Sugarcane is a major global crop for sugar and bioenergy in tropical and subtropical regions. Abiotic stresses such as drought and salinity severely impair sugarcane production. Aquaporins (AQPs), small integral membrane proteins that facilitate the transport of water and small solutes across biological membranes, have been implicated in crop response to abiotic stress. However, the AQP gene family has not yet been systematically characterized in sugarcane. In the present study, AQP genes were identified in the genomes of Saccharum spontaneum AP85-441 (38 genes, 141 alleles), Saccharum officinarum B48 (38 genes, 267 alleles), and the sugarcane cultivar XTT22 (39 genes, 441 alleles). Phylogenetic analysis further classified these genes into four clades: PIP, TIP, NIP, and SIP. Combined analysis of transcription factor-binding sites, transcriptomic data, and RT-qPCR data suggested that PIPs may function in water transport and tolerance to abiotic stresses. Eight PIPs were cloned from XTT22 and evaluated using yeast transformation under PEG 6000 or NaCl treatments. The results showed that the yeast cells expressing ScPIP2;4 exhibited the maximum growth inhibition under stress condition. ScPIP2;4 was subsequently overexpressed in Nicotiana. benthamiana plants. Transgenic N. benthamiana lines exhibited tolerance to PEG 6000 or NaCl treatments, which was associated with increased proline content and reduced malondialdehyde level. This study comprehensively identified the AQP family in the Saccharum genus, which provides insights on AQP functions in sugarcane and provide potential molecular targets for engineering osmotic-stress resistant sugarcane.

Abstract Background Magnesium (Mg²⁺) is essential for chlorophyll synthesis, enzyme activation, and photosynthesis, but the differential regulation of Mg²⁺ homeostasis between the two founding Saccharum species ( Saccharum officinarum and Saccharum spontaneum ) remains unknown. Results We systematically characterized the MGR gene family in S. spontaneum and S. officinarum and uncovered distinct physiological responses to Mg²⁺ availability between the two species. Comparative expression analysis across the leaf developmental gradient and diurnal cycles revealed species-specific transcriptional dynamics of MGR2 , suggesting divergent regulatory mechanisms underlying Mg²⁺ management. Functional complementation in the Mg²⁺-deficient Salmonella typhimurium MM281 mutant demonstrated that both SsMGR2 and SoMGR2 restore Mg²⁺ uptake, confirming their conserved transport capability. Overexpression of SsMGR2 in rice conferred increased biomass under Mg²⁺ deficiency and enhanced tolerance to Mg²⁺ excess, indicating a broad role for this gene in Mg²⁺ homeostasis. Promoter architecture and transcription factor prediction further revealed interspecific divergence, with BBX25, COL5, and WRKY19-2 exhibiting species-dependent regulatory interactions that potentially explain the observed differences in MGR2 expression. Conclusion Overall, the research results indicate that S. spontaneum and S. officinarum exhibit different Mg²⁺ responses and MGR2 regulatory patterns, highlighting the distinct strategies for Mg²⁺ homeostasis in these two founding species. This work provides new insights into the transport mechanism of Mg²⁺ in sugarcane and preliminarily identifies candidate genes and regulatory factors for improving nutrient efficiency and stress recovery ability.

