Soil-borne pathogens can severely compromise legume cultivation and, consequently, plant-based protein production by triggering root rot, particularly in pea (Pisum sativum L.). Although some pea genotypes exhibit enhanced performance compared to others under root rot stress, breeding efforts have so far achieved only limited resistance. Microbiome-mediated breeding might show more success in alleviating root rot. We hypothesized that some root‑associated microbes serve as resistance markers across diverse soils. We therefore determined whether certain fungi or mycobiome attributes consistently associated with a genotype's resistance across a diverse range of soils. Root-associated fungal communities of eight pea genotypes differing in root rot resistance were characterized by ITS amplicon sequencing in four soils with contrasting infestation levels under controlled conditions. We employed alpha and beta diversity, as well as differential abundance analyses, to detect genotype- and soil-specific patterns and associations with resistance traits. Both genotype and soil identity influenced alpha diversity. Evenness was reduced in infested soils, as OTU richness increased. Fungal community composition covaried with infestation level, genotype and previously defined resistance levels of the genotypes. A single OTU (OTU3), showing 100

The pea root rot complex is caused by various soil-borne pathogens that likely reinforce each other, influencing the composition of the root microbiome and leading to significant yield reductions. Previous studies have shown variations in the abundance of key microbial taxa and differences in disease susceptibility among plant genotypes. To better understand this relationship between plant genetics and microbiome dynamics, we conducted genetic analyses focusing on plant health and frequency of microbial taxa. Two hundred fifty-two diverse pea lines were grown in naturally infested soil under controlled conditions, genotyped, assessed for their disease symptoms at the seedling stage, and analyzed the associated root microbial communities using amplicon sequencing. Genome-wide association studies (GWAS) revealed genomic loci that influence the abundance of various fungal and bacterial operational taxonomic units (OTUs). We identified 54 independent quantitative trait loci (QTLs) significantly linked to the abundance of 98 out of 1227 detected OTUs, while an additional 20 QTLs were associated with more than one OTU. The most significant region was found on chromosome 6, influencing 50 OTUs across 10 distinct QTLs. When comparing genomic markers and microbial OTUs as predictors in a genomic prediction model for root rot resistance and seedling emergence, we found that the abundance of specific microbial groups provided a significantly better predictive ability than QTLs. The abundance of Fusarium species was correlated with increased infection levels, while others, such as those linked to Dactylonectria and Chaetomiaceae, positively correlated with resistance to root rot. These findings were validated by specific QTLs and high genetic heritability for OTU abundance. The results highlight two key points: (1) the presence and abundance of certain microbial groups in the pea root are influenced by distinct QTLs and, thus, determined by the plant genotype, and (2) these microbial communities show heritable correlations with the plant resistance to root rot. By combining plant and microbiome genetic markers—using a “holobiont” approach—we can improve predictions of root rot resistance compared to predictions based on plant genetics alone. These findings set a foundation for practical applications in breeding programs aimed at enhancing disease resistance through microbiome-assisted approaches.

Plants are constantly challenged by pathogens, which can cause substantial yield losses. The aggressiveness of and damage by pathogens depends on the host-associated microbiome, which might be shaped by plant genetics to improve resistance. How different crop genotypes modulate their microbiota when challenged by a complex of pathogens is largely unknown. Here, we investigate if and how pea (Pisum sativum L.) genotypes shape their root microbiota upon challenge by soil-borne pathogens and how this relates to a genotype’s resistance. Building on the phenotyping efforts of 252 pea genotypes grown in naturally infested soil, we characterized root fungi and bacteria by ITS region and 16 S rRNA gene amplicon sequencing, respectively. Pea genotype markedly affected both fungal and bacterial community composition, and these genotype-specific microbiota were associated with root rot resistance. For example, genotype resistance was correlated (R2 = 19

BACKGROUND:Root rot is one of the most threatening diseases to pea production. Root rot is caused by several interacting soil-borne pathogens which makes it challenging to manage. Breeding for resistance is a promising approach for sustainable pea production. While quantitative trait loci (QTL) for resistance against individual pathogens have been identified, the genetic basis underlying resistance against the pathogen complex is poorly understood. RESULTS:Using a previously described diverse panel of 254 pea genotypes and 18k single nucleotide polymorphism (SNP) markers, we identified a novel QTL for resistance to root rot on chromosome chr6LG2. This QTL co-locates with a mitochondrial Rho GTPase and an F-box gene model, which are promising candidates for disease control. A whole-genome prediction model explained up to 53% of the phenotypic variation and reached predictive abilities of up to 0.51 for root rot-related traits. We found that plant height and shoot biomass were unreliable indicators of plant health. Instead, these traits were related to the Mendelian Le locus, which controls stem length. CONCLUSIONS:Our results provide new insights into the genetic basis of quantitative root rot resistance in pea and provide novel tools that could accelerate the development of resistant pea lines through marker-assisted and genomic selection.

