Sugarcane ring spot disease significantly impacts crop yield, necessitating the development of resistant cultivars. This study investigated the pathogenicity, morphology, growth characteristics, and molecular identity of the causal fungal pathogen while assessing the resistance of various sugarcane genotypes. Morphological and molecular analyses identified Curvularia guangxiensis as the primary pathogen. Pathogenicity assays demonstrated that the strain FS1 exhibited greater virulence than the strain BH1, inducing more severe leaf lesions. FS1 also displayed a higher growth rate on potato dextrose agar, triggering earlier symptom onset. A multifactorial analysis of genotype, location, and year revealed significant effects on disease incidence, with broad-sense heritability estimated at 0.7, highlighting substantial genetic and environmental contributions. Cluster analysis categorized sugarcane genotypes into five resistance groups, identifying CP81-1258 and Q202 as highly resistant, while CP88-1762, FN07-2020, and GT94-119 were highly susceptible. These findings provide critical insights for breeding resistant sugarcane cultivars and optimizing disease management strategies.

Sugarcane (Saccharum spp.) is a vital sugar and bioenergy crop with an exceptionally complex polyploid genome (10-12 sets of chromosomes). This complexity resulted from nobilization-a historical breeding process involving interspecific hybridization and repeated backcrossing1. However, the extreme ploidy has long impeded efforts to elucidate the genetic basis of its considerable sucrose-storing capacity. Here we present a fully phased genome assembly of the foundational cultivar POJ2878, achieved using a Pore-C-based assembly algorithm. This assembly resolved 118 chromosomes, revealing extensive subgenome recombination and non-homologous chromosomal rearrangements. Using identity-by-descent and allele-specific expression profiling, we identified breeder-favoured haplotypes, including a SUS2 haplotype with enhanced sucrose content. Resequencing of 981 Saccharum accessions traced POJ2878's pervasive contribution to modern cultivars and identified key domestication and improvement sweeps. Genes under selection include CBL1 for cold tolerance, TIP1 for cell size regulation and TB1 for tillering control. A genome-wide association study tailored for polyploid genomes resolved loci associated with parenchyma cell size and sucrose storage capacity, including the functionally validated sucrose transporter Saccharum hybrid SUT2. These findings clarify the genetic architecture underlying sugarcane's biomass productivity and sugar yield, offering a genomic foundation for accelerating improvement in sugarcane and other polyploid crops critical for global food and bioenergy security.

Sugarcane (Saccharum spp.) is a major sugar crop, yet its growth and yield are frequently limited by soil salinization. Receptor-like cytoplasmic kinases (RLCKs) act as central signaling hubs in plants, regulating growth, development, immunity, and abiotic stress responses. However, the evolution of the RLCK gene family in sugarcane and its role in salt tolerance remain unclear. Using the high-quality genome of elite cultivar ‘Zhongzhe No.1’, we identified 262 ScRLCK genes, grouped into 15 subfamilies, all of which contain a typical protein kinase domain. Synteny analysis revealed that whole-genome and segmental duplications were the primary drivers of ScRLCK family expansion, accounting for 67.9% duplication events, while purifying selection predominated during their evolutionary trajectory. T Transcriptome profiling revealed widespread differential expression of ScRLCK genes under hormonal treatments and abiotic stresses; notably, ScRLCK53 was strongly upregulated by salt and other stresses. Functional characterization confirmed nuclear localization of the ScRLCK53. Transgenic Arabidopsis lines displayed markedly enhanced seed germination rates and increased seedling fresh weight under salt stress. Moreover, these overexpression lines exhibited heightened sensitivity to jasmonic acid (JA), accompanied by elevated endogenous JA levels, pronounced upregulation of key JA signaling markers, and enhanced expression of canonical salt-responsive genes. This study represents the first comprehensive characterization of the RLCK gene family in sugarcane, elucidating its evolutionary features, expression dynamics and functional roles, and provides compelling evidence that ScRLCK53 modulates salt tolerance through activation of the JA signaling pathway, providing a theoretical foundation and valuable genetic resources for the genetic enhancement of stress tolerance in sugarcane.

