Periodic Reporting for period 4 - GenTORE (Genomic management Tools to Optimise Resilience and Efficiency)
Berichtszeitraum: 2021-06-01 bis 2022-07-31
The arrival of genomics and its use in livestock farming has seen a step-change in breeding programmes. It has greatly improved selection accuracy and now offers many options for selecting more complex but highly relevant traits like animal efficiency and resilience. The use of genomics in livestock has been paralleled by the rapid expansion of Precision Livestock Farming (PLF) using on-farm technology, which enables large-scale cost-effective data collection and monitoring.
These technologies will vastly improve the cattle sectors’ ability to phenotype a much wider range of traits in increasing detail and in larger populations, and then to select on these complex traits. Over the last five years, the GenTORE EU project has successfully brought genomics and PLF together to provide on-farm management tools to sustainably improve efficiency using resilient animals.
These tools will help farmers focus on matching their animals to the options available to them, and to adapt their cattle farming to the challenges of climate change. This will include identifying which animals to breed, crossbreed or cull, thus making cattle enterprises more economically efficient, more appropriate to current and future environments, and better fitting for what consumers demand. To achieve this GenTORE has produced results and impact in the four areas described below, which will be important for future-proofing European cattle production.
These technologies will vastly improve the cattle sectors’ ability to phenotype a much wider range of traits in increasing detail and in larger populations, and then to select on these complex traits. Over the last five years, the GenTORE EU project has successfully brought genomics and PLF together to provide on-farm management tools to sustainably improve efficiency using resilient animals.
These tools will help farmers focus on matching their animals to the options available to them, and to adapt their cattle farming to the challenges of climate change. This will include identifying which animals to breed, crossbreed or cull, thus making cattle enterprises more economically efficient, more appropriate to current and future environments, and better fitting for what consumers demand. To achieve this GenTORE has produced results and impact in the four areas described below, which will be important for future-proofing European cattle production.
Tools to match cattle to their environment: Identifying which cattle genotype is best for current and future environments and sufficiently resilient requires finding the best blend of animal resilience and animal efficiency. However, given the diverse nature of European farm environments there is no one-size-fits-all best blend. Moreover, these traits are generally poorly defined and hard to measure. GenTORE scientists have developed two publically-available databases combining regional topographic with climatic and farm types to aid in forecasting climate change effects on dairy and beef cattle production systems by region. They have also produced animal-level lifetime performance prediction models for dairy and beef using efficiency measurements and environmental impact. This will enable breeders and farmers to identify whether the local production environment is likely to challenge animals. Then, by ranking their animals in terms of resilience and production efficiency, farmers will be able to decide which ones will best suit local conditions as pure-breds 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-variable traits. Moreover, we lack practical references, on a large scale, for predicting which young animals will make good cows. Technologies used in PLF can provide the kind of fine-grained longitudinal data needed to phenotype resilience and efficiency. GenTORE has developed new methods for quantifying resilience and efficiency such as a multiple trait random regression model using this high-frequency data to measure efficiency. This allows the assessment of efficiency not just in fixed periods but at all time points throughout the lactation in dairy cows and the growth period in beef cattle. It has also developed a scoring system to assess a lifetime resilience score (LRS), and methods to quantify resilience from the disturbances in the milk yield curve over lactation. The model will allow the farmer to evaluate the cow’s ‘ability to re-calve’ and gives an estimate of its productive life. Farmers will be able to use on-farm information collection to calculate individual animals’ LRS and rank all the cows in the herd, which will help them predict the LRS early in life to identify which cows to breed and keep. GenTORE has also explored the potential of new technologies such as drones to collect data when animals are at pasture. As this and other technologies become cheaper and more commonly deployed, ranking and prediction will become more accurate.
Genomics tools: There are four distinct ways genomic tools can provide solutions to the challenges facing farmers: provide the genomic tools for systematic crossbreeding in order to leverage the complementarity of different breeds to generate crosses particularly adapted to specific environments; improve modelling of genotype by environment interactions in order to leverage genetic data across different environments; incorporate more precise efficiency and resilience traits; and provide the tools for improved breeding management decisions on-farm. GenTORE has developed promising multi-breed genomic methods to evaluate jointly purebreds, crossbreds, and admixed individuals with complex patterns of genomic contributions from different breeds. A breed of origin single step BLUP method was tested in a large dataset with over 300,000 genotyped and millions phenotyped individuals of five major breeds and is implemented in a breeding industry available toolbox. Likewise, GenTORE has developed protocols and analysis pipelines for GxE models in which individual genomic variant effects may differ across environments These rely on mixed linear model methodologies that are already generally used by animal evaluation centres in cattle breeding.
