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

Citation

Slate, Jon (2022), Genomic prediction in the wild: a case study in Soay sheep, Dryad, Dataset, https://doi.org/10.5061/dryad.h44j0zpkq

Abstract

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.

Methods

The dataset describes SNP genotype and phenotype information, provided in Plink binary format. The data were collected from a wild population of Soay sheep, as part of a long-term study that has been running since 1985. SNP data are from the Illumina Ovine SNP50 beadchip array. Descriptions of the file contents are available as a readme document.

Usage Notes

Users are strongly advised to contact the corresponding author (j.slate@sheffield.ac.uk), for further details on the long-running St Kilda Soay sheep project and the methods used in the field and laboratory.

Funding

Natural Environment Research Council, Award: NE/M002896/1