Sugarcane leaf scald, caused by Xanthomonas albilineans, is a destructive bacterial disease that threatens sugarcane production. Successful disease development depends on the pathogen's ability to move, colonize host tissues, and spread within plants, yet the regulatory mechanisms underlying these processes remain poorly understood. In this study, we investigated the role of the histidine kinase RavS in the pathogenicity of X. albilineans. A ravS deletion mutant (ΔravS) exhibited significantly reduced swimming and swarming motility, impaired growth, and markedly decreased virulence on sugarcane compared with the wild-type strain. Genetic complementation restored all phenotypes to wild-type levels. Comparative transcriptome analysis revealed that deletion of ravS resulted in coordinated repression of genes involved in flagellar assembly and chemotaxis, processes that are essential for bacterial movement and host colonization. In contrast, tolerances to oxidative stress (H₂O₂), ionic stress (CaCl₂ and MgSO₄), and pH stress were unaffected. Together, these results demonstrate that RavS promotes the development of sugarcane leaf scald by regulating motility-associated pathways that enable X. albilineans to colonize and cause disease in sugarcane effectively.

Sugarcane is a globally important sugar crop, and stalk sugar content is a primary determinant of its industrial value. While ethephon is a commonly used ripening agent known to enhance sugarcane sugar accumulation, systematic field studies evaluating its optimal application remain limited. This research addresses this gap by presenting a detailed investigation into the field application of ethephon to maximize sugar accumulation in sugarcane. Using the medium-to-late maturing sugarcane cultivar ‘ZZ9’, this study investigated the interactive effects of ethephon application concentration, timing, and harvest time on sugar accumulation. Employing a rigorous orthogonal experimental design and Response Surface Methodology (RSM), we systematically dissected the spatial (internode-dependent) and temporal (application and harvest timing-dependent) effects governing ethephon application efficacy. Foliar application of ethephon at varied concentrations significantly enhanced sugar content in sugarcane stalks, specifically affecting these immature internodes. Spatiotemporal application of ethephon revealed optimized results: applying 400 mg/L ethephon approximately 250 days after emergence, followed by harvesting 11 days later, increased stalk sugar content by 0.73% (a 4.4% improvement over the control). Further optimization using RSM established a robust regression model, which predicted that spraying 480 mg/L ethephon at 243 days after emergence, followed by harvesting 10 days post-application, would increase Brix by 0.817% in the 4th internode, corresponding to a 12.16% relative enhancement compared to the control. Although ethephon application slightly reduced sugarcane yield and potentially accelerated leaf senescence, these effects were outweighed by the observed improvements in sugar enhancement under optimized conditions. This study successfully elucidated the optimal application parameters for ethephon to enhance sucrose accumulation in field-grown sugarcane. These findings provide a readily applicable protocol for growers aiming to improve sugar yields, offering valuable insight for enhancing cultivation efficiency and promoting sugar industry development.

BACKGROUND:Herbicide mixtures are widely used in post-emergence weed management to broaden control spectra and mitigate resistance evolution. However, mixture selection is often based on empirical ratios or average efficacy metrics that do not adequately account for heterogeneous weed communities. In practice, management failure is typically driven by the most tolerant species rather than the community's mean performance. Despite this, quantitative decision criteria that explicitly account for worst-case efficacy remain limited. RESULTS:A multi-stage decision-oriented framework was implemented in a sugarcane production system to optimize a ternary post-emergence herbicide mixture. The framework integrated ratio-dose response-surface modelling, interaction robustness screening, and conservative effective-dose mapping. Interaction analysis showed early positive deviations from additivity, which converged toward additivity at later assessments, indicating temporal dependence and limited persistence of synergistic effects. A conservative worst-case effective dose (ED90_worst), defined as the maximum ED90 across weed groups and assessment times, was used as the decision criterion for dose selection. At 25 days after application, ED90_worst ranged from 148.66 to 807.79 g a.i. ha-1 across mixture ratios. The 30:8 ratio achieved ED90 for five of six weed groups. A practical dose band of 652.22-717.44 g a.i. ha-1 satisfied worst-case efficacy requirements while maintaining crop safety across cultivars. CONCLUSION:By prioritizing robustness and worst-case performance rather than point-optimal efficacy, this framework provides a reproducible decision-support approach for optimizing herbicide mixtures in heterogeneous weed communities and supports resistance-aware post-emergence weed management. © 2026 Society of Chemical Industry.

