New methods and innovation - Genetic Adaptation for Future Agrifood Systems under planetary boundaries

What are the main challenges?

Human activities are imposing severe pressures on Earth. As a result, we have crossed several planetary sustainability boundaries such as climate change, land-system change, biodiversity and disturbed biogeochemical flows. This has led to several global-scale environmental crisis, which call for urgent actions. As a response, the European Green Deal reflects our long-term ambition towards a green, biobased EU, which requires a transformative, systemic transition in our society and agricultural production systems.


Key characteristics of the HUB

The Genetics HUB will combine expertise’s within quantitative genetics and genomics, holegenomics, molecular breeding and gene editing techniques. The expertise’s will combine quantitative approaches taking all gene effects into account, targeted qualitative approaches for targeted gene editing, and hologenomics approaches allowing us to understand the role of the environment including the role of microorganisms in or around the host organism and hence the resilience and adaptive potential of the species. This will ensure a more comprehensive understanding of genetic properties of organisms and their interaction with the environment in the agro food system.


What is your expected outcome of taking part in START?

The New methods and innovation - Genetic Adaptation for Future Agrifood Systems will have several outcomes. Characterizing genetic diversity will allow us to build resilience against new agricultural constraints: extreme weather events, regulatory or financial restrictions on agricultural inputs, new agroecological practices (e.g., polyculture and circular bioeconomy). Likewise, genetic improvement is an efficient and necessary way to adapt agriculture to be more sustainable and geographically appropriate. Furthermore, we must optimize our genetic offer for different consumer preferences (cultural, ethical and dietary appropriateness) while meeting the needs of various stakeholders: from farmers and industries, to consumers and policy makers. START is designed to integrate research across multiple disciplines focusing on stakeholders in the entire value chain and thus coordinating and focusing research to pursue genetic fitness for relevant and inclusive agrifood systems in a changing socio-ecological contexts. 

 

The genetic HUB will address the following START themes:

Food systems 2050, Novel food and feed, Connecting sea and land, and Circular resource sufficiency, valorization.

The genetics HUB will have a link to the following HUBS: Future agrifood systems, 2gether, Circularity in nutrients.

This is achieved by genetically adapting current and new agricultural species to the future agrifood systems by:

  • Characterizing species and varieties, which fit new niches, in circular bioeconomy, market segments, and climate or disease pressures.
  • Exploit the historical diversity in gene banks and conservatories and elite gene pool as well as new domestications

Examples of new valuable traits targeted for breeding could be:

    • Side stream upcycling, resilience, health and consumer preference, methane mitigation, socio-ecological conditions

And digital tools could play a central role in providing new phenotypes.

Examples of new breeding directions could be:

    • Nutrient and water efficient Crops that are resilient to future conditions and pathogens
    • Nutrient and energy efficient livestock and aquaculture species with a lower climatic impact in different systems
    • Insects specialized to upcycle waste to nutritious food and feed and improve soil health
    • Blue biomass as a novel mineral, protein, bio compound source and as a tool for nutrient recover to reducing environmental impact.
    • Optimize for host genome interactions to coexisting species: microbiomes of soils and guts, genetics of companion crops (e.g., in intercropping and mixed cropping) and pathogens.

What new knowelgde is necessary to meet these main challnges?

Agriculture relies first on biological organisms, livestock and crops, whose basic properties are defined by their genetic makeup and variability. A core element in the green transition lies in genetic adaptation of current and new agricultural species for future sustainable agrifood systems. The complexity of the problems we face call for more synergy between multiple actors, technologies and disciplines. Also, for new species and novel technologies to effectively contribute, consumers must accept and adopt the resulting products.

Characterization of genetic diversity  

Modern agriculture has globally reduced agrodiversity (fewer breeds, cultivars and species). However, the diversity of genes, variety and species is a crucial resource to ensure resilient agrifood systems. Therefore, we must use the tools of modern genetics to characterize the inter- and intra-specific genetic diversity that likely contains untapped potential to adapt for our future agrifood systems. These include describing and maintaining the genetics from various sources: the historical diversity in gene banks and conservatories, and the elite gene pool maintained in ongoing breeding programs. Likewise, as we must transition from linear to circular agrifood systems, we need to describe the species and varieties, which fit new niches, in circular bioeconomy, market segments, and climate or disease pressures. It is likely, that our current elite genetic pools is not adapted to these niches, many of these new roles may require evaluating underrepresented varieties or domesticating new species. Beyond mere characterization of genetic resources in crops, livestock, and new species, genetics will also describe the key biological components, which contribute to environmental contexts: microbiomes of soils and guts, genetics of companion crops (e.g., in intercropping and mixed cropping) and pathogens. 

