leaves and culms along development in the field. We retrieved 11 TOR, 23 RAPTOR, 55 LST8, 95 SnRK1α, 98 HXK, and 14 HXK-like putative full-length sequences containing all the conserved domains. Most of these transcripts seem to share a common origin with the three ancestral species of sugarcane: Saccharum officinarum , Saccharum spontaneum, and Saccharum barberi . We accessed the expression profile of sequences from one sugarcane transcriptome. We found the highest enzymatic activity of HXK in culms in the first month, which, at this stage, provides carbon (sucrose) and nitrogen (amino acids) for initial plant development. Our approach places novel sugar sensing sequences that work as a guideline for further research into the underlying signaling mechanisms and biotechnology applications in sugarcane.

Nitrogen (N) is a major component of the photosynthetic apparatus and is widely used as a fertilizer in crops. However, to the best of our knowledge, the dynamic of photosynthesis establishment due to differential N supply in the bioenergy crop sugarcane has not been reported to date. To address this question, we evaluated physiological and metabolic alterations along the sugarcane leaf in two contrasting genotypes, responsive (R) and nonresponsive (NR), grown under high- and low-N conditions. We found that the N supply and the responsiveness of the genotype determined the degree of senescence, the carboxylation process mediated by phosphoenolpyruvate carboxylase (PEPcase) and differential accumulation of soluble sugars. The metabolite profiles indicated that the NR genotype had a higher respiration rate in the youngest tissues after exposure to high N. We observed elevated levels of metabolites related to photosynthesis in almost all leaf segments from the R genotype under high-N conditions, suggesting that N supply and the ability to respond to N influenced photosynthesis. Therefore, we observed that N influence on photosynthesis and other pathways is dependent on the genotype and the leaf region.

Aims Respiration of sugar maple ( Acer saccharum ) surface fine roots has been shown to partially acclimate to experimentally increased soil temperature. In this study, we assessed how larger roots and roots at deeper depths responded to experimental warming. Methods We quantified specific root respiration and root biomass for three different diameter classes (<1, 1–2, and 2–10 mm) from three soil depths (0–10, 10–30, and 30–50 cm) in a sugar maple forest that had received a factorial combination of increased soil temperature (4 to 5 °C above ambient) and supplemental precipitation for three growing seasons. Results Partial temperature acclimation occurred for respiration of fine-roots (<1 mm) at 0–10 cm, limiting the increase to 30% above that for roots in the control treatment. In contrast, there was no evidence for acclimation of fine-roots at deeper depths, where soil warming caused respiration to more than double. There was evidence of acclimation for 1–2 mm roots at the 0–10 cm depth (20% reduction in respiration at an 18 °C reference temperature) but not for the larger diameter roots at any of the three soil depths. Root biomass was not altered by soil warming or moisture addition. Conclusions Despite partial thermal acclimation in surface fine-root respiration, soil warming caused an overall 41% increase in the C flux to the atmosphere from respiration of roots in the upper 30 cm of soil, from 21.3 to 30.1 μmol m −2  s −1 , potentially reducing C availability for biomass production.

Silicon (Si) is a relatively novel element that has found widespread application in various fields. Gibberellic acid (GA 3 ) is known to induce different physiological traits in a variety of plants. While Si and GA₃ independently improve plant performance, their interactive mechanisms and potential synergy are poorly understood. In the present study, different treatments of GA 3 (0, 10, 20, 50, 75 and 100 ppm) and Si (50 ppm) were applied as foliar and soil irrigation on sugarcane ( Saccharum officinarum L. cv. GT55) plants at specific time intervals, such as 60 and 90 days. The result findings indicated that the application of foliar and soil irrigation containing GA 3 and Si notably enhanced and/ or stabilized enzymatic and non-enzymatic activities, i.e., soluble protein, catalase, peroxidase, ascorbate peroxidase, superoxide dismutase, glutathione reductase, hydrogen peroxide, lipid peroxidation, proline, ascorbate, glutathione, oxidized glutathione, glutathione-S-transferase, dehydroascorbate, and plant hormones, such as indole-3-acetic acid, abscissic acid, and gibberellic acid in sugarcane plant leaves and roots after foliar and soil irrigation application. The results showed that the interactive applications of GA 3 and Si were not harmful to sugarcane plants, and positively affected their growth and development. The simultaneous application of Si and GA₃ is a safe and highly effective strategy to upregulate sugarcane growth and metabolic regulation. This innovative approach presents sustainable technology to enhance crop productivity and contribute to global food security goals without relying on conventional chemical inputs.

Main conclusion Silicon application at a concentration of 2 mM induced sugarcane resistance to Nigrospora oryzae by upregulating pathogen recognition and defense genes, thus increasing plant metabolic activities and productivity. Sugarcane is an important global food and industrial crop, but numerous pathogens threaten its productivity. Our team recently identified the fungus Nigrospora oryzae as a pathogen affecting sugarcane’s growth and productivity. Although silicon supplementation is active against most fungi, it remains unclear if it would enhance the resilience of sugarcane to N. oryzae , and molecular mechanisms underlying this process are yet to be explored. In this study, we explored the effects of four silicon concentrations (control, 1 mM, 2 mM, and 4 mM) on the growth and disease resistance of seedlings of the sugarcane variety ROC22 under fungal stress. Employing an integrative approach combining detailed phenotypic analysis with transcriptomic and metabolomic profiling, we elucidated the underlying molecular mechanisms of silicon’s protective effects. Results indicated that optimal concentrations (2 mM) of silicon enhanced disease resistance and significantly improved plant height, root characteristics, and enzymatic activities. Transcriptomic analysis revealed an upregulation of genes (826) involved in pathogen recognition and defensive response, while metabolomic analysis highlighted alterations in metabolic pathways pertinent to stress response. These findings suggest that silicon supplementation could effectively bolster sugarcane’s defense against fungal diseases, offering new insights into its role in plant pathology and paving the way for developing more resilient crop varieties. Graphical abstract

Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. Expression of sugar transporters might explain sucrose differences among genotypes, but an unexpected differential expression of histones were also identified between high and low Brix° genotypes. Lignin biosynthetic genes and bioenergetics-related genes were up-regulated in the high lignin genotype, suggesting that these genes are important for S. spontaneum to allocate carbon to lignin, while S. officinarum allocates it to sucrose storage. Co-expression network analysis identified 18 transcription factors possibly related to cell wall biosynthesis while in silico analysis detected cis-elements involved in cell wall biosynthesis in their promoters. Our results provide information to elucidate regulatory networks underlying traits of interest that will allow the improvement of sugarcane for biofuel and chemicals production.