Sugarcane mosaic virus (SCMV) causes substantial yield losses worldwide, yet the molecular basis underlying resistance and susceptibility in sugarcane remains incompletely understood. Here, we performed time-resolved transcriptome profiling of two contrasting sugarcane genotypes, the SCMV-susceptible cultivar Badila and its resistant somatic mutant FG1, across five infection stages. Absolute quantification revealed rapid viral RNA replication in Badila, whereas FG1 showed early suppression followed by SCMV clearance. Comparative transcriptomic analyses showed that FG1 mounted a rapid and sustained defence-associated transcriptional response, whereas Badila displayed delayed, predominantly repressive gene expression changes. Weighted gene co-expression network analysis identified gene modules strongly correlated with viral RNA levels and highlighted the small heat shock protein gene ScHSP17.5 as a central hub associated with susceptibility. Protein-protein interaction assays demonstrated that ScHSP17.5 and ScHSP17.9A specifically interact with the SCMV movement protein P3N-PIPO, but not with P3 or the coat protein. Functional assays in Nicotiana benthamiana further showed that overexpression of either ScHSP enhanced SCMV RNA replication, with co-expression producing a synergistic effect. Together, these results support a model in which SCMV exploits host small heat shock proteins via P3N-PIPO to promote viral accumulation, whereas early redox- and signalling-associated responses restrict infection in resistant sugarcane. This study provides mechanistic insight into SCMV-host interactions and identifies candidate targets for resistance breeding.

Sugarcane leaf scald, caused by Xanthomonas albilineans, is difficult to diagnose because latent infections often precede symptom development, allowing infected planting material to disseminate the pathogen unnoticed. Although quantitative PCR (qPCR) has substantially improved pathogen detection, most available assays target conserved ribosomal regions, which can limit species-level discrimination and offer little guidance for interpreting pathogen abundance. Comparative genomic analysis identified Xal_000736 as a candidate species-specific target for assay development. A TaqMan qPCR assay targeting this locus was developed and evaluated using purified genomic DNA, bacterial suspensions, plant matrix-matched standards, six X. albilineans isolates, 21 non-target bacterial strains, and naturally or artificially infected sugarcane samples. Assay performance was directly compared with that of the previously described 16S rRNA-based xal-FR assay. The biological significance of pathogen abundance was further examined using correlation analysis, logistic regression, receiver operating characteristic (ROC) analysis, and generalized linear mixed-effects models (GLMMs). The 0736 assay showed high amplification efficiency, excellent linearity, and reproducible quantification throughout the validated dynamic range. Quantitative performance was comparable between the two assays, whereas the 0736 assay achieved substantially greater analytical specificity against the bacterial panel examined. ROC analysis also produced a higher area under the curve for the 0736 assay, although the difference between assays was not statistically significant. Pathogen abundance increased with disease severity but overlapped considerably among adjacent symptom classes, indicating that bacterial abundance alone could not fully distinguish disease status. Logistic regression identified quantitative reference values associated with symptom transition and diagnostic classification, while mixed-effects modelling confirmed that the relationship between pathogen abundance and disease status remained significant after accounting for cultivar-related variation. Together, these results show that genome-guided target selection can improve analytical specificity without compromising quantitative performance. They also provide a quantitative basis for interpreting qPCR-derived pathogen abundance in sugarcane leaf scald. Because the proposed reference values were derived from the populations and sampling conditions included in this study, independent validation across additional cultivars, environments, and pathogen populations will be required before routine diagnostic or regulatory use.

Pokkah boeng disease (PBD), caused by Fusarium sacchari, is a devastating fungal disease that threatens global sugarcane production. Understanding the genetic basis of PBD resistance is crucial for molecular breeding under sugarcane’s complex autopolyploidy. Here, we evaluated an F1 population of 201 individuals derived from a cross between ‘ROC22’ (resistant) and ‘Zhongzhe 1’ (susceptible). Based on multi-year field trials and artificial inoculations, we established a robust phenotypic evaluation system using Best Linear Unbiased Prediction (BLUP) values. A k-mer-based genome-wide association study (GWAS) identified 759 associated loci, highlighting 22 stable major-effect loci detected across multiple environments. Time-series RNA-seq analysis revealed the transcriptional dynamics of infection, pinpointing 48 h post-inoculation (hpi) as the critical time point for resistance-susceptibility divergence. By integrating physical mapping with temporal expression patterns, we identified four key candidate genes: the sensor DUF4220, the signaling switch Ras-family protein, the defense executioner DDE superfamily endonuclease, and the homeostasis regulator T-complex protein. This study outlines a four-dimensional (perception-transduction-execution-monitoring) immune framework, revealing the molecular mechanisms by which resistant genotypes construct multiple defense barriers through precise temporal coordination. The identified major-effect loci and core genes provide pivotal targets and a scientific foundation for marker-assisted and genomic selection in sugarcane disease-resistance breeding.