Intercropping of legume and cereal crop species shows potential to reduce root disease pressures by changing root-associated microbiomes and improve nitrogen (N) use via soil N-dependent fixation of atmospheric N2 by symbiotic rhizobia. A two-year field study was conducted to evaluate the effect of pea-barley association on crop performance and on the root fungal community. Five pea cultivars (Alvesta, Karpate, Mytic, Respect, Vitra) were grown either in pure stands or mixed with one variety of barley (Atrika). We measured crop grain yield and root rot incidence and analyzed root fungal communities. In mixed stands, total grain yield was more stable compared with each pure stand, but pea root disease incidence was higher except for cv. Vitra and Karpate. The effect of cropping system on fungal alpha diversity depended on the cultivar, with cv. Vitra showing higher Shannon diversity and cv. Alvesta showing lower richness in mixed compared with pure stands. All four operational taxonomic units (OTUs) belonging to the Didymellaceae family were positively associated with pea root rot, and another disease-asssociated OTU in pea, Neoascoschyta exitialis, was found to be also part of the barley core microbiome. Eleven out of 12 OTUs belonging to the Glomeraceae family were associated with healthy roots and abundant in cv. Vitra. This study shows how the phenotype and fungal microbiome of different pea cultivars respond distinctly to intercropping. Furthermore, the identification of disease- and health-associated taxa in the pea root fungal community refines the characterization of different cultivar candidates for intercropping.

Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea ( Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea , were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world’s most important pulse crops of the world.

BackgroundApple blotch (AB) caused by Diplocarpon coronariae (Dc) has been established in Europe since 2010. AB is a serious apple disease, mostly in low input orchards and in cider production areas in Northern Italy, Switzerland, Austria and Germany. However, the epidemiology and population genetic structure of this pathogen is unknown.MethodsWe developed twelve Dc-specific microsatellite markers and screened DNA of both pure fungal isolates and infected apple leaves. The marker data of 313 European samples of Dc were compared to Dc isolates from Asia (n = 7) and the USA (n = 3).ResultsWe found 31 distinct multilocus genotypes (MLGs) in European samples, and seven additional MLGs in the Asian and USA samples. The European samples had the typical genetic signature of a recently introduced species including high clonality, a low number of private alleles and one dominant MLG across all the sampling sites. All European MLGs were genetically distant from those MLGs of Asian and USA origin. Based on the lack of linkage disequilibrium observed, there is evidence that Dc undergoes regular cycles of sexual recombination in the European population, although the sexual stage (apothecia) has not been observed in Europe.ConclusionsThe twelve newly developed SSR markers reported here provide a useful tool to characterize the population genetic diversity and structure of Dc in Europe. Our study supports the hypothesis that Dc is a recently introduced pathogen in Europe, but of currently unknown origin. Dc has a large effective population size during field epidemics, so we believe that the pathogen has substantial evolutionary potential. Application of the SSR markers to large-scale and diverse Dc samples will help to better understand the epidemiology of AB, which has become a global apple disease, and will help guide effective mitigation strategies based on disease management and resistance breeding.

Soil-​borne diseases in legumes, especially in peas, cause severe damage and can lead up to total yield loss. New science is providing solutions.

Apple blotch caused by Marssonina coronaria (Mc) is reported in Europe since 2001. It has become a serious problem in organic low input orchards and in cider production areas in Northern Italy, Switzerland, Austria and Germany. It is assumed that is has been introduced from East Asia where it is known since 1907. However, its invasion route to Europe and the genetic diversity of established populations in Europe is unknown. To better understand its epidemiology and to reveal its population genetic structure, we developed Mc specific SSR markers (SSR: short sequence repeats) and studied European samples. They showed the typical genetic signatures of a recently introduced species such as lower number of alleles per SSR markers, and higher clonality compared to samples from Asia. The observed low genetic diversity and high clonality suggests that management strategies (such as resistance breeding) might be successful, always supposing that further introduction of novel M. coronaria genotypes into Europe is prevented.

