Bioscience Methods 2025, Vol.16, No.2, 108-116 http://bioscipublisher.com/index.php/bm 111 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. 4 Development of Molecular Markers and Their Application in Disease-Resistant Breeding 4.1 Development of SNP and SSR markers associated with disease resistance The development of molecular markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) has greatly promoted the development of disease-resistant breeding. In cassava, researchers have developed and verified some SNP markers associated with cassava mosaic disease resistance sites that have high prediction accuracy against traits (Ige et al., 2021). Similarly, SSR markers associated with resistance to multiple diseases were also found in other crops. For example, SSR markers in peanuts are associated with resistance to premature spot disease, SSR markers in rice are associated with resistance to brown planthoppers (Shabanimofrad et al., 2015), while SSR markers in cotton are associated with resistance to jassid (Venkatesulu et al., 2023). These markers are of great significance for identifying disease-resistant genotypes and promoting the application of marker-assisted selection (MAS) in breeding. 4.2 Association analysis between markers and disease resistance traits Researchers use correlation analysis to link DNA markers to disease resistance in plants. They discovered specific SSR markers linked to early spot disease resistance in peanuts, which helps breeders develop better varieties (Zongo et al., 2017). Research on rice showed the same SSR markers linked to resistance to brown planthoppers, explaining some of the defensive traits of the plants. Tobacco researchers also discovered SSR markers linked to resistance to potato Y virus, enabling breeders to select resistant plants using novel tools (Darvishzadeh et al., 2016). The marker research helps to confirm which genetic markers truly predict disease resistance and whether they work in real breeding programs so that crop improvement can become more precise and efficient. 4.3 Application of marker-assisted selection in disease-resistant breeding Marker-assisted selection (MAS) has become a core tool in disease-resistant breeding programs. In rice, SSR-labeled MAS was successfully selected to breed species that resist brown planthoppers (Shabanimofrad et al., 2015). In cassava, SNP markers are used to accelerate the introduction of resistance alleles such as mosaicism in breeding populations (Ige et al., 2021). In addition, SSR markers are also used for selective breeding in shrimp breeding to enhance their resistance to viral and bacterial pathogens (Yin et al., 2023). These applications show that MAS has significant results in improving the disease resistance of crops and breeding species and accelerating the breeding process. 5 Integration of Multi-Omics and Optimization of Disease-Resistant Breeding Strategies 5.1 Integrated analysis of genomic and transcriptomic data Scientists are linking genetic and gene expression data to better comprehend how sugarcane can resist disease. Scientists could find useful disease-resistance genes and how they work by studying the DNA of the plant as well as what genes are turned on when infected (Pimenta et al., 2023). For example, to evaluate mosaic virus resistance, they applied GWAS and RNA sequencing for gene network assembly, which showed that genes of photosynthesis and stress response are involved in the plant defense. Another smut disease research utilized WGCWA to uncover how groups of genes interact with each other during disease infection, stress-related genes being an important feature (Wu et al., 2022). These complementing methods offer a better picture of the natural resistance of sugarcane and allow scientists to ascertain the most valuable genes to utilize in breeding healthier, disease-free sugarcane varieties.
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