Pokkah Boeng disease (PBD), caused by Fusarium sacchari, has severely impacted the yield and quality of sugarcane, resulting in significant economic losses. However, the molecular interaction mechanisms between F. sacchari and sugarcane remain poorly understood. In this study, we identified the GH12 family protein FsEG1, secreted by F. sacchari, as a critical virulence factor. Further analysis demonstrates that the hydrolase activity of FsEG1 is essential for the full virulence of F. sacchari. The enhanced immune responses and cell death induced by FsEG1 in N. benthamiana depend on the recognition of oligosaccharide elicitors derived from the degradation of host cell walls by FsEG1, which are detected by membrane-localised receptors NbWAKs and NbCERK1, and this process also necessitates RAR1 and MAP3Kα to facilitate intracellular signal transduction. Consequently, FsEG1 activates DTI (DAMP-triggered immunity) rather than the conventional PTI. The stable transgenic sugarcane plants carrying the FsEG1 RNAi hairpin construct displayed high levels of resistance to F. sacchari and decreased FsEG1 expression, production of specific FsEG1 siRNA in transgenic HIGS sugarcane plants was confirmed by stem-loop qRT-PCR; at the same time, the stable transgenic sugarcane plants with ectopic expression of FsEG1 also showed enhanced PBD resistance with activated expression of defence-related genes. Overall, these findings establish a foundational basis for investigating the molecular mechanisms that govern the interactions between F. sacchari and sugarcane and offering valuable insights into enhancing sugarcane's resistance to PBD.

Fusarium oxysporum is the causal agent of Pokkah Boeng disease (PBD) in sugarcane. Lysine acetylation (Kac) is a dynamic and reversible post-translational modification that plays a critical role in regulating diverse cellular processes. Although Kac is known to significantly influence protein function, its specific role within the F. oxysporum secretome during PBD pathogenesis remains poorly understood. In this study, we conducted a comprehensive analysis of the lysine acetylome across the F. oxysporum secretome. Utilizing highly sensitive immunoaffinity purification coupled with high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 291 acetylation sites within 85 potentially secreted proteins. Bioinformatics analysis revealed that these acetylated proteins are involved in a wide array of biological functions and exhibit diverse subcellular localizations. Notably, these secreted proteins represent a valuable resource for identifying novel effectors; specifically, eight upregulated genes encoding Kac proteins were identified as potential players during the initial asymptomatic stages of infection. Collectively, these findings provide a global overview of the F. oxysporum secretome acetylome and offer a foundational resource for elucidating the functional significance of lysine acetylation in sugarcane PBD pathogenesis.

Pokkah boeng disease has been reported in nearly all countries where sugarcane is commercially cultivated. Historically, this disease was regarded as a minor concern; however, due to the impacts of climate change, it has now escalated into a significant issue. The causative agents of this disease are fungi, specifically belonging to the Fusarium fungal complex, with Fusarium sacchari being the predominant species in Guangxi Zhuang Autonomous Region, China. However, the pathogenic mechanism remains largely unknown. In this study, we have identified and characterized an effector protein designated as FsP4H1, which contains a prolyl-4-hydroxylase domain and is crucial for the virulence of F. sacchari. FsP4H1 localizes to the host cytoplasm and nucleus, and its nuclear localization is required for the immune suppression in the host. We demonstrate that FsP4H1 interacts with the transcription factor DPb, a positive regulator of plant immunity, and facilitates degradation of DPb via the 26S proteasome. This degradation leads to downregulation of catalase genes, ScCAT9, ScCAT34 or NbCAT, which are direct transcriptional targets of DPb and play a crucial role in maintaining hydrogen peroxide (H2O2) homeostasis. Consequently, in the interaction between F. sacchari and sugarcane, F. sacchari secretes FsP4H1 into the hosts' nuclei, resulting in the disruption of the DPb-CAT module to enhance host susceptibility. Our study reveals a novel virulence strategy in which a fungal effector hijacks a conserved plant transcriptional network to suppress antioxidant defences, providing potential targets for resistance breeding in sugarcane.

