Mining of Candidate Genes and Developing Molecular Markers Associated with Pokkah Boeng Resistance in Sugarcane (Saccharum spp.)

Sugarcane Pokkah Boeng (PB), a fungal disease caused by Fusarium spp., poses a significant threat to sugar industries globally. Breeding sugarcane varieties resistant to PB has become a priority, and the mining of PB resistance genes and the development of molecular markers provide a solid foundation for this purpose. This work comprehensively analyzes the genetic components of sugarcane's resistance to PB using transcriptome sequencing. A segregating population was created by crossing the susceptible parent ROC25 with the resistant parent Yunzhe89-7, which is a traditional cultivar known for its PB resistance. Transcriptome analysis uncovered many differentially expressed genes (DEGs) associated with PB resistance. Utilizing weighted gene co-expression network analysis (WGCNA), we identified gene modules closely related to disease phenotypes. We annotated their functions with bioinformatics tools, particularly focusing on genes enriched in the plant immune response's MAPK signaling pathway and ABC transporter synthesis pathways. In addition, by integrating whole-genome resequencing data of parental lines and transcriptome data of progeny, we identified a series of putative molecular markers that potentially effectively differentiate between highly resistant and susceptible materials. Our study provides crucial genetic resources and molecular methodologies that are essential for the advancement of sugarcane varieties with improved resistance to PB. These innovations are expected to accelerate the breeding process greatly.