The effect of background selection and stabilising selection on genetic architecture in domestic animals

Background

Genetic architecture refers to the number, allele frequency distribution and effect size of genetic variants that contribute to traits. Genetic research suggests that many traits that matter to the productivity, health and welfare of domestic animals have complex architectures, shaped by population history and selection. The details, however, are hard to study in real data, as most causative variants have individually small effects.

Aims

This project aims to describe the genetic architecture of trait that we expect to see in domestic animals, based on their population history, historical stabilising selection, and background selection against linked deleterious variants. To achieve this, the project will use computational models of genomes under selection.

Project description

The project will use the genetic simulation environment SLiM to simulate cattle populations with mutation, selection and realistic population history, using parameters from the literature and real data. The project will vary population genetic parameters including mutation rates, strength of selection, the distribution of effects and dominance coefficients of deleterious variants, and characterise their effect on the genetic architecture.

Genetic architecture will be described with different simple and more complex statistics, including the distributions of allele frequency at causative variants, their linkage disequilibrium, polygenicity and the distribution of effect sizes.

Optionally, the project can also describe fixations of causative variants during breeding, selective sweeps, effects on genomic prediction accuracy, structure of the genomic relationship matrix, and the power and resolution of genome-wide association studies.

Specifications

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