Genome-wide association studies in complex polyploids are hindered by genotyping ambiguity and allele dosage complexity. Here we present KMERIA, a k-mer-based framework specifically designed to address these challenges, enabling efficient genotyping and robust association mapping in complex polyploid genomes. Rigorous benchmarking with simulated and empirical datasets demonstrates that KMERIA surpasses existing methods in accuracy and statistical power. By applying KMERIA to 290 wild sugarcane (Saccharum spontaneum) accessions and integrating a 15-accession graph pangenome to capture structural variations, we identified new genes regulating sucrose biosynthesis (SsMGT) and tillering (for example, SsERF14, SsNGA5, SsNAC, SsARF8, SsLOG and SsSCR). These findings elucidate the genetic architecture of yield-related traits and provide actionable targets for sugarcane breeding. Collectively, KMERIA bridges a critical methodological gap in polyploid genomics, while our graph-pangenome integration provides a powerful framework for deciphering genotype-phenotype relationships in crops with complex architectures.

Summary statement The transcription factor TaDREB2B enhances sugarcane drought tolerance through two complementary pathways: it represses aquaporin genes in an ABA‐independent manner to reduce water loss and interacts with ScGTE10 to synergistically activate the ABA‐dependent ScSnRK2.8 signalling cascade.

Pokkah Boeng disease caused by Fusarium sacchari seriously threatens the yield and quality of sugarcane worldwide. Effectors play a crucial role in the infection and colonization of pathogens. However, there were few reports on the virulence functions of F. sacchari effectors. To characterize effector functions and unravel the pathogenic mechanisms of F. sacchari, we identified an effector FsSCR6, which was vital for the virulence of F. sacchari. Gene knockout mutants showed no difference in growth rates and colony morphology from wild-type. However, the virulence of knockout mutants was severely impaired. Agrobacterium-mediated transient expression assays in Nicotiana benthamiana showed that FsSCR6 and FsSCR6Δsp (without signal peptide) performed cell death-suppressive activity inside plant cells. 3'3-diaminobenzidine staining and aniline blue staining assays showed that FsSCR6 significantly reduced the accumulation of reactive oxygen species and callose deposition triggered by BCL-2-Associated X protein (BAX) in N. benthamiana leaves. FsSCR6 significantly suppressed the relative expression of the marker genes of the hypersensitive responses and salicylic acid (SA)-, jasmonic acid (JA)-, and ethylene-dependent immunity in N. benthamiana. Overall, FsSCR6 is required for F. sacchari virulence; it performs a function inside plant cells and suppresses the plant immune responses by regulating the SA-, JA- and ethylene-mediated defense pathways. These results clarify the function of this effector from F. sacchari and assist in dissecting the interaction between sugarcane and F. sacchari, ultimately contributing to sugarcane production.

The sugarcane genus Saccharum is characterized by complex genomes with diverse ploidy levels. We developed a multiscale graph–based pangenome representation, which integrates nine genome assemblies into a unified reference, representing modern cultivars and founding species. Each homo(eo)logous (encompasses both homologous and homeologous relationships) chromosome set retains 47 to 57 haplotypes and ~74,000 to 271,000 gene alleles. This framework enables multiomics exploration, encompassing homo(eo)log systems and epigenomic signatures. The pangenome facilitates population genomics analyses of 417 mixed-ploidy Saccharum accessions, revealing convergent selection and identifying the Andropogoneae TB1 homolog linked to tillering as a promising gene-editing target to boost cane yield. Additionally, the pangenome supports dosage-informed genome-wide association study, improving heritability estimates and identification of sugar or leaf-angle–associated loci, including SaIRX10 and SaBAK5 . Our analytical framework establishes a foundation for graph-based genetic studies in sugarcane and other polyploid genomes.

