Genomic management tools
Future-proofing European cattle production: GenTORE results and their potential impact
The issues:
GenTORE aims to contribute to a diversity rich breeding for efficiency and resilience, in which adaptation of breeds to local conditions are considered and add to the richness of future opportunities. We foresee four distinct ways in which genomic tools may improve efficiency and resilience on the individual as well as on the system level.
Genotype by environment interactions: First, we can work with ways to model GXE interactions in order to use genetic data across different environments, while selecting efficiently for individuals that are better adapted to individual environments.
Systematic crossbreeding: Second, we can work more systematically with systems that utilize the advantages of crossbreeding. Advantages include that the complementary forces of different breeds can be combined to make crosses that are particularly adapted to specific environments. This can bring faster changes in production animals and may therefore result in a more resilient cattle production system as environments or policies change. A major limitation to utilizing the benefits of crossbreeding is, that genomic tools that handle the mixture of multiple pure breeds, crossbreds, and admixed breeds do not exist.
Efficiency and resilience traits: The third way to improve genomic tools for efficiency and resilience is to improve the availability of needed phenotypes as well as modelling. For both traits records are scarce and are often not available in large scale systems.
Management decisions: The final contribution is to integrate genomic information of additive and non-additive individual effects of individuals in decision management tools, that farmers use to take more informed decisions.
GenTORE aims to contribute to a diversity rich breeding for efficiency and resilience, in which adaptation of breeds to local conditions are considered and add to the richness of future opportunities. We foresee four distinct ways in which genomic tools may improve efficiency and resilience on the individual as well as on the system level.
Genotype by environment interactions: First, we can work with ways to model GXE interactions in order to use genetic data across different environments, while selecting efficiently for individuals that are better adapted to individual environments.
Systematic crossbreeding: Second, we can work more systematically with systems that utilize the advantages of crossbreeding. Advantages include that the complementary forces of different breeds can be combined to make crosses that are particularly adapted to specific environments. This can bring faster changes in production animals and may therefore result in a more resilient cattle production system as environments or policies change. A major limitation to utilizing the benefits of crossbreeding is, that genomic tools that handle the mixture of multiple pure breeds, crossbreds, and admixed breeds do not exist.
Efficiency and resilience traits: The third way to improve genomic tools for efficiency and resilience is to improve the availability of needed phenotypes as well as modelling. For both traits records are scarce and are often not available in large scale systems.
Management decisions: The final contribution is to integrate genomic information of additive and non-additive individual effects of individuals in decision management tools, that farmers use to take more informed decisions.
GenTORE contributions to solutions:
Genotype by environment interactions
GenTORE has developed protocols and analysis pipelines for GXE models in which individual SNP effects may differ across environments. The advantage of the method is, that it relies on mixed linear models’ methodologies that are already generally used by evaluation centers in cattle breeding.
Systematic crossbreeding
GenTORE has developed a promising multi-breed genomic prediction method to evaluate simultaneously pure breeds and crossbreds and admixed individuals with complex patterns of genomic contributions from different breeds (Karaman et al. 2021, GSE). This Bayesian sampling-based method is computationally demanding, which limits its applicability for industrial scenarios. Therefore, GenTORE worked with methods to scale to full industry level applications. A similar BLUP based method was also tested on the ProCROSS system (Croiseau et al., 2022 WCGALP).
First, a method to blend phenotypes and genotypes from crossbreeds with summary statistics (SNP effects and accuracies) from e.g. purebred individuals (Clasen et al., 2022 WCGALP). This is highly relevant for e.g. rotational breeding scenarios, with relatively small population of crossbreds and large purebred populations. The method also eliminates the need for sharing raw data across countries, which could be problematic for privacy reasons. In GenTORE this method is implemented and aim to test on the rotational crossing program ProCROSS.
The second strategy is to develop a BLUP based method that, given estimated variance components using the Bayesian method, can evaluate large scale multi-breed and admixed breeds scenarios. Based on results from GenTORE, such a method is implemented in the LMT (Linear Models Toolbox) and was tested in a large Irish dataset with over 300.000 genotyped and millions of phenotyped individuals of 5 major breeds and their crossbreeds using a breed of origin single-step BLUP method. A validation of the improvement of prediction for crossbred individuals in this scenario was presented in the 4th annual GenTORE meeting (Guillenea et al, 2021). This means that the methods have been implemented to be able to handle any industry level problems.
Efficiency and resilience traits
The perspective of improved phenotypes for efficiency and resilience is discussed in more detail in the theme dedicated to this topic.
Management decisions
GenTORE has contributed to the development of management indexes based on the future profit potential of cattle to decide if a particular heifer or cow is a candidate for further breeding or for sale, or for culling. The indexes can be used in tandem to help farmers make decisions. This can be undertaken either at the point of sale or on the farm itself when a farmer is trying to decide the fate of the animal
Applications and potential impact
In several cases, GenTORE is developing methods and models using industry level data. The results are therefore either ready to be adapted by industry, or at least very close to be so. Also, results and expertise’s knowledge are communicated to other stakeholders that potentially will adapt the methodologies developed. In this connection, results and methods are communicated in a broader community in the Nordic countries, Ireland, France, and will in part be subject of the GenTORE summer school in Wageningen 2022.
As examples, the BOA models for crossbred individuals are planned to be implemented both in the Nordic countries and in France. The culling index (called COW) in Ireland is fully deployed via a webservice at the Irish Cattle breeding Federation. It is routinely used at two main time points in conjunction with the national breeding index (which is correlated with a value of 0.63 with the COW index).
The transaction index (renamed to Commercial beef Value CBV in Ireland) has been deployed nationally with considerable interest. The plan is that in 2022 all electronic boards at the time of sale of calves will display the CBV.
Tools were also developed and deployed in France to reflect the expected heterogeneity in the progeny of individual bulls. Breeders of the next generation will seek heterogeneity in offspring in the pursuit of identifying a genetically elite outlier extreme relative to the mean; producers on the other hand will strive for a more homogenous herd. French breeding companies are using this tool to help accelerate genetic gain.
As a result, GenTORE will lead to better utilization of and selection in crossbreeding systems, better selection within and across environments, and better management decisions leading to more efficient and resilient cattle systems. The entry point for the aforementioned applications is the gentore.eu website