IntroductionSugarcane mosaic disease (SCMD) poses a severe threat to global sugarcane yield. Since conventional field management is insufficient to restrict viral transmission, unraveling the underlying defense mechanisms is imperative for targeted breeding. The primary objective of this study was to delineate the molecular and metabolic networks governing SCMD resistance by comparing highly resistant (XIDAZHE10-19, YT94-128) and susceptible (HP, XTT22) cultivars.MethodsWe employed metabolomic profiling and integrated transcriptomic data to investigate the genetic basis driving host responses. To further elucidate the functional and regulatory mechanics of identified key hub genes, we conducted weighted gene co-expression network analysis (WGCNA) alongside AlphaFold-driven structural predictions and interactome profiling.ResultsMetabolomic profiling identified critical defense-associated metabolites --including alcoholamines and glycerol derivatives --that strongly correlate with disease incidence. Transcriptomic integration yielded two major findings. First, pathway enrichment revealed a striking dichotomy in defense strategies: XIDAZHE10-19 preferentially orchestrated the autophagy pathway and aromatic amino acid biosynthesis, whereas YT94-128 relied heavily on calcium signaling and peroxisome-mediated reactive oxygen species (ROS) homeostasis. Second, WGCNA pinpointed ShNDK as a core hub gene exhibiting robust upregulation in susceptible cultivars. AlphaFold predictions further revealed that ShNDK potentially assembles into dimers and physically associates with canonical immune transcription factors (e.g., bZIP, Dof) and pathogenesis-related (PR) proteins.DiscussionThe novelty of this work lies in uncovering divergent, cultivar-specific defense strategies and identifying novel genetic hubs through a multi-omics and structural biology approach. Together, these findings unveil a complex, multi-layered defense network against SCMD. The characterization of ShNDK and the elucidation of cultivar-specific synergistic crosstalk provide a crucial mechanistic foundation and promising genetic targets for developing sugarcane cultivars with heritable, broad-spectrum resistance.

Abstract Tripidium arundinaceum , a wild perennial grass with exceptional stress tolerance, has been tested in sugarcane breeding. Its complex polyploid genome has hindered understanding of its evolution and adaptive traits. Here, we present a high-quality, haplotype-resolved reference genome for autohexaploid T. arundinaceum Hainan92-105 (2 n = 6 x = 60). T. arundinaceum is likely originated from a diploid ancestor approximately 1.31 million years ago and contains abundant repetitive sequences from two major recent bursts of long terminal repeat retrotransposons following polyploidization. Phylogenetic analyses place Saccharum closer to Sorghum bicolor than to T. arundinaceum , indicating that the polyploidizations in these two lineages occurred independently. Population genomics analysis reveals southwestern China (Yunnan) as a diversity center for T. arundinaceum within China. Genotype–environment associations highlight temperature and precipitation as key local adaptation drivers mediated by stress-associated genes. This study provides a genomic resource for understanding polyploid evolution and climate adaptation in T. arundinaceum .

Epigenetic editing enables programmable and potentially reversible regulation of chromatin states without altering DNA sequences. By establishing a framework of programmable chromatin engineering, epigenetic editing provides new opportunities for designing climate-resilient crops and advancing next-generation precision breeding.

Modern sugarcane cultivar XTT22 is characterized by high sucrose content and favorable agronomic traits and is widely cultivated as well as extensively used as a backbone parental line in sugarcane breeding. However, the molecular regulation of sucrose accumulation remains poorly understood due to its complex polyploid genome. Recently, our team successfully assembled and resolved the XTT22 genome, providing a robust foundation to explore these complex regulatory mechanisms. Here, we quantified sucrose content across six key developmental stages and profiled gene expression in leaf, upper stem, central stem, and lower stem tissues. Multivariate and pairwise analyses revealed pronounced expression divergence between the upper stem and the central/lower stem during the rapid sucrose accumulation. Integration of spatiotemporal transcriptome profiling with weighted gene co-expression network analysis (WGCNA) identified three region-specific modules comprising 19 candidate genes with putative roles in sucrose accumulation. Functional annotation indicated spatial specialization: the upper stem was enriched for genes associated with sucrose biosynthesis, transport, and auxin-mediated regulation; the central stem for stress responses and auxin signaling/transport; and the lower stem for stress-response pathways. Four hub genes, including IAA30 and ARF2, were identified, highlighting the central role of auxin signaling. Beyond the predominant negative correlations, two positive correlations emerged between photosynthesis-related genes and hub genes, suggesting a more complex source-sink relationship during sucrose accumulation than previously appreciated. Haplotype-resolved mapping showed that upper-stem candidates predominantly originated from the high-sucrose S. officinarum, whereas central/lower-stem candidates were mainly derived from the stress-tolerant S. spontaneum, reflecting their ancestral contributions. Overall, our results demonstrate spatiotemporal specialization of gene expression underlying sucrose accumulation in XTT22 and highlight auxin signaling potentially serving as a key regulatory module. These findings provide new insights into the molecular basis of sucrose accumulation and offer candidate genes with potential for targeted improvement of sugarcane cultivars.

