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Genomic management Tools to Optimise Resilience and Efficiency

Periodic Reporting for period 3 - GenTORE (Genomic management Tools to Optimise Resilience and Efficiency)

Reporting period: 2020-06-01 to 2021-05-31

The European cattle sector is facing challenges: ensuring food security, managing natural resources, mitigating and adapting to climate change. In this context, the objective of GenTORE is to develop innovative genome-enabled selection and management tools to optimise cattle resilience and efficiency (R&E) in widely varying environments. There is a need to develop genomic indexes for multi-breed selection on R&E over different environments. Crossbreeding is bringing R&E and diversity-rich breeding into dairy and beef production, as it capitalises on the complementarity between breeds and heterosis effects. However, genomic tools are lacking for multi-breed analysis in admixed populations. GenTORE aims to develop these tools. It also aims to provide farmers and breeders with tools to rank the animals in their herds based on observed performance and genomic information. Such tools will allow bespoke genomic management on-farm.
Improved phenotyping of R&E is needed, and this on a large enough scale to enable genomic evaluation for these traits. Accordingly, GenTORE aims to develop precision phenotyping using on-farm sensor technology, and to elucidate the relationship between R&E with the aim of finding the balance of R&E that leads to sustainable gains in farm efficiency and resilience for a given environment. European (and global) livestock production systems are highly diverse and solutions need to be tailored to local production environments. Thus, GenTORE aims to map this diversity, to improve modelling of genotype environment interactions (GxE), and to incorporate these elements into prediction tools. Given that climate change is expected to negatively affect cattle production, it is important to be able to predict for future farming scenarios. The right breeding, genetic and herd management choices can help farmers to adapt and respond to these changes by having animals that are resilient to environmental perturbations as well as being efficient users of available resources. GenTORE ensures stakeholder participation throughout the project and communicates the project results and outcomes to a wider audience.
Significant advances have been made towards all of the above aims, as detailed in a growing list of peer-reviewed publications ( GenTORE has quantified the potential of sensor technologies to phenotype indicators of R&E using at or near market technologies with prediction accuracies of 52% for categorizing high vs low efficiency animals, and 46% for resilience. In the challenging context of outdoors grazing, AI-models using drone imagery have achieved accuracies of >88% for detecting, identifying, and characterizing cow postures. Further, models that combine location with accelerometer data can accurately classify (>78%) cow behaviour in an outdoor setting. It has also shown that data available on national scale can estimate animal and herd resilience. In tandem, improved methods for quantifying R&E have been developed. These methods better exploit the dynamic nature of the data increasingly available on farm, and extend the phenotyping of R&E from being “snapshot” measures to considering the accumulated consequences over a productive lifetime. These new methods, and the associated repositories of experimental data, feed into the work on genomic evaluation of R&E.
A novel method has been developed that allows genomic evaluation for any individual in a population of multiple pure-breeds and crossbred individuals. This is being tested in rotational crossbreeding scenarios. An analysis protocol that allow for heterogeneous SNP (co)variances in genomic GxE models was developed, and GxE models based on multitrait and reaction norm models were tested. In addition, implementation of the practical efficiency trait 'Age at slaughter' is being made for multiple country evaluations. In the domain of genomic management tools, indexes were developed for valuing a dairy female, and a beef heifer if she was slaughtered versus retained as a replacement female in a herd. Validation found that the transaction index is a relatively good predictor of animal value. Efficient and effective tools were also developed (and now used by industry partners) to quantify the expected variability in offspring from a given sire or mating.
With respect to forward prediction, the farm typology database constructed in GenTORE, describing cattle farm types across all the EU, was used to study regional impacts of climate stress, and to provide scenarios for individual animal-based herd prediction models and a social life cycle assessment tool. These models have shown that genetic correlations between feed efficiency at lactation level and feed efficiency at lifetime level changed depending on the nutritional environment. Considerable focus has been on combining the different strands of work. E.g. the different approaches for phenotyping are being combined into a demonstration software for farm R&E assessment. Likewise, breeding simulation and lifetime performance models are being combined to predict impacts of R&E selection strategies in diverse environments. Stakeholder consultation has been an important element for tool development, with continued showcasing of GenTORE results and development of training material for stakeholders.
GenTORE has made contributions that advance the state-of-the-art by approaching the project aims in the light of the possibilities offered by recent innovations in livestock production, i.e. genomics and on-farm sensor technology, whilst taking into account the diversity of European cattle farming systems and the impending threats from climate change. The project has assembled significant data resources to describe animals, environments, and farm systems that should have lasting impact. GenTORE has significantly advanced our understanding of R&E, leading to definitions of resilience, and the optimum balance between R&E, that are of great practical help to farmers. It has provided proof-of-principle for: length of productive life as a proxy for the accumulated consequences of resilience, and for phenotyping cattle kept outside using drone technologies. GenTORE has developed beyond state-of-the art methods for: phenotyping resilience for housed cattle, e.g. variability in milk yield; quantifying the time profiles of efficiency using multitrait random regression; genomic evaluation of multibreed and admixed populations; and for estimating gametic variation.
The decision support tools being developed will have impact by allowing farmers to identify their most (and least) resilient and efficient animals. Two international first management indexes were developed for beef cattle to better inform the value of a given animal; these can be used to identify which females should be slaughtered versus graduated to the mature herd. The impact is improved, more-informed decisions. While genotyping of female is often cited as an approach to increase gains, a tool to quantify the return-on-investment which is sufficiently generic for different populations was not available until developed here. Further impact will come from the combination of tools, in particular with respect to predicting consequences for farm R&E in future scenarios.
This progress will be given added impact by outreach and dissemination activities. It is expected to address societal concerns of a larger, younger audience and support end-users in facing new challenges.