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.
Tianyou Wang, Qin Zhang, Qiutao Xu et al.· Journal of Integrative Plant...· 0 citations
Introduction Sugarcane 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. Methods We 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. Results Metabolomic 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. Discussion The 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.
Mingjie You, Hui Li, Yan Xie et al.· Frontiers in Plant Science· 0 citations