Pea (Pisum sativum L.) is a valuable and healthy protein source for food and feed. In addition to the nutritional benefits, pea is an invaluable agro-ecological asset for sustainable cropping systems through positive effects on soil fertility and soil microbial diversity. The symbiosis with nitrogen-fixing bacteria allows pea and other legume crops to supply the soil with nitrogen and, therefore, to significantly reduce the application of external nitrogen fertilisers. Therefore, pea plays an important role especially in low-input farming systems. The growing market for plant- based protein supply is likely to promote pea cultivation in the near future. However, pea production is severely challenged by various soil-borne pathogens that form a Pea Root Rot Complex (PRRC) causing root-rot diseases. Despite considerable progress in resistance breeding against individual pathogens, current pea varieties lack resistance against multiple interacting pathogens. The overall goal of this thesis was to contribute to the understanding of resistance against root rot pathogen complexes in pea. Chapter 1 gives an overview of the importance of pea as a future key player in agricultural systems and the food sector before introducing the pea root rot complex concept and its relevance for research on resistance. Furthermore, the most recent developments in molecular biology relevant for molecular plant breeding of pea are briefly summarised and an overview of quantitative real-time PCR relevant for research on microbial interactions in the pea root rot complex is given. Chapter 2 reviews the current knowledge of resistance against root- rot pathogens in major grain legumes, highlights the importance of the host genotype in determining the composition of plant-associated microbial communities and how the root associated microbiome relates to plant health. In addition, major findings on the role of root exudation in disease susceptibility and resistance of grain legumes are summarised. Finally, it delineates how this knowledge could be integrated in resistance breeding of grain legumes. In Chapter 3, a resistance screening assay was established based on infested soil from an agricultural field that showed severe pea root rot pressure. This approach was chosen in order to account for the whole rhizosphere microbiome - including the naturally occuring pathogen complex - in the assessment of root rot resistance in pea. The initial ITS- amplicon sequencing of the fungal rhizosphere community of diseased pea roots grown in the infested soil showed a root community of evenly abundant fungal taxonomic units not dominated by a few taxa. This finding points at complex interactions within the PRRC. Two hundred and sixty-one pea cultivars, landraces and breeding lines were screened for resistance on the naturally infested field soil in a controlled conditions experiment. The screening system allowed for a reproducible assessment of disease parameters among the tested genotypes. Broad sense heritabilities on the infested soil were H2 = 0.89 for plant emergence, H2 = 0.43 for root rot index and H2 = 0.51 for relative shoot dry weight. The resistance ranking was verified in an on-farm experiment with nine pea genotypes in two field sites: The controlled conditions root rot index showed a significant correlation with the resistance ranking in the field site with high PRRC infestation (Spearman's ρ = 0.73, p = .03). The screening system offers a tool for selection at early stages of the plant development, and for the study of plant resistance in the light of complex plant-microbe interactions. For Chapter 4, a subset of five resistant and three susceptible pea genotypes was selected based on the initial screening. In analogy to the previous experiment, a controlled conditions experiment was setup up in order to assess and validate resistance of the eight pea genotypes on four soils. Plant growth was significantly reduced on the three sick soils compared to the healthy soil. Despite the significantly different levels of disease pressure in the three infested soils (ANOVA: p < .001) and the strong genotype effect (p < .001), no significant soil × genotype interaction (p < .342) was found for plant growth reduction. In addition to disease assessments, ten key microbial taxa (eight putative pea pathogens and two putative beneficials) were quantified in the roots by quantitative real-time PCR (qPCR). Fusarium solani, F. oxysporum and Aphanomyces euteiches were the most abundant pathogens in diseased roots from the three sick soils. Further, various levels of the pathogens F. avenaceum, F. redolens, Rhizoctonia solani, D. pinodella and Pythium sp. as well as the potential antagonist Clonostachys rosea were quantified by qPCR. The contribution of individual pathogens to root rot and growth reduction differed among the three sick soils: F. solani and F. oxysporum showed significant correlations (Spearman correlations; p < 0.05) with root rot index and relative shoot dry weight in the two soils with the highest infestation level; A. euteiches showed significant relations with disease in two sick soils from Germany. The quantities of arbuscular mycorrhizal fungi were negatively correlated with root rot index and positively correlated with relative shoot dry weight in all sick soils. Furthermore, the root microbial composition differed significantly among the pea genotypes (PERMANOVA; p < .0001) and the soils (p < .0001) and a significant pea genotype × soil interaction was evidenced (p < .0001). In addition, resistant pea genotypes showed significantly lower F. solani and A. euteiches, and higher arbuscular mycorrhizal fungi abundance in the roots (Wilcoxon rank-sum test; p < .05). These results give insights into the complex interaction between key microorganisms of the PRRC and the plant, by pointing out potential key microorganisms in the root rot pathobiome. Further disentanglement of this complex and the validation of key microbial players can be harnessed by resistance breeding. Chapter 5 reviews the experimental approaches and results from the previous chapters before discussing the major findings and implications for future research and resistance breeding. I also raise the question if and how knowledge about complex soil microorganisms-plant feedbacks can be incorporated in resistance screenings and breeding efforts to conclude that today we are at a point where information on microbial complexes could indeed assist resistance breeding. However, our current state of knowledge does not yet allow to design specific microbiome-enabled selection-tools. This last chapter will also give short outlooks and indicate possible future lines of research in the field of microbe-mediated plant resistance.

