Sugarcane (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. To 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. Our 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.

Sugarcane (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. To 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. We 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.

Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. However, genetic improvement through conventional breeding is constrained by long breeding cycles, low genetic gain, and considerable operational complexity arising from its highly allopolyploid and aneuploid genome. With the increasing global demand for sustainable food and renewable energy, sugarcane breeding programs must accelerate the development of high-yielding, stress-tolerant cultivars through the integration of advanced biotechnological tools with traditional breeding approaches. Recent advances in genetic engineering, genomic selection (GS), and high-throughput omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and phenomics, have substantially enhanced the efficiency of trait improvement related to growth, development, yield, and stress resilience. The integration of multi-omics data enables the dissection of regulatory networks linking genotype to phenotype, improves predictive accuracy, and provides deeper insights into the molecular mechanisms underlying complex traits. These integrative approaches support more informed selection decisions and accelerate genetic gain in sugarcane breeding programs. This review synthesizes recent technological developments and their practical applications in sugarcane improvement. It highlights the strategic implementation of transgenic and genome-editing technologies, genomic selection, and multi-omics integration to enhance yield potential and resistance to biotic and abiotic stresses, thereby contributing to sustainable sugarcane production and global food and bioenergy security.

Flowering often perturbs carbon allocation in sugarcane, yet its transcriptomic–metabolomic basis remains unclear. We profiled two contrasting cultivars, Gui Tang 16-3285 (sugar increases during flowering) and Gui Tang 44 (sugar decreases), sampling apical tissues at five stages (Non-spikelet-bearing stage (NSB), Early booting stage (ESB), Late booting stage (LSB), Tasseling stage (TS), and Flowering stage (FS)). RNA-seq and untargeted LC–MS revealed a strong stage/genotype structure (PCA) with high reproducibility. Pairwise contrasts (FS vs. earlier stages) and time series clustering (Mfuzz) showed extensive, stage-resolved reprogramming with small cross-cultivar overlaps. GO/KEGG indicated that GT16 is enriched for central carbon processes and glucose response, whereas GT44 favors cell-wall remodeling (xylan/xyloglucan), amino/nucleotide sugar, and phenylpropanoid pathways. Integrated analysis identified opposing temporal features across omics layers: in GT16, late-rising metabolites—including sedoheptulose—were consistent with enhanced pentose phosphate/Calvin coupling that regenerates fructose-6-phosphate for sucrose biosynthesis; in GT44, early activation of wall and secondary sinks, together with trehalose/(trehalose-6-phosphate) T6P signatures, paralleled declining soluble sugars. Across cultivars we resolved 11 and 18 genes in reciprocal opposite-trend sets (most with clear temporal order) and eight vs. five metabolites with mirrored dynamics, nominating actionable biomarkers (e.g., sedoheptulose/S7P) and regulatory nodes. These results provide a mechanistic framework linking flowering stage to carbon partitioning and suggest practical levers—timing growth moderation/ripeners, prioritizing sucrose phosphate synthase/Sucrose Phosphate Phosphatase, tempering wall flux, to sustain sucrose during reproductive development and inform breeding for high-sugar, flowering-resilient ideotypes.

Background. Water channel proteins, also called aquaporins, are integral membrane proteins from major intrinsic protein (MIP) family and involved in several pathways including not only water transport but also cell signaling, reproduction, and photosynthesis. The full cDNA and protein sequences of aquaporin inChorispora bungeanaFisch. & C.A. Mey (C. bungeana) are still unknown.Results. In this study, PCR and rapid amplification of cDNA ends approaches were used to clone the full cDNA of LRB7 (GenBank accession number: EU636988) ofC. bungeana. Sequence analysis indicated that it was 1235 bp, which had two introns and encoded a protein of 250 amino acids. Structure analysis revealed that the protein had two conserved NPA motifs, one of which is MIP signature sequence (SGxHxNPAVT), six membrane helix regions, and additional membrane-embedded domains. Phylogenetic analysis suggested that the protein was from TIP2 subgroup. Surprisingly, semiquantitative RT-PCR experiment and western blot analysis showed that LRB7 and TIP2 were only detectable in roots, unlikeArabidopsisandRaphanus. Connecting with our previous studies, LRB7 was supported to associate with chilling-tolerance inC. bungeana.Conclusion. This is the first time to characterize the full sequences of LRB7 gene and water channel protein inC. bungeana. Our findings contribute to understanding the water transports in plants under low temperatures.