Bayesian marker-based principal component ridge regression – a flexible multipurpose framework for quantitative genetics in wild study systems

Abstract

AbstractAs larger genomic data sets become available for wild study populations, the need for flexible and efficient methods to estimate and predict quantitative genetic parameters, such as the adaptive potential and measures for genetic change, increases. Animal breeders have produced a wealth of methods, but wild study systems often face challenges due to larger effective population sizes, environmental heterogeneity and higher spatio-temporal variation. Here we adapt methods previously used for genomic prediction in animal breeding to the needs of wild study systems. The core idea is to approximate the breeding values as a linear combination of principal components (PCs), where the PC effects are shrunk with Bayesian ridge regression. Thanks to efficient implementation in a Bayesian framework using integrated nested Laplace approximations (INLA), it is possible to handle models that include several fixed and random effects in addition to the breeding values. Applications to a Norwegian house sparrow meta-population, as well as simulations, show that this method efficiently estimates the additive genetic variance and accurately predicts the breeding values. A major benefit of this modeling framework is computational efficiency at large sample sizes. The method therefore suits both current and future needs to analyze genomic data from wild study systems.