The power of genome-wide association studies in commercial crossbred animals

Background

In pig and poultry breeding, commercial animals are three-way or four-way terminal crossbreds, that combine the genetics of 3-4 genetically distinct purebred lines. Breeding happens in the pure lines, but for practical as well as scientific reasons genetics research is often performed in crossbreds. Samples and phenotypes from crossbred animals may be more accessible than the pure lines, and the environment of the commercial crossbred animals may be more relevant to practice.

Aims

This project aims to quantify the power and precision of genome-wide association studies of commercial crossbred animals, and describe contributions of genetic variance in crossbreds. To achieve this, the project will use genetic simulation and theoretical power calculations.

Project description

The project will use the genetic simulation environment AlphaSimR to simulate breeding programs with terminal crossbreeding, including selection within lines and crosses between them.

The resulting distributions of causative variants in crossbred animals will be used to quantify the power of genome-wide association studies for variants under selection in the pure lines. Variants will be classified based on their differentiation between lines, effect size, and contribution to genetic variance in the crossbreds. Parameters of the breeding program, such as the polygenicity of the traits and differences in selection between lines, will be varied to describe their impact.

Optionally, the project can also implement genome-wide association studies on the simulated data to check the numerical predictions of power and describe the mapping resolution due to long-range linkage disequilibrium, and make comparisons to real genotype data from crossbred laying hens.

Specifications

The project is suitable for students in animal science or bioinformatics who are interested in modelling, animal breeding and genetic mapping.