The potential to breed for genetic legacy effects in sustainable farming systems

Legume crops provide protein-rich food, critical disease breaks in cereal rotations, and contribute to soil fertility through symbiotic nitrogen fixation. However, crop improvement programs typically focus on individual crop performance rather than system-level benefits. We hypothesise that legacy effects (the influence of one crop’s genotype on subsequent crop performance) are under genetic control and could be leveraged in breeding programs. To test this, we evaluated how 309 genetically diverse mungbean genotypes influence subsequent wheat performance. The mungbean panel was grown, followed by a single wheat cultivar sown in the same plot locations. Remarkably, wheat yield varied by nearly 1 t ha⁻¹ (2.52-3.49 t ha⁻¹) depending solely on the preceding mungbean genotype, with legacy traits displaying moderate heritability (H²: 0.43-0.65), demonstrating untapped genetic potential for breeding. Integrated analyses of traits, soil properties, and volatile organic compounds identified potential biological drivers including root architecture, symbiotic nitrogen fixation and soil microbiome. Haplotype mapping identified genomic regions in mungbean associated with wheat yield and protein, revealing trade-offs between direct and legacy performance. Genetic simulations using empirically derived marker effects compared genomic selection strategies targeting mungbean yield, wheat yield, or both simultaneously. Balanced selection (50:50 weighting) achieved simultaneous gains in both crops (19.5% and 7.6%), highlighting the opportunity to breed for system-level productivity with reduced input requirements.