Integrating k-mer GWAS and time-series transcriptomics to dissect the genetic architecture and immune defense networks against pokkah boeng disease in polyploid sugarcane

Pokkah boeng disease (PBD), caused by Fusarium sacchari , is a devastating fungal disease that threatens global sugarcane production. Understanding the genetic basis of PBD resistance is crucial for molecular breeding under sugarcane’s complex autopolyploidy. Here, we evaluated an F 1 population of 201 individuals derived from a cross between ‘ROC22’ (resistant) and ‘Zhongzhe 1’ (susceptible). Based on multi-year field trials and artificial inoculations, we established a robust phenotypic evaluation system using Best Linear Unbiased Prediction (BLUP) values. A k-mer-based genome-wide association study (GWAS) identified 759 associated loci, highlighting 22 stable major-effect loci detected across multiple environments. Time-series RNA-seq analysis revealed the transcriptional dynamics of infection, pinpointing 48 h post-inoculation (hpi) as the critical time point for resistance-susceptibility divergence. By integrating physical mapping with temporal expression patterns, we identified four key candidate genes: the sensor DUF4220, the signaling switch Ras-family protein, the defense executioner DDE superfamily endonuclease, and the homeostasis regulator T-complex protein. This study outlines a four-dimensional (perception-transduction-execution-monitoring) immune framework, revealing the molecular mechanisms by which resistant genotypes construct multiple defense barriers through precise temporal coordination. The identified major-effect loci and core genes provide pivotal targets and a scientific foundation for marker-assisted and genomic selection in sugarcane disease-resistance breeding.