H2020 GenTORE Project: Genomic management tools to optimize resilience and efficiency
- Type Project
- Status Filled
- Execution 2017 -2022
- Assigned Budget 6.999.999,75 €
- Scope Europeo
- Main source of financing H2020
- Project website Proyecto GenTORE
The objective of GenTORE is to develop innovative genome-based selection and management tools to optimize the resilience and efficiency (R&E) of livestock in highly diverse environments. These tools, which incorporate genetic and non-genetic variables, will be applicable across all systems (beef, dairy, and mixed), thereby increasing the economic, environmental, and social sustainability of European beef and dairy production systems. To achieve this, GenTORE brings together:
- Multidisciplinary scientific expertise in genomics, environmental assessment, nutritional physiology, health management, precision livestock farming, mathematical modeling, and socioeconomics.
- Partners and stakeholders representing breeding organizations, agricultural technology companies, agricultural and veterinary advisory services, and agricultural sectors (organic, pastoral, etc.).
- A unique database that includes more than one million genotypes.
This multi-stakeholder team will develop tools for: multi-breed selection for R&E, characterization of diverse agricultural environments, large-scale phenotyping of R&E using in situ technology, in situ management of breeding and culling decisions, and prediction of the consequences of changes in breeding and management for livestock farm resilience. These tools are designed to be applicable under commercial conditions at the end of the project. They will enable greater use of genomic diversity in livestock breeds, for example, through the use of selective crosses to optimize the local production environment.
They will also enable livestock farm managers, their advisors, and policymakers to assess the relative importance of breeding for animal resilience versus breeding for efficiency, relative to system resilience. As such, GenTORE will not only enable the use of genomic information to facilitate predictive biology of efficiency- and resilience-related traits, but will also increase the resilience of livestock production to the current and future challenges of climate change and food security.
Tools to adapt cattle to their environment: Identifying which cattle genotype is best suited to current and future environments, and is sufficiently resilient, requires finding the optimal combination of resilience and animal efficiency. However, given the diversity of European agricultural environments, there is no one-size-fits-all solution. Furthermore, these traits are often poorly defined and difficult to measure. GenTORE scientists have developed two public databases that combine regional topography with climate information and farm types to help forecast the effects of climate change on dairy and beef cattle production systems by region.
They have also developed lifetime performance prediction models for dairy and beef cattle, using efficiency and environmental impact metrics. This will allow breeders and ranchers to identify whether the local production environment may present challenges for their animals. By then classifying their animals based on resilience and production efficiency, ranchers can decide which animals will be best suited to local conditions, such as purebreds or crossbreds, or whether they should be sold. This means the best animals are selected for the local environment. Improved phenotyping for resilience and efficiency: Resilience and efficiency are complex and time-varying traits. Furthermore, we lack practical, large-scale references to predict which young animals will make good cows. The technologies used in PLF can provide the accurate longitudinal data needed to phenotype resilience and efficiency. GenTORE has developed new methods to quantify resilience and efficiency, such as a multi-trait random regression model that uses these high-frequency data to measure efficiency. This allows efficiency to be assessed not only at fixed periods, but at all stages of lactation in dairy cows and the growth period in beef cattle. A scoring system has also been developed to assess the Lifetime Resilience Score (LRS) and methods to quantify resilience to changes in the milk production curve during lactation. The model will allow farmers to assess a cow's ability to calve again and provides an estimate of her productive lifespan. Farmers will be able to use on-farm information collection to calculate each animal's LRS and classify all cows in the herd.
This will help them predict LRS at early life stages to identify which cows to breed and maintain. GenTORE has also explored the potential of new technologies, such as drones, to collect data when animals are grazing. As this and other technologies become cheaper and more widely deployed, classification and prediction will become more accurate. Genomic tools: There are four distinct ways in which genomic tools can provide solutions to the challenges faced by farmers: providing the genomic tools for systematic crossbreeding to leverage the complementarity of different breeds to generate crosses particularly adapted to specific environments; improving the modeling of genotype-environment interactions to leverage genetic data in different environments; incorporating more accurate efficiency and resilience traits; and providing the tools to improve on-farm breeding management decisions. GenTORE has developed promising multi-breed genomic methods to jointly evaluate purebred, crossbred, and mixed individuals with complex patterns of genomic contributions from different breeds.
