Multi-Level Data Integration Decodes the Metabolic Strategies of Kawisari Coffee Hybrid Resistance to Hemileia vastatrix

Plants have developed mechanisms to regulate carbon metabolism during growth and development under both optimal and stressful conditions. In the biotrophic interaction between Coffea spp. and Hemileia vastatrix, the plant restricts pathogen access to nutrients, whereas the fungus attempts to manipulate host metabolism. Here, we elucidate the metabolic mechanisms underlying post-haustorial resistance of the Kawisari coffee hybrid to H. vastatrix by integrating metabolomic, starch, enzymatic, and gene expression analyses to distinguish between resistant (R) and susceptible (S) responses. Polar untargeted metabolomics (GC-TOF-MS) revealed distinct modulation of sugars, amino acids, polyamines, and phenolics between R and S responses. Combining these metabolomic profiles with starch quantification, semi-high-throughput enzyme activity assays, and RT-qPCR gene expression analysis revealed a strategic reallocation of carbon in the resistant response. Specifically, resistance was associated with the activation of the pentose phosphate pathway, providing reducing power and precursors for secondary metabolism (phenolic defenses), coordinated with a tight control of starch utilization and nitrogen remobilization (namely through asparagine and ornithine) and polyamine signaling. These findings underscore the pivotal role of primary metabolic networks in supporting resistance to H. vastatrix and identify promising biochemical targets for breeding coffee cultivars with enhanced resistance to rust under climate change scenarios.