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AGRIBIOME – breeding for plant microbiome recruitment

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Projektdaten

  • Projekt-Nr: GRS-082/19 
  • Förderbeitrag: CHF 299'000 
  • Bewilligung: 30.10.2019 
  • Dauer: 04.2020 - 03.2024 
  • Handlungsfeld:  Microbials, seit 2016

Projektleitung

Projektbeschreibung

AGRIBIOME will advance sustainable crop production by developing novel, microbiome-based breeding tools. These tools will generate resilient plants recruiting a functional microbial community that synergistically interacts with its host.
We envisage that microbiome-based ecosystem services can be steered by bio-inoculation and breeding. The main goals of AGRIBIOME are to (i) identify microbial hubs (highly connected taxa in microbial networks) regulated by plant genotype while mitigating biotic stresses, (ii) develop molecular markers for plant traits associated with recruitment of beneficial microbes, (iii) establish a new generation of plant probiotics that predictably and consistently enhance crop resilience and (iv) utilize knowledge on microbiome engineering to predict crop disease resistance towards holobiont-based breeding programmes. The outcome of this project will set a precedent for other crop species and cultivation issues employing the holobiont concept that regards the crop species as an ecological unit consisting of the plant and its associated microbial community.
AGRIBIOME will develop innovative tools to harness microbiome functions for breeding and seed health strategies while addressing the demand for less dependency on soybean imports and fuel-based inputs, thus, achieving more sustainable and circular food production in Europe as requested by civil societies and policy makers. This will strengthen environmental and climate-smart primary plant production and provide consumers with healthy and safe food along with affordable diets.

Stand/Resultate

AGRIBIOME started in 2020 by genotyping a panel of 254 pea lines. These pea lines had previously been phenotyped for their resistance towards root rot when grown in infested field soil under controlled conditions. Genome-wide association studies (GWAS) revealed one major genomic region on chromosome 6, explaining up to 15% of the observed root rot resistance. Further analysis revealed that genomic prediction models can explain up to 50% of the observed variation in root rot resistance. To understand the relationship between root rot resistance and the root microbiome, root fungal and bacterial communities were determined by amplicon sequencing of the whole panel of 254 pea lines grown under root rot stress. The pea genotype showed substantial effects on the fungal and bacterial diversity indices, while the origin of the pea lines (genetic resources, European cultivars, Swiss breeding lines) was of minor importance. Microbiota community composition was associated with the resistance level of the pea against root rot. Key fungi and bacteria linked to root rot resistance have been identified. Some of these potentially beneficial microbes were shown to be highly heritable and highly connected within the microbial network (hub taxa). GWAS were conducted to find plant genomic regions associated with microbiome features and individual microbes related to disease resistance. Several genomic regions were found to affect the abundance of potentially beneficial microbes. The strongest correlation was found at the same genomic locus on chromosome 6 as for the disease resistance. Next, GWAS on root rot resistance were conducted following a holobiont approach by incorporating plant genotypic data and the abundance of individual microbes. The holobiont approach markedly increased the prediction ability of pea root rot resistance.
Based on our findings, plant genetic markers were developed for root rot resistance and the recruitment of potentially beneficial microbes. These markers were used to screen the breeding lines of two breeding companies. In future collaborations, these markers will further be applied to conduct marker-assisted selection for direct and microbiome-mediated disease resistance. Validation of the different selection schemes will be done in field trials. Within this project, the disease resistance of the most contrasting genotypes was validated in replicated field trials in 2021, 2022 and 2023 on a Swiss field with severe symptoms of soil fatigue triggered by root rot pathogens. In parallel, the first bio-inoculation experiments with potentially beneficial microbes have been conducted at three research sites in Switzerland and Germany.
AGRIBIOME is a multidisciplinary and multi-actor team led by FiBL in close collaboration with the large breeding company KWS AG, the non-profit organic breeder gzpk and experts from ETH Zurich: Prof Bruno Studer for molecular plant breeding and Prof. Martin Hartmann for microbiome analysis. To fully exploit the findings of this project, the work is continued within Swiss and European projects. AGRIBIOME delivered promising results for future research on breeding resilient cultivars through the recruitment of beneficial microbial communities and developing microbial seed inoculants as an alternative to synthetic seed treatments.

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Am Projekt beteiligte Personen

Dr. Valentin Gfeller, Project lead, Scientist Microbiome-assisted breeding, FiBL
Dr. Monika Messmer, Head of Plant Breeding, interims project lead, FiBL
Dr. Natacha Bodenhausen, Team Leader microbiome, FiBL
Dr. Michael Schneider, Scientist for MAS and genomic prediction, FiBL
Prof. Dr. Bruno Studer, Head of Molecular Plant Breeding, ETH Zurich
Daniel Ariza Suarez, Molecular Plant Breeding, ETH Zurich
Dr. Martin Hartmann, Senior Scientist, Sustainable Agroecosystems, ETH Zurich
Dr. Klaus Oldach, Pre-breeder, KWS Saat SE
Dr. Nora Temme, Manager Biologicals, KWS Saat SE
Sebastian Kussmann, Breeder, Getreidezüchtung Peter Kunz
Miriam Kamp Breeder, Getreidezüchtung Peter Kunz

Letzte Aktualisierung dieser Projektdarstellung  28.03.2024