A single-step breed-of-origin BLUP method was tested on a large dataset with over 300,000 genotyped and millions phenotyped individuals from five major breeds and is implemented in a toolset available to the breeding industry. Similarly, GenTORE has developed protocols and analysis pipelines for GxE models where the effects of individual genomic variants may differ between environments. These are based on linear mixed model methodologies already commonly used by animal assessment centers in livestock breeding. GenTORE has also incorporated enhanced resilience and efficiency phenotyping into genomic assessment of resilience and efficiency, and has provided on-farm breeding management tools that incorporate genomic information. These tools will lead to more efficient and resilient livestock systems through improved utilization and selection in crossbreeding systems, improved selection within and between environments, and better management decisions.
Breeding strategies for mitigation: Genetic tools can be used to reduce emissions per kilogram of product by improving productivity and efficiency, reducing waste at the herd level, and reducing emissions through direct selection when individual animal emissions are measurable. GenTORE has explored and evaluated several strategies that reduce management costs as well as emissions, including:
- Improved fertility: Reducing the intervals between calvings and inseminations would result in shorter unproductive periods.
- Greater resilience and longevity: Reducing the number of growing replacement females would generate fewer emissions and additional costs for the farmer.
- Better health: Reducing unproductive periods or minimizing production losses, as well as involuntary culling, would generate economic and environmental benefits.
- Increased feed efficiency: For example, selection for improved feed intake would directly affect emissions; animals that eat less for the same level of production tend to produce fewer greenhouse gases (GHGs). It would also indirectly affect emissions by reducing emissions associated with feed production.
The advent of genomics and its application in livestock farming has radically changed breeding programs. It has significantly improved the precision of selection and now offers numerous options for selecting for more complex but highly relevant traits, such as efficiency and animal resilience.
The use of genomics in livestock farming has been accompanied by the rapid expansion of Precision Livestock Farming (PHF) technology on livestock farms, which enables large-scale, cost-effective data collection and monitoring. These technologies will greatly enhance the livestock sector's ability to phenotype a much wider range of traits in greater detail and in larger populations, and subsequently select for these complex traits.
For the past five years, the EU GenTORE project has successfully combined genomics and GPP to provide farm management tools that can sustainably improve efficiency using resilient animals. These tools will help farmers focus on matching their animals to available options and adapt their livestock to the challenges of climate change. This will include identifying animals to breed, crossbreed, or cull, making livestock businesses more economically efficient, better suited to the current and future environment, and more responsive to consumer demands.
To achieve this, GenTORE has generated results and impact in the four areas described below, which will be important for ensuring the future of European livestock production.
The objective of GenTORE is to develop innovative genome-based selection and management tools to optimize the resilience and efficiency (R&E) of cattle in highly diverse environments. These tools, which incorporate genetic and non-genetic variables, will be applicable across the full range of systems (beef, dairy, and mixed) and will therefore increase the economic, environmental, and social sustainability of European beef and dairy production systems. To achieve this, GenTORE brings together:
- Multidisciplinary scientific expertise in genomics, environmental assessment, nutritional physiology, health management, precision livestock farming, mathematical modeling, and socioeconomics.
- Partners and stakeholders representing breeding organizations, agricultural technology companies, agricultural and veterinary advisory services, and agricultural sectors (organic, pastoral, etc.).
A unique database including more than 1 million genotypes. This multi-stakeholder team will develop tools for: selecting multiple breeds for R&D, characterizing diverse farming environments, large-scale R&D phenotyping using on-farm technology, on-farm management of breeding and selection decisions, and predicting the consequences of changes in breeding and management for farm resilience. These tools are designed to be applicable under commercial conditions by the end of the project. They will enable greater use of genomic diversity in livestock breeds, e.g., the use of selective crossbreeding to better exploit the local production environment.