Soil-borne pathogens cause severe root rot of pea (Pisum sativum L.) and are a major constraint to pea cultivation worldwide. Resistance against individual pathogen species is often ineffective in the field where multiple pathogens form a pea root rot complex (PRRC) and conjointly infect pea plants. On the other hand, various beneficial plant-microbe interactions are known that offer opportunities to strengthen plant health. To account for the whole rhizosphere microbiome in the assessment of root rot resistance in pea, an infested soil-based resistance screening assay was established. The infested soil originated from a field that showed severe pea root rot in the past. Initially, amplicon sequencing was employed to characterize the fungal microbiome of diseased pea roots grown in the infested soil. The amplicon sequencing evidenced a diverse fungal community in the roots including pea pathogens Fusarium oxysporum, F. solani, Didymella sp., and Rhizoctonia solani and antagonists such as Clonostachys rosea and several mycorrhizal species. The screening system allowed for a reproducible assessment of disease parameters among 261 pea cultivars, breeding lines, and landraces grown for 21 days under controlled conditions. A sterile soil control treatment was used to calculate relative shoot and root biomass in order to compare growth performance of pea lines with highly different growth morphologies. Broad sense heritability was calculated from linear mixed model estimated variance components for all traits. Emergence on the infested soil showed high (H-2 = 0.89), root rot index (H-2 = 0.43), and relative shoot dry weight (H-2 = 0.51) medium heritability. The resistance screening allowed for a reproducible distinction between PRRC susceptible and resistant pea lines. The combined assessment of root rot index and relative shoot dry weight allowed to identify resistant (low root rot index) and tolerant pea lines (low relative shoot dry weight at moderate to high root rot index). We conclude that relative shoot dry weight is a valuable trait to select disease tolerant pea lines. Subsequently, the resistance ranking was verified in an on-farm experiment with a subset of pea lines. We found a significant correlation (r(s) = 0.73, p = 0.03) between the controlled conditions and the resistance ranking in a field with high PRRC infestation. The screening system allows to predict PRRC resistance for a given field site and offers a tool for selection at the seedling stage in breeding nurseries. Using the complexity of the infested field soil, the screening system provides opportunities to study plant resistance in the light of diverse plant-microbe interactions occurring in the rhizosphere.

