Pathogen infection seriously affects plant development and crop productivity, sometimes causing total crop failure. In this study, artificial stab inoculation was used to inoculate sugarcane smut. The changes in leaf gas exchange, chlorophyll fluorescence variables, and related defense enzyme activities were measured in sugarcane cultivar ROC22 after pathogen infection. The results showed that the net photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (Tr) downregulated in the first three days after smut infection and upregulated on the fourth day; intercellular CO₂ concentration (Ci) increased in the first three days of smut infection and reduced on the fourth day. The chlorophyll fluorescence parameters, i.e., Fo, Fm, Fv/Fm, Fs, and Fv′/Fm′ decreased at the initial stage of pathogen infection but increased rapidly up to 3 days after smut infection. It can be seen that sugarcane seedlings showed a positive response to pathogen infection. The correlation coefficient relationship between Pn, gs, and Tr reached above 0.800, showing a significant correlation; Ci was positively correlated with Fv′/Fm′ and ΦPSII, reaching above 0.800 and showing a significant correlation; Fo positively correlated with Fv/Fm, Fs, and ETR; Fv /Fm was positively correlated with Fv′/Fm′; Fs significantly correlated with Fv′/Fm′; and Fv′/Fm′ positively correlated with ΦPSII. After inoculation with smut, the related defense enzymes, i.e., POD, SOD, PPO, and PAL, were increased and upregulated; photosynthetic parameters can be associated with an increase in enzymatic activities. The results of this study will help to further study of the response mechanism to smut in the sugarcane growing period and provide a theoretical reference for sugarcane resistance to smut breeding.

Sugarcane, a cash crop, is easily affected by low temperature, which results in a decrease in yield and sugar production. Breeding a new variety with cold tolerance is an essential strategy to reduce loss from cold stress. The identification of germplasms and genes/proteins with cold tolerance is a vital step in breeding sugarcane varieties with cold tolerance via a conventional program and molecular technology. In this study, the physiological and biochemical indices of 22 genotypes of S. spontaneum were measured, and the membership function analysis method was used to comprehensively evaluate the cold tolerance ability of these genotypes. The physiological and biochemical indices of these S. spontaneum genotypes showed a sophisticated response to low temperature. On the basis of the physiological and chemical indices, the genotypes were classified into different cold tolerance groups. Then, the high-tolerance genotype 1027 and the low-tolerance genotype 3217 were selected for DIA-based proteomic analysis by subjecting them to low temperature. From the four comparison groups, 1123, 1341, 751, and 1693 differentially abundant proteins (DAPs) were identified, respectively. The DAPs based on genotypes or treatments participated in distinct metabolic pathways. Through detailed analysis of the DAPs, some proteins related to protein homeostasis, carbohydrate and energy metabolism, amino acid transport and metabolism, signal transduction, and the cytoskeleton may be involved in sugarcane tolerance to cold stress. Furthermore, five important proteins related to cold tolerance were discovered for the first time in this study. This work not only provides the germplasms and candidate target proteins for breeding sugarcane varieties with cold tolerance via a conventional program and molecular breeding, but also helps to accelerate the determination of the molecular mechanism underlying cold tolerance in sugarcane.

Sugarcan e is a major crop for sugar and biofuel production and is cultivated in tropical and subtropical areas worldwide. Sugarcane growth is constrained because of winter’s low-temperature stress, and cold resistance is an important limitation in sugarcane growth enhancement. Therefore, in this study, we identified a gene involved in the low-temperature stress response of sugarcane. Calcineurin B-like (CBL) protein is a calcium signal receptor involved in the cold stress response. Five sugarcane CBL genes were cloned, sequenced, and named SoCBL1, SoCBL3, SoCBL5, SoCBL6, and SoCBL9. The protein sequences of these genes were analyzed. The calculated molecular weight of these proteins was 24.5, 25.9, 25.2, 25.6, and 26.3 kD, respectively. Subcellular localization analysis revealed that SoCBL1, SoCBL3, SoCBL6, and SoCBL9 were situated in the cytoplasm, while SoCBL5 was present in mitochondria. Secondary structure analysis showed that these five CBL proteins had similar secondary structures. Conserved domain analysis displayed that each sugarcane CBL protein contained three conserved EF domains. According to the self-expanding values of the phylogenetic tree, the CBL gene family was divided into four groups. The CBL1 and CBL9 genes were classified into one group, illustrating that these two genes might possess a similar function. The expression analysis of the SoCBL gene under low temperatures showed that SoCBL3 and SoCBL5 were affected significantly, while SoCBL1 and SoCBL9 were less affected. These results demonstrate that the CBL genes in sugarcane have similar characteristics and present differences in genetic diversity and gene expression response to low temperatures. Therefore, these genes might be novel candidates for fighting cold stress in sugarcane.

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.

Ratoon stunt caused by Leifsonia xyli subsp. xyli (Lxx) is widely spread across sugarcane planting regions. Here, transcriptomics and cytology were conducted to analyze the changes in gene expression levels and chloroplast ultrastructures after Lxx inoculation. A total of 90.26 Gb clean bases, 156,713 unigenes and 406 differentially expressed genes were obtained. The genes of HSP and ACS were continuously differentially expressed. The photosynthesis-related genes of PsbO, PsbQ, PsaD, PsaE, PsaG and PsaH were up-regulated. PIRH2, WRKY, NCED, AHP and GST were identified as the important specific genes that responded to Lxx inoculation. Lxx inoculation also altered the shape and damaged the membrane of chloroplasts in sugarcane leaves. Sugarcane responds to Lxx infection likely via changing the expression levels of some specific genes and interfered with photosynthesis. A possible molecular regulation network induced by Lxx was speculated. These findings broaden the understanding to the mechanisms of the interaction between sugarcane and Lxx.

Sugarcane (Saccharum officinarum L.) faces significant challenges in China, including labor-intensive cultivation, low yields, and environmental stresses. Enhancing root development and stress tolerance through phytohormones and molecular breeding is a promising approach to boosting productivity. Indole-3-butyric acid is a phytohormone known for promoting root development and stress resistance. However, its effects on sugarcane root development under low temperature remain poorly understood. This study demonstrated that IBA markedly promoted root initiation, elongation, and biomass under low temperature, and significantly increased the levels of phytohormones, including GA₃, ABA, JA, IAA, and ZT, suggesting the activation of multiple signaling pathways. Transcriptome analysis revealed numerous differentially expressed genes related to metabolic pathways such as glycolysis, the tricarboxylic acid cycle, and glutathione metabolism. Weighted gene co-expression network analysis identified core gene modules correlated with phytohormone activities, highlighting their role in the IBA-mediated stress response. Eleven core genes, including GSTU6, FAR1, and BCAT3, and nine hub genes, such as Ub-CEP52-1 and ACS1, were identified as critical components for IBA-induced root development and stress mitigation. These findings provide insights into the molecular mechanisms underlying IBA-induced root development and stress tolerance in sugarcane, offering candidate genes for breeding high-yield, stress-tolerant varieties and demonstrating IBA’s potential as a strategy to enhance productivity under challenging conditions.