They will also enable farm managers, their advisors, and policymakers to assess the relative importance of breeding for animal resilience versus breeding for efficiency, with respect to system resilience. As such, GenTORE will not only enable the use of genomic information to facilitate predictive biology of efficiency- and resilience-related traits, but will also increase the resilience of livestock production to the current and future challenges of climate change and food security.
Not all cows are the same. By analyzing each cow's genome and phenotype, the GenTORE project promises to increase the economic, environmental, and social sustainability of European livestock production systems. Livestock farming, including the separation of breeding stock from slaughter stock, relies heavily on intuition and speculation. But what if farmers could base their decisions on accurate genetic and non-genetic information? In this new reality, each animal's value and suitability for breeding would be determined by specialized management tools. This is precisely what the EU-funded GenTORE (Genomic Management Tools for Optimizing Resilience and Efficiency) project aims to achieve. "Farmers often have many questions about their animals, and the answers depend primarily on their innate capabilities—their genotype—and their current state, or phenotype," explains Nicolas Friggens, INRAE researcher and GenTORE project coordinator. Until recently, both could only be roughly estimated. But the advent of genomics and automated farm monitoring technologies has the potential to change this completely. "It could provide highly accurate information to guide farmers' most crucial decisions," says Friggens. Drawing directly on these advances, GenTORE provides a suite of tools that optimize livestock management at every stage of the process.
These tools enable multibreed selection for increased resilience and efficiency (R&E) in cattle, the characterization of diverse cattle environments, large-scale R&E phenotyping using in-situ technology, and on-site management of breeding and slaughter decisions. Farmers can even use GenTORE to predict the consequences of changes in breeding and management on overall farm resilience. Cattle Management Under the Microscope: With GenTORE, farmers can rank their cows based on their milk value. With this information, they can decide which of their cows should be bred with dairy semen and which with beef breeds that increase the value of calves for beef production. However, the range of possibilities is broader: “With this genomic information about their cows, farmers will be able to select bulls that present the most favorable genetic combination. GenTORE has already developed these tools, and breeding companies and farmers are implementing them,” Friggens notes.
To achieve this level of accuracy, the GenTORE consortium had to compile a unique database of over one million genotypes and combine them with R&E phenotypes. This was perhaps the most challenging part of the project. “In some situations, typically in extensive beef production systems, data availability was very limited. We had to conduct specific trials within GenTORE,” says Friggens. He adds: “We also wanted to test the feasibility of remote animal monitoring. Given the lack of available information, we conducted our own studies using drone technology. These show that such technology has potential, but is not yet ready for deployment.” Many other tools are. In addition to the classification tool, the GenTORE team has successfully developed a European map that combines geophysical, meteorological, and farm-type information, providing key insights into the local production context. They have also developed improved methods for R&E phenotyping using farm technologies that measure both animal performance (milk production, body weight, etc.) and other aspects such as activity and temperature.
Finally, they created new methods to improve the genomic evaluation of crossbred animals. “We hope our work will enable new generations of cows better adapted to their local production environments. Better-adapted animals translate into improved welfare, greater longevity, and sustainable efficiency for livestock production systems.” On-farm management tools will also allow farmers to adapt their breeding strategies to produce the right number of animals based on their needs. This means fewer replacement animals, which is good news for the environmental footprint of livestock production. “Finally, the long-term prediction models developed in GenTORE will enable farm advisors and farmers to better anticipate and adapt to the impacts of climate change in their regions,” Friggens concludes.
Conclusion: GenTORE has made significant progress in its short life. Its research findings and tools for genomic management will be invaluable to livestock producers, breeders, and researchers seeking to improve the sustainable efficiency of the livestock sector.
For more information, please visit www.gentore.eu, which details each of the four topics presented, as well as a full list of GenTORE outcome publications and a variety of videos describing the topics.
- INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT (INRAE)
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