In the fall of 2015, four projects started that are funded by the Partnership program STW-Breed4Food. The Animal Breeding and Genomics Centre is an important partner in each of those four projects. The four projects collectively involve 8 PhD students and 3 post-docs. Each of the four projects will develop knowledge and tools that will guide the Breed4Food breeding companies in the design of their future breeding programs.
Topbreed aims to develop statistical genetic methodology to increase the accuracy of genomic prediction for complex phenotypic traits by optimal use of sequence information. These new prediction methods will depend on the identification of the causal SNPs/genomic regions. With statistical and bioinformatics approaches, we will first identify the potential contributions of different types of genetic variation to total genetic variation, and then develop optimal differential weighting schemes for the various genetic effects in genomic prediction models.
SMARTBREED investigate the applicability of advanced machine learning methods to get insight in the variation in phenotypic patterns over time, and in the value of adding data on the life history of an animal to the genomic information to improve the prediction of the animal’s future phenotype. The amount of data that is accumulating over the lifespan of animals is increasing very rapidly, in particular with the emergence of sensor technology. Integration of this information with the genomic ability would allow for both early detection of reduced health and for prediction of future performance of an animal.
GenoMiX aims to utilize crossbred information to accelerate genetic progress. Using crossbred instead of purebred information is advantageous when the breeding goal is to improve crossbred performance, and when the correlation between purebred and crossbred performance is lower than one. GenoMiX will therefore develop and investigate methods and strategies to use crossbred performance for selection decisions in genomic breeding programs.
From sequence to phenotype aims to develop methods to identify potentially deleterious variants in livestock species. To achieve this, we will exploit the wealth of whole genome sequence information that is already available at Wageningen University for chicken, turkey, pigs and cattle. The project will integrate available genome annotation, evolutionary conservation and functional genomics data. The project also will explore to what extent knowledge obtained from other species (human) can be transferred to livestock species.
The projects are a collaboration between the Animal Breeding and Genomics Centre of Wageningen UR, the four Breed4Food breeding companies (Cobb, CRV, Hendrix Genetics, and Topigs Norsvin), and several other research institutes: Biometris-Wageningen UR, Wageningen University Bioinformatics Group, University of Groningen, Radboud University, Delft University of Technology and Leiden University Medical Centre.