Whole-genome approaches for causal variant detection in cattle

• Applicant: Professor Dr. Hubert Pausch
• Subject Area: Animal Breeding, Animal Nutrition, Animal Husbandry
• Term: from 2015 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 282765794

The availability of comprehensive genotype data facilitates to identify trait-associated regions in genome-wide association studies. However, common genotyping arrays provide genotypes for a limited number of polymorphic sites only, rendering the precise localisation of causal variants effectively impossible. Whole-genome sequencing of key ancestors now enables to assess a population's entire genomic variation. Once these ancestors have been sequenced, their sequence variants can be inferred in all descendants that have been genotyped with dense arrays. Association studies with imputed sequence variants facilitate to directly test causal variants for association with traits of interest in a large number of animals. The objective of this proposal is to exploit whole-genome sequence data for the identification and characterisation of causal variants underlying complex phenotypes. A computationally efficient approach for accurately imputing sequence variants into tens of thousands of animals will be implemented. Subsequently, association studies with imputed sequence variants will be carried out applying different statistical approaches with a special emphasis on multi-trait and multi-breed methods. Different approaches will be compared regarding both runtime and power to identify trait-associated variants. The effect of trait-associated variants will be validated in large independent populations. Moreover, a functional characterisation of candidate causal variants is envisaged. All investigations will be carried out using real data from different cattle breeds.

• DFG Programme: Research Fellowships
• International Connection: Australia
• Host: Professor Benjamin Hayes