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

Van Haeften, S.; Brunner, S.; Dinglasan, E.; Fabreag, E.; Eyre, J.; Mens, C.; Hayes, B. J.; Udvardi, M.; Alahmad, S.; Eglinton, M.; McQuinn, R.; Ryan, M.; van der Meer, S.; Smith, M. R.; Hickey, L.

doi:10.1101/2025.11.03.686422

bioRxiv · 10.1101/2025.11.03.686422

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

Van Haeften, S.·Brunner, S.·Dinglasan, E.·Fabreag, E.·Eyre, J.·Mens, C.·Hayes, B. J.·Udvardi, M.·Alahmad, S.·Eglinton, M.·McQuinn, R.·Ryan, M.·van der Meer, S.·Smith, M. R.·Hickey, L.

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Abstract

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 within-crop performance rather than system-level benefits. We hypothesise that legacy effects (the influence of one crops 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{square}{superscript 1} (2.52-3.49 t ha{square}{superscript 1}) depending solely on the preceding mungbean genotype, with legacy traits displaying moderate heritability (H{superscript 2}: 0.43-0.65), demonstrating untapped genetic potential for breeding. Analyses of mungbean traits, soil properties, and volatile organic compounds implicated root architecture, symbiotic nitrogen fixation and soil microbiome as potential biological drivers of legacy effects. Haplotype mapping identified genomic regions in mungbean associated with wheat yield and protein, revealing trade-offs between within-crop 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.

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Van Haeften, S., Brunner, S., Dinglasan, E., Fabreag, E., Eyre, J., Mens, C., Hayes, B. J., Udvardi, M., Alahmad, S., Eglinton, M., McQuinn, R., Ryan, M., van der Meer, S., Smith, M. R., Hickey, L.. 2025-11-05. The potential to breed for genetic legacy effects in sustainable farming systems. https://doi.org/10.1101/2025.11.03.686422

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