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.

Sugarcane (Saccharum spp.) is a globally important C4 crop that contributes substantially to sugar production and renewable bioenergy systems. Modern sugarcane cultivars were derived from interspecific hybridization between high-sucrose S. officinarum and stress-resilient wild S. spontaneum, followed by extensive backcrossing and selection. Such breeding trajectory has generated an extremely complex polyploid genome marked by high ploidy, pervasive aneuploidy, mosaic subgenome composition, and a reticulate evolution history. For decades, this complexity has resulted in persistent taxonomic ambiguities, constrained genomic analyses, complicated genetic dissection of agronomic traits, and limited breeding efficiency. The rapid development of third-generation long-read sequencing, haplotype-resolved assembly, and polyploid-aware computational approaches has fundamentally revolutionized sugarcane research. This review synthesizes recent progress in Saccharum taxonomy, polyploid genome architecture and evolution, high-quality genomic resource development, germplasm exploration, and genome-informed breeding strategies. We propose an integrated framework connecting taxonomic refinement, genome biology, and breeding applications. Critical challenges are elaborated, including the taxonomy-genomics disconnect, diploid-centric analytical bias, insufficient haplotype resolution, the lack of polyploid-aware genetic models, and underutilization of wild germplasm. Finally, we outline future priorities toward predictive and design-oriented sugarcane improvement by addressing unresolved core questions. This review provides a comprehensive and forward-looking perspective for accelerating genetic improvement in sugarcane and other highly complex polyploid crops.

Traditionally viewed as cytoplasmic catalysts, plant metabolic enzymes are now known to moonlight in the nucleus. This forum article highlights emerging mechanisms by which nuclear-localized metabolic enzymes couple plant metabolic status to development and stress responses via chromatin regulation, providing a conceptual framework for metabolic-epigenetic crosstalk and future crop improvement.

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.

In Poaceae, the rho whole-genome duplication (ρ-WGD) event gave rise to three Paleo-duplicated chromosome pairs (PdCPs) that are enriched in resistance genes (nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes) but show low transcriptional levels. Despite their evolutionary importance, systematic family-wide studies of PdCPs have been lacking. We analyzed 37 Poaceae genomes using karyotyping and evolutionary analyses, mapped NBS-LRR genes distributions, and examined transcriptomic and epigenomic patterns across representative species to characterize the evolution and regulation of PdCPs. Our findings show that PdCPs have persisted throughout the evolutionary history of Poaceae, exhibiting distinct patterns of rearrangements among different subfamilies. Notably, one PdCPs is consistently enriched in disease resistance genes across multiple subfamilies and displays conserved low transcriptional activity. This PdCPs also exhibits conserved CHH hypomethylation around transcription start site regions. Further analyses suggest that this PdCPs maintains a more closed chromatin state, associated with repressive histone modifications that suppress gene expression. These results imply that the low transcriptional levels of genes on this PdCPs may be regulated by multiple epigenetic mechanisms. This study advances our understanding of the formation, diversification, and epigenetic regulation of PdCPs following the ρ-WGD in Poaceae.

A high-quality reference genome requires not only accurate DNA sequences but also well-defined gene-structure annotations. However, many existing tools depend predominantly on automated pipelines that perform poorly when confronted with complex gene architectures, such as overlapping loci, alternative splicing patterns, and lowly expressed isoforms, resulting in incomplete or inaccurate annotations. To overcome these limitations, we developed GSAman, a standalone, ready-to-use tool that enables intuitive, what-you-see-is-what-you-get (WYSIWYG) editing of gene-structure annotations. In contrast to web-based platforms such as Apollo2, which generally require server deployment and do not provide full offline functionality, GSAman delivers a fully local, responsive interface for real-time annotation refinement, thereby improving accessibility across research settings. GSAman supports both fine-scale curations of individual genes and large-scale annotation of entire genomes. By enabling precise curation of gene models across varied genomic contexts, it directly facilitates downstream applications, including pan-genome construction, gene family evolutionary analyses, and precision crop enhancement. Using a telomere-to-telomere rice genome (MH63) annotation project as a case study, we demonstrate the practical utility of GSAman in producing a complete and accurate reference annotation, improving Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness to 99.63% following manual curation. We believe GSAman will serve as a critical resource for advancing functional genomics across diverse species.

