Sugarcane is an important sugar and energy crop that is widely planted in the world. Among the environmental stresses, the water-deficit stress is the most limiting to plant productivity. Some groups have used PCR-based and microarray technologies to investigate the gene expression changes of multiple sugarcane cultivars under water stress. Our knowledge about sugarcane genes in response to water deficit is still poor. A wild sugarcane type, Saccharum narenga, was selected and treated with drought stress for 22 days. Leaves from drought treated (DTS) and control (CK) plants were obtained for deep sequencing. Paired-end sequencing enabled us to assemble 104,644 genes (N50 = 1605 bp), of which 38,721 were aligned to other databases, such as UniProt, NR, GO, KEGG and Pfam. Single-end and paired-end sequencing identified 30,297 genes (> 5 TPM) in all samples. Compared to CK, 3389 differentially expressed genes (DEGs) were identified in DTS samples, comprising 1772 up-regulated and 1617 down-regulated genes. Functional analysis showed that the DEGs were involved in biological pathways like response to blue light, metabolic pathways and plant hormone signal transduction. We further observed the expression patterns of several important gene families, including aquaporins, late embryogenesis abundant proteins, auxin related proteins, transcription factors (TFs), heat shock proteins, light harvesting chlorophyll a-b binding proteins, disease resistance proteins, and ribosomal proteins. Interestingly, the regulation of genes varied among different subfamilies of aquaporin and ribosomal proteins. In addition, DIVARICATA and heat stress TFs were first reported in sugarcane leaves in response to water deficit. Further, we showed potential miRNAs that might be involved in the regulation of gene changes in sugarcane leaves under the water-deficit stress. This is the first transcriptome study of Saccharum narenga and the assembled genes are a valuable resource for future research. Our findings will improve the understanding of the mechanism of gene regulation in sugarcane leaves under the water-deficit stress. The output of this study will also contribute to the sugarcane breeding program.

The N⁶-methyladenosine (m⁶A) methylation of mRNA is involved in biological processes essential for plant growth. To explore the m⁶A modification of sugarcane and reveal its regulatory function, methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to construct the m⁶A map of sugarcane. In this study, m⁶A sites of sugarcane transcriptome were significantly enriched around the stop codon and within 3′-untranslated regions (3′UTR). Gene ontology (GO) analysis showed that the m⁶A modification genes are associated with metabolic biosynthesis. In addition, the m⁶A modification of drought-resistant transcript mRNA increased significantly under drought (DR) treatment, resulting in enhanced mRNA stability, which is involved in regulating sugarcane drought resistance. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results showed that differentially methylated peak (DMP) modification of differentially expressed genes (DEGs) in DR were particularly associated with abscisic acid (ABA) biosynthesis. The upregulated genes were significantly enriched in the ABA metabolism, ethylene response, fatty acid metabolism, and negative regulation of the abscisic acid activation signaling pathway. These findings provide a basis and resource for sugarcane RNA epigenetic studies and further increase our knowledge of the functions of m⁶A modifications in RNA under abiotic stress.

Sugarcane is an important industrial crop with a high sugar yield that has become a leading energy crop worldwide. It is widely cultivated in tropical and subtropical regions. Various diseases beset the cultivation of sugarcane. The molecular study of disease resistance in sugarcane is limited by its complicated genome. In our study, RNA-seq was employed to detect the mechanism of twisted leaf disease tolerance in modern cultivar sugarcane, which derived from Narenga porphyrocoma. We completed high-throughput transcriptomic sequencing of 12 samples, including three stages of a susceptible (NSBC1_T “H3–8”) and an unsusceptible cultivar (NSBC1_CK “H-19”) with two biological repeats, respectively. Using the Saccharum spontaneum genome as reference, the average mapping ratio of the clean data was over 70%. Among the differentially expressed genes between H3–8 and H3–19, we focused on the analysis of hormone pathways and resistance (R) genes. The results showed that twisted leaf disease triggers hormone networks and around 40% of R genes conditioned lower expression in the susceptible cultivar. One of the possible reasons for H3–8 being susceptible to twisted leaf disease might be the null/retarded response of R genes, especially in pre-onset stage (46% down-regulated) of pathogens infection.

Sugarcane is highly sensitive to the variations in soil moisture content capacity, and upregulated water stress efficiency restricts its development and crop output. Rhizospheric microbes and metabolites play key roles to mitigate the adverse effects of abiotic stresses, i.e., drought stress. The drought-tolerant wild sugarcane relative, Saccharum arundinaceum Retz., remains poorly characterized with respect to its rhizosphere microbial community dynamics under water limitation. To address this, we analyzed drought-associated shifts in the rhizosphere microbiome and metabolome by comparing native plants from a long-term arid habitat in Guangxi, China, with plants from an irrigated cultivation environment. We analyzed the effects of agronomic traits, soil properties, enzyme activities, and 16S rRNA sequencing and untargeted metabolomics to characterize microbial communities and metabolites, with correlation analyses. Results demonstrated that wild plants possessed thicker stems, higher proline levels, and increased antioxidant enzyme activity. Their rhizospheres were enriched with Actinobacteria, Proteobacteria, and Chloroflexi, which exhibited upregulated urease and acid phosphatase activities. Metabolites linked to phosphotransferase systems and sugar metabolisms were also more abundant. Positive correlations between these microbes, metabolites, and drought traits reveal site-specific microbial–metabolic modules that confer drought resilience, providing valuable insights for sugarcane breeding programs.

Sugarcane production in China is severely constrained by frequent seasonal droughts, especially in the major planting region of Guangxi. Identifying drought-resistant varieties is crucial for ensuring yield stability. This study aimed to comprehensively evaluate the drought resistance of 15 sugarcane varieties and screen key identification indicators. A pot experiment was conducted with both well-watered (control) and drought-stress treatments. Fifteen agronomic and physiological traits were measured, and drought resistance was assessed using the comprehensive drought resistance evaluation value (D value), the comprehensive drought resistance coefficient (CDC), and the weighted drought resistance coefficient (WDC). Results showed significant variations in trait responses to drought: green leaf number (NGL) decreased the most (66.06%), while proline (Pro) increased the most (88.09%). PCA reduced 15 traits to 5 principal components, with a cumulative variance contribution rate of 82.26%. Comprehensive evaluation using D values, comprehensive drought resistance coefficients (CDCs), and weighted drought resistance coefficients (WDCs) showed consistent overall drought resistance rankings, with slight differences in individual varieties. Cluster analysis based on D values classified the 15 varieties into three groups: 10 drought-resistant (66.67%, e.g., YZ08-1609, LT5), 3 moderately drought-resistant (e.g., GT08-56), and 2 drought-sensitive (GT10-612, ZT13-012). Grey relational analysis identified single stalk weight (SSW), number of leaves (NL), and number of green leaves (NGL) as key indicators closely associated with drought resistance. This study provides a scientific basis for establishing a drought-resistant sugarcane variety evaluation system and lays the foundation for breeding drought-resistant varieties.