Abstract
Agricultural intensification has led to a significant reduction in cultivated biodiversity, with global food production increasingly dependent on a limited number of species. This trend has contributed to climate change, biodiversity loss, and human health concerns. One major consequence of crop genetic homogenization is the increased vulnerability of agricultural systems to pests, diseases, and weeds at both field and landscape levels. In contrast, diversification has emerged as a promising strategy for sustainable, pesticide-free agriculture by enhancing resilience and stability. At the national scale, diversification broadens crop variety, while at the farm level, techniques such as extended crop rotations, cover cropping, intercropping, and cultivar mixtures improve pest and disease control.The French collaborative project MoBiDiv explores the role of diversification in influencing the establishment and evolution of plant diseases, pests, and weeds. Specifically, we aim to assess how diversification enhances the durability of disease resistance and alters disease susceptibility within mixed cropping systems. Additionally, we seek to determine whether intra-plot diversification drives genetic co-selection between interacting plants.To evaluate the impact of intercropping on fungal disease incidence, we conducted field trials using two intercropping systems: (i) wheat-perennial prairie, and (ii) wheat-pea. Disease assessments focused on key fungal pathogens, including septoria tritici blotch in wheat, and anthracnosis in pea. Our findings demonstrated that intercropping effectively reduced disease severity, particularly in anthracnosis affecting pea. However, no significant effect was observed on wheat fungal diseases in the wheat-pea system, while septoria incidence was lower in wheat intercropped with prairie. This highlights the potential of certain intercropping combinations in mitigating specific disease pressures.To further investigate the genetic mechanisms underlying these effects, we analyzed potential co-selection between plants that might influence susceptibility to fungal diseases in wheat intraspecific mixtures. We conducted the first co-Genome Wide Association Study (co-GWAS) between two interacting plants and tested whether loci involved in inter-individual interactions exhibited signatures of selection. We calculated Tajima’s D values to detect selection traces, expecting co-selected loci to show more negative values than control regions. Linkage disequilibrium (LD) was also assessed between interacting loci, hypothesizing that co-selected regions would exhibit high r² values. Finally, we compared intra- and inter-subgenome interactions, postulating that co-selection would primarily occur within sub-genomes in ancestral wheat lines predating polyploidization. Our analyses did not detect clear evidence of co-selection. This suggests that intra-plot diversification influences disease suppression primarily through eco-physiological mechanisms rather than co-evolutionary genetic adaptation. Understanding the impact of these underlying mechanisms on disease reduction is important to optimize diversification strategies and resistance management.