Key message Multi-omics assisted prediction of disease resistance mechanisms using machine learning has the potential to accelerate the breeding of resistant legume varieties. Abstract Grain legumes, such as soybean ( Glycine max (L.) Merr.), chickpea ( Cicer arietinum L.), and lentil ( Lens culinaris Medik.) play an important role in combating micronutrient malnutrition in the growing human population. However, plant diseases...