Resistant and susceptible pea lines harbour different root-rot pathogens and antagonistic fungi

Summary

Disease resistance encompasses the mechanisms that allow a plant to withstand or ward off a pathogen. The molecular responses of plants under pathogen attack and the underlying genetics have been extensively studied. However, resistance is not only a trait defined by the warfare between pathogen and host. In fact, resistance is an emergent phenotype of the interactions between the microbial community and the host. Fungal root diseases threaten pea (Pisum sativum L.) cultivation, and therefore a valuable protein source and important crop in low-input farming systems. Resistance in current pea varieties against multiple root pathogens is lacking. In order to acknowledge the rhizosphere microbiome as an integral part of the environment, 261 pea genotypes were screened for resistance on naturally infested field soil in a pot-based experiment. Thereof, eight lines with contrasting disease levels were selected and tested on four soils with different disease pressure in a follow-up pot experiment. Along root rot assessments, pea pathogens (F. solani, F. oxysporum, F. avenaceum, A. euteiches, P. ultimum and D. pinodella) and arbuscular mycorrhizal fungi were quantified in diseased roots using qPCR assays. The amount of fungal DNA detected in the roots differed among the pea genotypes and the four soils and a significant pea genotype x soil interaction was evidenced for several pathogen species. For example, the quantity of F. avenaceum in the roots mostly depends on the soil (two-way ANOVA, p < 0.01) and differs significantly between pea genotypes (p = 0.013). F. oxysporum and F. solani quantities showed significant pea genotype x soil interactions (p < 0.01 for both species). Significant correlations were found between F. avenaceum and F. solani quantity and root rot index (rs = 0.38, p < 0.01 and rs = 0.56, p < 0.01, respectively ). On the other hand, F. oxysporum quantity shows no relationship with root rot (rs = 0.007, p = 0.95). These results suggest differential roles of the microbes in the pea root rot and highlight the importance of incorporating the complexity of the soil microbiome at early stages of resistance screenings and breeding efforts. Resistance breeding against root rot will be challenged by the fact that soil microbes interact with each other and the plant and that their composition varies between different soils. Further insights into plant-microbe interactions and emerging molecular plant breeding tools will fuel future plant breeding.