Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK.
Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Korea.
Mol Ecol Resour. 2018 Jul;18(4):877-891. doi: 10.1111/1755-0998.12778. Epub 2018 Apr 16.
High-density SNP microarrays ("SNP chips") are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high-density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
高密度单核苷酸多态性微阵列（“SNP 芯片”）是一种快速、准确和高效的方法，可对大量个体中的数十万个多态性进行基因分型。虽然 SNP 芯片在人类遗传学以及动植物育种中得到了常规应用，但在进化和生态研究中应用较少。在本文中，我们描述了一种高密度 Affymetrix Axiom 芯片的开发和应用，该芯片约有 50 万个 SNP，旨在对大山雀（Parus major）种群进行基因组学研究。我们证明，每个 SNP 的基因型错误率远低于 1%，并且该芯片还可用于识别结构或拷贝数变异。该芯片用于探索探索行为（EB）的遗传结构，EB 是一个在大山雀和其他物种中广泛研究的人格特质。没有 SNP 达到全基因组显著水平，包括候选基因 DRD4。然而，EB 是可遗传的，并且似乎具有多基因结构。开发类似 SNP 芯片的研究人员可能会注意到：（i）先前在替代平台上分型的 SNP 更有可能转化为有效的检测方法；（ii）通过多个管道和独立数据集检测 SNP，可以确保高比例的有效检测方法；（iii）通过在多个种群的个体中进行 SNP 发现，可以最小化等位基因频率确定偏差；（iv）调用率最低的样本往往也具有最高的基因分型错误率。