GenTORE has also incorporated the improved phenotyping of resilience and efficiency into genomic evaluation of resilience and efficiency, and provided on-farm breeding management tools that incorporate genomic information. These tools will lead to more efficient and resilient cattle systems through better utilization of and selection in crossbreeding systems, better selection within and across environments, and better management decisions.
Breeding strategies for mitigation: Genetic tools can be used to reduce emissions per kg product through improving productivity and efficiency, reducing wastage at the herd level, and reducing emissions by 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 calving intervals and inseminations would result in shorter unproductive periods;
- Improved resilience and longevity: reducing the number of growing replacement females required would produce less additional emissions and costs for the farmer;
- Improved health: again, reducing unproductive periods or minimising production losses, as well as reducing involuntary culling, would provide both economic and environmental benefits;
- Improved feed efficiency: for example, selection for improved residual feed intake would directly affect emissions, animals that eat less for the same production level tend to produce fewer Greenhouse Gases (GHGs). Also, indirectly, by reducing emissions associated with feed production.
Improved phenotyping for resilience and efficiency: Resilience and efficiency are complex and time-variable traits. Moreover, we lack practical references, on a large scale, for predicting which young animals will make good cows. Technologies used in PLF can provide the kind of fine-grained longitudinal data needed to phenotype resilience and efficiency. GenTORE has developed new methods for quantifying resilience and efficiency such as a multiple trait random regression model using this high-frequency data to measure efficiency. This allows the assessment of efficiency not just in fixed periods but at all time points throughout the lactation in dairy cows and the growth period in beef cattle. It has also developed a scoring system to assess a lifetime resilience score (LRS), and methods to quantify resilience from the disturbances in the milk yield curve over lactation. The model will allow the farmer to evaluate the cow’s ‘ability to re-calve’ and gives an estimate of its productive life. Farmers will be able to use on-farm information collection to calculate individual animals’ LRS and rank all the cows in the herd, which will help them predict the LRS early in life to identify which cows to breed and keep. GenTORE has also explored the potential of new technologies such as drones to collect data when animals are at pasture. As this and other technologies become cheaper and more commonly deployed, ranking and prediction will become more accurate.
Genomics tools: There are four distinct ways genomic tools can provide solutions to the challenges facing farmers: provide the genomic tools for systematic crossbreeding in order to leverage the complementarity of different breeds to generate crosses particularly adapted to specific environments; improve modelling of genotype by environment interactions in order to leverage genetic data across different environments; incorporate more precise efficiency and resilience traits; and provide the tools for improved breeding management decisions on-farm. GenTORE has developed promising multi-breed genomic methods to evaluate jointly purebreds, crossbreds, and admixed individuals with complex patterns of genomic contributions from different breeds. A breed of origin single step BLUP method was tested in a large dataset with over 300,000 genotyped and millions phenotyped individuals of five major breeds and is implemented in a breeding industry available toolbox. Likewise, GenTORE has developed protocols and analysis pipelines for GxE models in which individual genomic variant effects may differ across environments These rely on mixed linear model methodologies that are already generally used by animal evaluation centres in cattle breeding.
GenTORE has also incorporated the improved phenotyping of resilience and efficiency into genomic evaluation of resilience and efficiency, and provided on-farm breeding management tools that incorporate genomic information. These tools will lead to more efficient and resilient cattle systems through better utilization of and selection in crossbreeding systems, better selection within and across environments, and better management decisions.
Breeding strategies for mitigation: Genetic tools can be used to reduce emissions per kg product through improving productivity and efficiency, reducing wastage at the herd level, and reducing emissions by 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 calving intervals and inseminations would result in shorter unproductive periods;
- Improved resilience and longevity: reducing the number of growing replacement females required would produce less additional emissions and costs for the farmer;
- Improved health: again, reducing unproductive periods or minimising production losses, as well as reducing involuntary culling, would provide both economic and environmental benefits;
- Improved feed efficiency: for example, selection for improved residual feed intake would directly affect emissions, animals that eat less for the same production level tend to produce fewer Greenhouse Gases (GHGs). Also, indirectly, by reducing emissions associated with feed production.
Conclusion: GenTORE has made huge progress in its short lifespan. Its research findings and tools for genomic management will be of great value to farmers, breeders, and researchers wanting to improve the sustainable efficiency of the cattle sector. If you want to learn more go to www.gentore.eu where each of the four themes presented here is elaborated in greater detail, as well providing a full list of GenTORE results publications and a range of videos describing GenTORE.