Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 110 Figure 1 Transcriptome analysis of genes in the RNA-seq dataset of sugarcane (Adopted from Jiang et al., 2023) Image caption: Transcriptomic analysis in multiple RNA-seq datasets. (A) Differential expression analysis of S. spontaneumand S. officinarumalleles. (B) Differentially expressed NBS-LRR genes in multiple diseases. (Adopted from Jiang et al., 2023) 3.3 Construction and analysis of key disease resistance pathways Researchers are studying how the synergy of sugarcane genes operates when they resist disease. Through one method called WGCNA, sets of genes were discovered to collaborate in resisting smut disease (Wu et al., 2022). These sets of genes control critical processes in the plant like the synthesis of glutathione and flavonoids that function as a protective role. By comparing gene activity data to biological networks, scientists have gained more insight about disease-resistance genes called RGAs and how they work with other defense systems (Rody et al., 2021). The study is revealing sugarcane's natural defense while helping to decide on the best genes to employ in breeding healthier, disease-resistant sugarcane. The study provides vital information for breeding sugarcane that will be more resistant to disease but also maintain quality production. 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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