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.

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.

基因组预测（Genomic prediction）是指通过个体的基因组估算其表型遗传组分的技术，该技术已彻底重塑动植物育种与医学遗传学领域。尽管该技术于近二十年前首次被提出，却始终未被研究野生生物的进化遗传学学界广泛采用。本研究对索艾羊（Soay sheep）野生种群的8个性状开展基因组预测分析。该种群是一项持续逾30年的进化生态学研究的核心观测对象，学界对其重点关注的孟德尔性状与数量性状的遗传结构已有较为充分的解析。研究结果表明，所有性状的基因组预测准确率均处于较高水平，其中携带大效应分离位点的性状表现尤为突出。本研究对比了5种不同的分析方法，其中可在同一模型中兼容零效应位点与大效应位点的两种方法表现最优。若其他野生种群的基因组预测准确率与此相近，则无需构建系谱的分子数量遗传学研究即可在更多野生种群中开展——当前相关学术文献多由那些需耗时数十年野外数据采集以构建足够详实系谱的研究主导。最后，本文还探讨了基因组预测在野生种群中的各类潜在应用场景。

方法
本数据集包含Plink二进制格式的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因型与表型信息。相关数据采集自索艾羊的野生种群，属于1985年启动的长期研究项目的一部分。SNP数据来源于Illumina Ovine SNP50 beadchip芯片阵列。文件内容的详细说明可通过自述文档获取。