New breeding goals 

Throughout the 20th century, breeders have improved the productivity of crops and livestock, but have focused on production under conventional systems (plant monoculture, controlled livestock environments). Under the ongoing green transition, we must define and quantify valuable traits: side stream upcycling (e.g., composting, carbon sequestration, nitrogen recovery), consumer preference (e.g., taste, nutritional value), and resilience (e.g., biotic and abiotic stress resistance, nutrient use efficiency). Building on the characterization of agrodiversity, genetic variation for these novel traits must be identified for broader resources in plant and animal breeding. Moreover, understanding the relationship between genomes and environments will allow breeders to define breeding goals and choose optimal gene variants under new production systems and changing environments. As new constraints arise (e.g., pest pressure, climate change, new policy regulations), breeding goals must be dynamically updated. Then, geneticists must implement efficient techniques for fast genetic gains, which include genomic speed breeding for genome-wide changes, and molecular breeding techniques for targeted genetic edits.

Genomic speed breeding  

Complex traits like yield, production efficiency, quality, and resilience depend on many genes which interact among themselves and with the environment, in an intricate manner. Therefore, improvement of these traits has relied on selection of best parents without mechanistic understanding of genetic effects. Traditionally, such selection has been slow (at most one cycle of selection and mating per year). To accelerate this process of selection, speed breeding dramatically shortens life cycles under controlled conditions (e.g., up to three cycles per year in plants). To realize this potential, we must combine this technology with genomics-assisted breeding techniques like genomic prediction, which detects traits of interest using only DNA information. Speed breeding combined with genomic prediction (genomic speed breeding) can modify plant and animal genomes much more efficiently than traditional breeding, which relies on measurements under field conditions. For an effective deployment of genomic speed breeding, geneticists must develop accurate genomic prediction models, which maintain their accuracy over many successive generations by integrating information on genes and genetic networks affecting the phenotypic traits.

Molecular breeding techniques 

New Genomic Techniques, such as CRISPR and cisgenesisis suited for simpler traits impacted by relatively few genes with high effect. This is particularly relevant to  lower pesticide requirements (e.g., disease resistance) and increase productivity under stressful environments (e.g., tolerance to drought, heat, or heavy metals), but can also modify cell wall constituents in feed crops, so greenhouse gas emissions during livestock production is decreased. Desired variants can be introduced in genomes by molecular techniques for precise DNA changes: CRISPR-based editing for modifying specific genes or DNA sites or naturally occurring disease resistance genes can be combined in elite variants to produce high and durable disease resistance. Though currently limited by European regulations, NGTs holds great promise for improving crop species, because it induces or combines new genetic variants which may not be available. Moreover, this technology holds key advantages over mutagenesis by chemicals or radiations: it relies on few constraints to target exact sites for mutation; it results in few off-target edits; and it is widely applicable across plant varieties. Furthermore, CRISPR represents the most effective technology for translating research knowledge already existing from model species into real crops, thus potentially capitalizing on the huge investment done in basic research over the last several decades.


Academic Coordinators


Mogens Sandø Lund

Centre Director Center for Quantitative Genetics and Genomics

Aarhus University

Phone: +45 20 75 12 22

E-mail: 

Mogens.lund@qgg.au.dk

Kåre Lehmann Nielsen

Department of Chemistry and Bioscience

Aalborg University

Phone: +45  27 87 98 30

E-mail:

kln@bio.aau.dk


Tom Gilbert

Center for Evolutionary Hologenomics

University of Copenhagen

Phone: +45 23 71 25 19

E-mail:

tgilbert@snm.ku.dk


Torben Asp

Center for Quantitative Genetics and Genomics

Aarhus University

E-mail: 

torben.asp@qgg.au.dk

Administrative Coordinators


Bodil Hjarvard

Academic Employee

Email: bohj@agro.au.dk

Phone: +45 93 52 29 26



Kristine Engel Arendt

Special Consultant

Email: kea@science.ku.dk

Phone: +45 35 33 28 00