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.

Papaya is a trioecious species with XX females, XY males, and XYh hermaphrodites. Any combination of Y and Yh chromosomes is lethal. The gene underlying YY lethality is pivotal in the transition from stage 2 to stage 3 in sex chromosome evolution. Here, we identify and functionally validate the YY lethality gene in papaya, CpYYL. Loss of CpYYL function accelerates glycolysis and reduces sucrose accumulation in embryo, causing embryo abortion. CpYYL interacts with CpAKRP and overexpression of both genes partially rescues seed abortion in the heterozygous emb506 and akrp mutants, indicating conserved role in plastid differentiation and embryo development. Viable YYh and YhYh plants are generated through genetic engineering and crossing, although both genotypes show high seedling mortality. Crossing YYh male with XX female papaya shows 1:1 ratio of male to hermaphrodite plants without recombination between MSY and HSY. Identification of CpYYL fills a critical gap in papaya sex chromosome evolution, and provides new resources for genomic and epigenetic studies. Papaya is a trioecious species with XX females, XY males, and XYh hermaphrodites, and the combination of Y and Yh chromosomes is lethal. Here, the authors identify the degeneration of the YY lethality gene on the Y chromosome as the causal balancing lethal factor that reenforces dioecy and stabilizes balanced sex ratios.

Traditional sugarcane breeding, reliant on phenotypic selection, is being transformed by genomic tools. However, the crop's highly polyploid genome and significant genotype-by-environment interactions pose challenges that conventional models cannot adequately address. Although the integrated genomic-enviromic prediction (iGEP) framework offers a promising path forward, its application to a complex clonal crop such as sugarcane requires significant extension. This review provides the first comprehensive road map for implementing iGEP in sugarcane, systematically addressing its unique biological constraints, and synthesizes a tailored "three-model" computational framework (genetic, environmental, and phenotypic) to decode polyploid allelic dosage, quantify high-resolution environmental drivers through an "isoenvironment" design, and predict clonal performance. In addition, we describe extensions of artificial intelligence (AI) and iGEP models to leverage clonal propagation, optimize multi-trait selection, and overcome perennial ratoon dynamics. Finally, we present a phased road map for construction of an AI model, outlining a transformative path from digitization to synthetic design. By combining cutting-edge predictive analytics with the distinctive biology of sugarcane, this work establishes a new paradigm for accelerating genetic gain in this vital crop and offers a transferable strategy for other species with complex genomes.

Fusarium sacchari, the causal agent of pokkah boeng disease (PBD), is a globally devastating pathogen of sugarcane that causes substantial economic losses. During infection, the fungus employs elicitors to induce necrosis in plant tissues, thereby enhancing pathogen fitness. However, the key elicitors in F. sacchari and the mechanism by which plants recognize them remain unclear. Here, we identified a predicted glycosylated phosphatidylinositol (GPI)-anchored protein FsEcm33 as an elicitor that activates plant immunity. FsEcm33 is perceived in the apoplast of Nicotiana benthamiana by the receptor-like protein NbRE02 and induces cell death in a manner that requires the co-receptors NbBAK1 and NbSOBIR1. Purified FsEcm33 triggers basal immune responses in N. benthamiana and enhances disease resistance in multiple plant species, including sugarcane, rice, wheat, and star anise. In F. sacchari, FsEcm33 localizes to the cell surface, where its recognition by the host limits pathogen colonization. Notably, FsEcm33 specifically interacts with a 14-3-3 protein, FsBmh1, which reduces its accumulation at the fungal cell surface, suggesting a spatial sequestration mechanism that helps F. sacchari evade host immunity. Together, these findings establish FsEcm33 as a cell-surface elicitor perceived by NbRE02 and reveal an evolutionary strategy in which FsBmh1 sequesters FsEcm33 to evade host recognition and facilitate infection in F. sacchari.