Sugarcane growth crack accelerates internal water loss and increases susceptibility to biotic stress, significantly affecting quality. However, the molecular mechanism underlying this phenomenon is poorly understood. This study evaluated eight crack-related traits across 94 sugarcane germplasms. These results of multivariate statistical analysis showed that number of growth crack internodes (NGCI) and growth crack rate (GCR) can be used to evaluate the growth crack of sugarcane. Applying this system to 392 germplasms, two extremes were found: 16–091 (no growth crack) and 16–0946 (severe growth crack). Both varieties exhibited comparable tissue water content, but 16–0946 absorbed more water after soaking, suggesting rapid water uptake within a short time is a key driver of crack growth. In addition, its peel contained significantly higher lignin content, with slightly reduced cellulose and unchanged hemicellulose and pectin. These results indicate that relatively high lignin content in the stem peel is a crucial factor contributing to growth crack. Transcriptomic and metabolomics analysis further supported this hypothesis, with upregulated differentially expressed genes (DEGs) were significantly enriched in lignin biosynthesis pathways, and downregulated DEGs were significantly enriched in regulation of jasmonic acid signaling pathway and regulation of response to water deprivation. The upregulated differentially accumulated metabolites (DAMs) were significantly enriched in the phenylpropanoid biosynthesis pathway, a key metabolic route contributing to lignin biosynthesis. Furthermore, lignin biosynthetic genes (e.g. PAL, COMT, and CCoAOMT) exhibited elevated expression levels in 16–0946. Collectively, these findings enhance understanding of the occurrence mechanism of growth crack and identify potential genetic improvement targets for sugarcane.

Contemporary sugarcane cultivars originate from interspecific hybridization between Saccharum officinarum and Saccharum spontaneum, resulting in highly complex polyploid genomes. Dissecting chromosomal inheritance and structural variation is critical for accelerating molecular breeding in sugarcane. Here, we applied chromosome-specific painting using ten probes, together with S. spontaneum-specific probes, to resolve chromosomal composition and translocation patterns in the cultivar CT89-103 and its derived hybrids. High-resolution physical map was constructed in sugarcane cultivar CT89-103 that harbors 111 chromosomes, with 7-12 copies of each chromosome (1-10), and exhibits 13 distinct chromosomal translocation types. Its genome comprises 7.14% S. spontaneum-derived chromosomes and 24.11% interspecific recombinant chromosomes. The hybrids contain 108-116 chromosomes, with 5-15 copies of chromosomes 1-10 converging toward ~12 copies, and show similar genomic composition (8.20% S. spontaneum and 23.88% recombinant chromosomes). These findings demonstrate that S. spontaneum chromosomal segments and parental translocations are largely transmitted through n + n inheritance. Notably, extensive structural variation was observed, with 35 translocation types predominating in the hybrids. Altogether, this study provides a high-resolution view of chromosomal inheritance and structural variation in sugarcane, offering a cytogenetic framework for sugarcane hybridization.

Sugarcane smut, caused by Sporisorium scitamineum, is a major disease threatening global sugarcane production. Biological control agents (BCAs) offer environmentally sustainable alternatives to chemical fungicides, with Bacillus velezensis recognized for its broad-spectrum antifungal properties. In this study, B. velezensis ZHR0 was isolated from sugarcane leaves and evaluated for its antifungal activity through in vitro dual-culture assays and in vivo greenhouse trials. Field application of a ZHR0-based biofertilizer achieved a maximum disease control efficiency of 43.86%. Whole-genome sequencing revealed a 4.04 Mb genome with a GC content of 46.48%, encoding 4,150 genes, including multiple biosynthetic gene clusters (BGCs) associated with secondary metabolite production. In vitro assays showed that ZHR0 inhibited the growth of S. scitamineum by 53.20% and reduced disease incidence in sugarcane seedlings by 45.74%. Notably, BGCs for iturin, fengycin, surfactin, and difficidin were identified, and liquid chromatography-mass spectrometry (LC-MS) confirmed the production of iturin, supporting its role in antifungal activity. These findings demonstrate the biocontrol potential of B. velezensis ZHR0 against sugarcane smut and provide integrated genomic and metabolomic evidence for its application as a sustainable biocontrol agent in sugarcane cultivation.