Genomic prediction in the wild: a case study in Soay sheep

Genomic prediction, the technique whereby an individual’s genetic
component of their phenotype is estimated from its genome, has
revolutionised animal and plant breeding and medical genetics. However,
despite being first introduced nearly two decades ago, it has hardly been
adopted by the evolutionary genetics community studying wild organisms.
Here, genomic prediction is performed on eight traits in a wild population
of Soay sheep. The population has been the focus of a >30 year
evolutionary ecology study and there is already considerable understanding
of the genetic architecture of the focal Mendelian and quantitative
traits. We show that the accuracy of genomic prediction is high for all
traits, but especially those with loci of large effect segregating. Five
different methods are compared, and the two methods that can accommodate
zero-effect and large-effect loci in the same model tend to perform best.
If the accuracy of genomic prediction is similar in other wild
populations, then there is a real opportunity for pedigree-free molecular
quantitative genetics research to be enabled in many more wild
populations; currently the literature is dominated by studies that have
required decades of field data collection to generate sufficiently deep
pedigrees. Finally, some of the potential applications of genomic
prediction in wild populations are discussed.