Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 109 2 Sugarcane Genomic Resources and Identification of Disease Resistance Genes 2.1 Complexity of the sugarcane genome and recent assembly achievements Sugarcane harbors highly complex DNA that is difficult to handle. Scientists have identified some vital sets of genes that make the plant disease resistant. Experiments show that NBS-LRR genes are the key to ensuring sugarcane's immunity to infections. Wild sugarcane species, especially Saccharum spontaneum, contribute precious disease-resistance genes to the cultivated sugarcane. Researchers have also cloned catalase genes that make it possible for sugarcane to cope with stresses in the environment. These results reveal how sugarcane's complex genetic makeup enables it to survive. The findings indicate the value of wild sugarcane types for breeding hardier, disease-resistant crops (Jiang et al., 2023). 2.2 Identification and annotation of disease-related gene families Researchers have identified a number of disease-resistant genes in sugarcane using various genetic analysis methods (Parvaiz et al., 2021). One of the significant discoveries is resistance gene analogues (RGAs) - these genes have differential patterns of activity in disease-resistant sugarcane compared to susceptible ones, clearly demonstrating their protective role (Rody et al., 2019). Recent studies with improved genetic network analysis identified interrelated groups of genes involved in smut disease prevention as a group and in plant stress alleviation (Wu et al., 2022). These all give the insight into sugarcane's natural defense mechanisms. The research shows how certain genetic studies result in the discovery of sugarcane's innate protection networks, providing prospective knowledge for creating more resistant varieties of sugarcane. 2.3 Functional validation and expression analysis of resistance genes Functional verification and gene expression analysis are very critical to understanding the mechanism of action of disease-resistant genes. Studies have found that some genes (such as ScCAT1) are upregulated under pathogen stress, which can enhance disease resistance by regulating reactive oxygen levels (Wu et al., 2023). In addition, the expression of some specific disease-resistant genes (such as PR10 and HCT1) has been shown to be related to early infection processes and disease-resistant mechanisms (Hidayah et al., 2021). These findings emphasize the importance of functional verification in identifying key disease-resistant genes and also provide the possibility of its application in breeding. 3 Application of Transcriptome Analysis in Studying Disease Resistance Mechanisms 3.1 Transcriptomic changes in sugarcane under pathogen infection Transcriptome analysis plays an important role in revealing the response mechanism of sugarcane to pathogenic infection. For example, during Sporisorium scitamineum infection, studies have found a large number of differentially expressed genes (DEGs), showing a complex stress response mechanism in sugarcane (McNeil et al., 2018). Similarly, many DEGs associated with metabolic processes and phytohormone signaling were also detected after Xanthomonas albilineans infection, which are crucial for plant defense responses (Figure 1). These studies show that sugarcane has dynamic changes in its gene expression during its resistance to pathogen invasion. 3.2 Screening and functional classification of differentially expressed genes Scientists have been studying how sugarcane genes respond when the plant is sick. They have noticed that there are certain genes that get expressed when disease hits. These genes are associated with certain important defense responses in the plant. There are certain genes that act through stress response pathways. Some of these include the MAPK signaling pathway that functions as an alarm system, hormone signaling pathways, and pathways that assist the plant in fighting germs (Ntambo et al., 2019). Scientists found out that most of these active genes assist in making special chemicals that combat diseases. These are crucial for protecting the plant. In a surprising turn of events, even genes that regulate basic plant processes seem to play a role in defense. These are photosynthesis genes (the process by which plants generate food from sun energy) and amino acid biosynthesis genes (protein precursors) (Zhang et al., 2022). These findings confirm that sugarcane utilizes many different systems to protect itself against disease, along with its special defense genes. The plant's normal processes also help keep it in good health.
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