Overarching all our work in food systems, is the call from the UN Agenda 2030 Sustainable Development Goals (SDGs) to find shared solutions to the world’s urgent challenges. For the upcoming UN Food Systems Summit in 2021, five action tracks have been defined that drive food system transformation. Each track is designed to address synergies as well as possible trade-offs with other tracks, and to identify bold new actions, innovative solutions, and strategies that can deliver wide-reaching benefits across all of the SDGs. This year, as the COVID-19 pandemic threatens the lives and livelihoods of people around the world, it also has exposed dangerous deficiencies in our food systems. Sharing research working towards sustainable food systems is as critical as ever. These times have also made us all rethink how we share and interact. We are, therefore, excited to present food systems research at ETH Zurich in a different format, namely in two distinct online events. The first is a webinar with presentations and panel discussions focused on plant breeding for global food security. The second is a reimagining of our Networking Poster Session, providing young scientists a platform to share and connect with others in the food systems arena. Both events highlight how work at ETH Zurich contributes to food systems transformation. This webinar, with presentations and panel discussion, focuses on plant breeding and the implications for global food security. Presentations from World Food System Center Research Programs will be featured and give insight into the applications of plant breeding. The panel discussion, with its various perspectives, will further highlight how the research contributes to the future of plant breeding and its implications for global food security and a planetary health diet. • Welcome: Michael Siegrist, World Food System Center, ETH Zurich • Presentations • Lukas Wille, Research Institute of Organic Agriculture (FiBL): Pea root rot: Will understanding plant-microbiota interaction support resistance breeding? • Beat Keller, ETH Zurich: Advancing bean breeding through genomic selection • Panel Discussion with Questions from Audience • Monika Messmer, Research Institute of Organic Agriculture (FiBL) • Bruno Studer, ETH Zurich • Clare Mugisha Mukankusi, Alliance Bioversity-CIAT (International Center for Tropical Agriculture) • Robert Santiago Andrade, Alliance Bioversity-CIAT • Martijn Sonnevelt, World Food System Center, ETH Zurich • Moderator: Jeanne Tomaszewski, World Food System Center, ETH Zurich

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.

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.

Lukas Wille beschaftigt sich mit Erbsen. Als Doktorand im Projekt «ResPEAct» forscht er daran, wie Erbsensorten gegen bodenburtige Krankheiten widerstandsfahiger werden konnen. Wie er das macht, zeigt er dir heute auf higgs.

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.

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.

Root and foot diseases severely impede pea (Pisum sativum) cultivation worldwide, and therefore a valuable protein source and important crop in low-input farming systems. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in the field. Moreover, resistance depends on the interactions between the plant associated microbial community and the host, and there is increasing evidence for the existence of genetic variation in the regulation of plant–microbe interactions that can be exploited by plant breeders. In order to acknowledge the entire native soil microbiome as a key element of plant resistance we designed a resistance screening experiment on naturally infested field soil. In a first step, DNA from diseased roots and rhizosphere soil from infected plants was isolated. Sequencing of the fungal ITS region in the roots and rhizosphere showed the presence of several know pea pathogens along putative antagonists. Subsequently, 261 pea lines were grown under controlled conditions and evaluated after three weeks. Along significant genotypic differences, moderate to high heritabilities could be revealed for root rot resistance and growth performance traits. Relating different resistance traits allowed to distinguish between highly susceptible, tolerant and resistant lines and between resistance at different time points in plant development (i.e. emergence and young plant stage). The evaluation of a subset of pea lines on two field sites with moderate and high root-rot potential, respectively, confirmed the resistance ranking obtained under controlled conditions. Furthermore, we used quantitative real-time PCR targeting selected fungal pathogen species to show that the pathogen DNA detected in the roots differs among resistant and susceptible pea genotypes, respectively. Our results indicate the replicability and usefulness of naturally infested field soil based screening systems. Such systems will allow to pursue research on plant-microbiome interactions and on the role specific pathogen species or potential beneficial microbes play in plant disease resistance.

Der Biolandbau benotigt dringend angepasste Sorten. Die Biopflanzenzuchtung soll deshalb vorangetrieben werden. Ein Schritt in diese Richtung ist das Vernetzen der verschiedenen Akteure. An der ersten Biopflanzenzuchtungstagung am FiBL in Frick stand das Vorstellen der nationalen und europaischen Pflanzenzuchtungsprojekte im Vordergrund.

Pea (Pisum sativum L.) is highly prone to soil-borne pathogens and rotation breaks of up to ten years are recommended to avoid the build-up of high pathogen loads in the field. This stands in conflict with efforts to increase acreage of pea to strengthen low input farming systems and meet the pro- tein demand of a growing world population. Pea cultivars resistant against individual pathogen species exist, but not against pathogen complexes present under field conditions. Incorporating the microbial complexity present in the rhizosphere into plant variety testing is a potential means to harness beneficial plant-microbe interactions for resistance breeding programs.