Sugarcane smut can cause losses in cane yield and sugar content that range from 30% to total crop failure. Losses tend to increase with the passage of years. Sporisorium scitamineum is the fungus that causes sugarcane smut. This fungus has the potential to infect all sugarcane species unless a species is resistant to biotrophic fungal pathogens. However, it remains unclear how the fungus breaks through the cell walls of sugarcane and causes the formation of black or gray whip-like structures on the sugarcane plants. Here, we report the first high-quality genome sequence of S. scitamineum assembled de novo with a contig N50 of 41 kb, a scaffold N50 of 884 kb and genome size 19.8 Mb, containing an estimated 6,636 genes. This phytopathogen can utilize a wide range of carbon and nitrogen sources. A reduced set of genes encoding plant cell wall hydrolytic enzymes leads to its biotrophic lifestyle, in which damage to the host should be minimized. As a bipolar mating fungus, a and b loci are linked and the mating-type locus segregates as a single locus. The S. scitamineum genome has only 6 G protein-coupled receptors (GPCRs) grouped into five classes, which are responsible for transducing extracellular signals into intracellular responses, however, the genome is without any PTH11-like GPCR. There are 192 virulence associated genes in the genome of S. scitamineum, among which 31 expressed in all the stages, which mainly encode for energy metabolism and redox of short-chain compound related enzymes. Sixty-eight candidates for secreted effector proteins (CSEPs) were found in the genome of S. scitamineum, and 32 of them expressed in the different stages of sugarcane infection, which are probably involved in infection and/or triggering defense responses. There are two non-ribosomal peptide synthetase (NRPS) gene clusters that are involved in the generation of ferrichrome and ferrichrome A, while the terpenes gene cluster is composed of three unknown function genes and seven biosynthesis related genes. As a destructive pathogen to sugar industry, the S. scitamineum genome will facilitate future research on the genomic basis and the pathogenic mechanisms of sugarcane smut.

Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.

The MADS-box transcription factor (TF) gene family is pivotal in various aspects of plant biology, particularly in growth, development, and environmental adaptation. It comprises Type I and Type II categories, with the MIKC-type subgroups playing a crucial role in regulating genes essential for both the vegetative and reproductive stages of plant life. Notably, MADS-box proteins can influence processes such as flowering, fruit ripening, and stress tolerance. Here, we provide a comprehensive overview of the structural features, evolutionary lineage, multifaceted functions, and the role of MADS-box TFs in responding to biotic and abiotic stresses. We particularly emphasize their implications for crop enhancement, especially in light of recent advances in understanding the impact on sugarcane (Saccharum spp.), a vital tropical crop. By consolidating cutting-edge findings, we highlight potential avenues for expanding our knowledge base and enhancing the genetic traits of sugarcane through functional genomics and advanced breeding techniques. This review underscores the significance of MADS-box TFs in achieving improved yields and stress resilience in agricultural contexts, positioning them as promising targets for future research in crop science.

To understand the molecular basis of sugarcane-smut interaction, it is important to identify sugarcane genes that respond to the pathogen attack. High-throughput tag-sequencing (tag-seq) analysis by Solexa technology was performed on sugarcane infected withSporisorium scitaminea, which should have massively increased the amount of data available for transcriptome profile analysis. After mapping to sugarcane EST databases in NCBI, we obtained 2015 differentially expressed genes, of which 1125 were upregulated and 890 downregulated by infection. Gene ontology (GO) analysis revealed that the differentially expressed genes involve in many cellular processes. Pathway analysis revealed that metabolic pathways and ribosome function are significantly affected, where upregulation of expression dominates over downregulation. Differential expression of three candidate genes involved in MAP kinase signaling pathway,ScBAK1(GenBank Accession number: KC857629),ScMapkk(GenBank Accession number: KC857627), andScGloI(GenBank Accession number: KC857628), was confirmed by reverse transcription polymerase chain reaction (RT-PCR). Real-time quantitative PCR (qRT-PCR) analysis concluded that the expression of these genes were all up-regulated after the infection ofS. scitamineaand may play a role in pathogen response in sugarcane. The present study provides insights into the molecular mechanism of sugarcane defense toS. scitamineainfection, leading to a more comprehensive understanding of sugarcane-smut interaction.

Summary: Sugarcane smut is a worldwide fungal disease caused by Sporisorium scitamineum, which seriously jeopardizes the healthy and sustainable development of the sugarcane industry. WRKY transcription factors are actively involved in plant responses to pathogen infection; however, the mechanisms by which WRKY mediates resistance to sugarcane smut remain elusive. Here, we obtained a nucleus‐localized transcription factor ScWRKY2, which was down‐regulated in smut‐resistant but up‐regulated in smut‐susceptible sugarcane cultivars. Overexpression of the ScWRKY2 gene in sugarcane enhanced its sensitivity to smut disease. Besides, an immune‐related gene ScLRR‐RLK, directly regulated by ScWRKY2, was identified through a combination of transcriptome and DNA affinity purification sequencing. Interestingly, ScWRKY2 suppressed the expression of the ScLRR‐RLK gene by binding to the W‐box element in its promoter region. Furthermore, protein–protein interaction assays demonstrated that ScWRKY2 interacted with the ScPsbP protein in the nucleus. Notably, co‐overexpression of ScWRKY2 and ScPsbP enhanced the sensitivity of plants to pathogens by inducing the expression of reactive oxygen species (ROS) scavenging‐related genes. Collectively, our study revealed that ScWRKY2 negatively regulated sugarcane resistance to smut disease by repressing the expression of the ScLRR‐RLK gene, followed by interacting with the chloroplast protein ScPsbP, and thus inducing the expression of ROS scavenging‐related genes to maintain ROS homeostasis. These findings provided a theoretical basis and gene resources for sugarcane disease resistance breeding.

Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common. Expression of differential miRNAs under S. scitamineum challenge was mostly downregulated, with similar trends in the two varieties. Gene ontology (GO) analysis showed that the target gene classification of known miRNAs was similar to that of the newly identified miRNAs. These were mainly associated with cellular processes and metabolic processes in the biological process category, as well as combination and catalytic activity in the molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these predicted target genes involved in a series of physiological and biochemical pathways or disease resistance-related physiological metabolism and signal transduction pathways, suggesting that the molecular interaction mechanism between sugarcane and S. scitamineum was a complex network system. These findings also showed certain predicted target genes of miR5671, miR5054, miR5783, miR5221, and miR6478 play roles in the mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, and plant-pathogen interaction. Quantitative real-time PCR (qRT-PCR) analysis showed that majority of the known miRNAs and its predicted target genes followed a negatively regulated mode. Seven out of eight predicted target genes showed identical expression after 12 h treatment and reached the highest degree of matching at 48 h, indicating that the regulatory role of miRNAs on the target genes in sugarcane was maximized at 48 h after S. scitamineum challenge. Taken together, our findings serve as evidence for the association of miRNA expression with the molecular mechanism underlying the pathogenesis of sugarcane smut, particularly on the significance of miRNA levels in relation to the cultivation of smut-resistant sugarcane varieties.