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

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

Improving disease resistance of pea - clues from plant-microbe interactions

Pea (Pisum sativum L.) is a valuable protein source for food and feed. Pea is able to significantly improve soil fertility and, hence, represents an ecologically important crop in low-input farming systems. Despite their importance, pea cultivation remains below expectations due to low and unstable yields caused by a complex of soil-borne pathogens. The goal of this project is to improve our understanding of resistance mechanisms of pea against soil-borne diseases. To achieve this goal, more than 300 pea lines were evaluated for resistance in pot-experiments and a subset of susceptible and resistant pea genotypes has been identified. In a next step, key pathogens and beneficials in the pea rhizosphere and the role of root exudates in determining the occurrence of these microbes will be investigated. The study will shed light on the complex interactions between pea genotypes and soil microbes, and promote resistance breeding programmes for legumes

Improving disease resistance of pea through selection at the plant-soil interface

Pea (Pisum sativum L.) belongs to the legume family (Fabaceae). Legumes form mutualistic symbiosis with nitrogen fixing rhizobacteria and, thereby, are able to improve soil fertility. Legume crops are important protein source for food and feed and contribute to the nitrogen demand of succeeding crops. Despite their importance, cultivation of cool-season legumes in temperate zones remains below expectations due to low and unstable yields. Soil fatigue is caused by a complex of different soil-borne pathogens and thought to be the main reason for yield losses, especially in pea. Plants have the ability to actively shape the community of root associated microbes through root exudations. Evidence is growing that there is considerable genetic variation for plant traits involved in the regulation of plant-microbe interactions, and that these genetic resources can be exploited by plant breeders. The overall goal of this project is to improve resistance of pea against soil-borne diseases. So far, more than 300 pea accessions have been screened for resistance in a standardised growth chamber pot-experiment and a subset of susceptible and tolerant pea genotypes has been identified. The results of the pot-experiment will be verified in on-farm trials with repeated pea cultivation in the recent crop rotation history or clear evidence for soil fatigue. In a next step, key pathogens and beneficials will be assessed by quantitative real-time PCR and linked to root exudate profiles of pea varieties with contrasting resistance levels. The role of root exudates in shaping the plants’ own detrimental or beneficial microbial community in the rhizosphere will be investigated using High-Performance-Thin-Layer-Chromatography. Furthermore, we will identify resistance associated quantitative trait loci (QTL) via genome-wide association study. The study will shed light on the complex interactions between pea and soil microbes and promote resistance breeding programmes for legumes

Genome-wide association study for resistance of pea against a complex of root rot pathogens

Fungal root diseases severely narrow yield in pea (Pisum sativum L.) cultivation, threatening this highly valuable protein source and important crop in low input-farming systems. Adequate resistance in current pea varieties against various root pathogens is largely lacking. The control of these pathogens is challenging, as they occur as pathogen complexes in the field, themselves embeded in entangled interactions in the rhizosphere. Plants have the ability to actively shape their rootassociated microbiome and genetic variation for rhizosphere related traits exists that can potentially be harnessed in resistance breeding. Results from a controlled pot-based resistance screening of 312 pea cultivars, advanced breeding lines and gene bank accessions on naturally infested soil will be presented. Based on different disease assessments, significant differences in resistance level between pea lines were identified. Validation of a subset of most contrasting lines in the field confirmed significant differences for diseases susceptibility. ITS amplicon sequencing of the fungal rhizosphere community showed a root community of evenly abundant fungal taxonomic units not dominated by a few taxa. This finding points at complex interactions within the fungal community. Along the microbiome sequencing approach, quantitative real-time PCR assays targeting the most important pathogen species are being implemented for the analysis of pot and field rhizosphere samples. Finally, first results of a genome-wide association study on resistance to root rot will be presented

Improving disease resistance of pea through selection at the plant-soil interface

Legumes are able to improve soil fertility via a mutualistic symbiosis with nitrogen-fixing rhizobacteria. Therefore, they represent ecologically important crops for sustainable farming systems. Besides their ecological function, grain legumes considerably contribute to the dietary protein N needs of humans (Graham and Vance 2003). Despite their importance, legume cultivation remains low due to low and unstable yields (Rubiales and Mikic 2015). Soil fatigue, also called legume yield depression syndrome, is caused by a complex of different soil-borne pathogens and thought to be the main reason for these yield losses, especially in pea (Pisum sativum) (Fuchs et al. 2014). The overall goal of this project is to improve the resistance of pea against soil-borne diseases. More than 250 pea lines (varieties, advanced breeding material and GenBank accessions) will be screened for resistance in standardised growth chamber experiments and on-farm. A screening tool for breeders will be developed in collaboration with Getreidezüchtung Peter Kunz. The role of root exudates in shaping the plants’ own detrimental or beneficial microbial community in the rhizosphere will be investigated by HPTLC in collaboration with Giessen University, Germany, and CAMAG, Switzerland. Key pathogens and beneficials will be characterised by quantitative real-time PCR and linked to root exudate profiles of pea varieties with contrasting resistance levels. In addition, we will identify resistance associated quantitative trait loci via genome-wide association study. Our study will shed light on the complex interactions between pea and soil microbes and promote resistance breeding programmes for legumes. This project is supported by the Mercator Foundation Switzerland and the Swiss Federal Office of Agriculture

Breeding for microbiome-mediated disease resistance

Plant-associated microbial communities play a crucial role for the expression of various plant traits including disease resistance. Increasing evidence suggests that host genotype influences the composition and function of certain microbial key groups, which, in turn, effects how the plant reacts to environmental stresses. Several studies indicate that modern plant breeding may have selected against plant traits essential for hosting and supporting beneficial microbes. However, they also highlight the presence of an exploitable genetic base for the regulation of the rhizosphere microbiota. We illustrate the concept of breeding for microbial symbioses with pea (Pisum sativum L.). Firstly, genotypic variation for the efficiency of a mycorrhizal symbiosis is shown, as measured by an estimation of the plant benefit per symbiotic unit. Secondly, we extend the view towards the wider fungal community using ITS amplicon sequencing. Two pea genotypes with contrasting resistance levels against pathogen complexes are investigated to provide information on the functional diversity of the rhizosphere microbiome in a naturally infested agricultural soil. In the near future, microbial hubs and diversity indices will be linked with root exudation in order to elucidate the plant’s capacity to influence the microbial composition leading to disease susceptibility or resistance. Current and future research activities of our group aim to make use of plant-microbiome interactions to develop advanced screening tools for breeders for an improved expression and stability of important plant traits