Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
Mol Ecol. 2013 Feb;22(3):757-73. doi: 10.1111/j.1365-294X.2012.05757.x. Epub 2012 Sep 24.
Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. The candidate gene approach has been applied to studies of a number of traits in various species, in an attempt to elucidate their genetic basis. Here, we test the application of the candidate gene approach to identify the loci involved in variation in gastrointestinal parasite burden, a complex trait likely to be controlled by many loci, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources between cattle and sheep were used to generate a list of candidate genes. In a pilot study, these candidates, along with 50 random genes, were then sequenced in two pools of Soay sheep; one with low gastrointestinal nematode burden and the other high, using a NimbleGen sequence capture experiment. Further candidates were identified from single nucleotide polymorphisms (SNPs) that were highly differentiated between high- and low-resistance sheep breeds. A panel of 192 candidate and control SNPs were then typed in 960 individual Soay sheep to examine whether they individually explained variation in parasite burden, as measured as faecal egg count, as well as two immune measures (Teladorsagia circumcincta-specific antibodies and antinuclear antibodies). The cumulative effect of the candidate and control SNPs were estimated by fitting genetic relationship matrices (GRMs) as random effects in animal models of the three traits. No more significant SNPs were identified in the pilot sequencing experiment and association study than expected by chance. Furthermore, no significant difference was found between the proportions of candidate or control SNPs that were found to be significantly associated with parasite burden/immune measures. No significant effect of the candidate or control gene GRMs was found. There is thus little support for the candidate gene approach to the identification of loci explaining variation in parasitological and immunological traits in this population. However, a number of SNPs explained significant variation in multiple traits and significant correlations were found between the proportions of variance explained by individual SNPs across multiple traits. The significant SNPs identified in this study may still, therefore, merit further investigation.
鉴定自然种群表型变异的基因可以为进化过程提供新的见解。候选基因方法已应用于许多物种的一些特征的研究，试图阐明其遗传基础。在这里，我们测试了候选基因方法在鉴定胃肠道寄生虫负担变化相关基因座中的应用，胃肠道寄生虫负担是一种复杂的特征，可能由许多基因座控制，在一个野生的斯澳绵羊群体中。我们综合了文献综述、基因本体论数据库和牛和羊之间的比较基因组资源，生成了一份候选基因列表。在一项初步研究中，这些候选基因与 50 个随机基因一起，使用 NimbleGen 序列捕获实验，在低胃肠道线虫负担和高胃肠道线虫负担的两组斯澳绵羊中进行了测序。从高抗和低抗绵羊品种之间高度分化的单核苷酸多态性 (SNP) 中进一步鉴定了候选基因。然后，在 960 只斯澳绵羊个体中对 192 个候选基因和对照基因的 SNP 进行了分型，以研究它们是否能单独解释粪便虫卵计数、两种免疫措施（circumcincta 特异性抗体和抗核抗体）的寄生虫负担变化。候选基因和对照基因的累积效应通过在三种特征的动物模型中拟合遗传关系矩阵 (GRM) 作为随机效应来估计。在初步测序实验和关联研究中，没有比预期更多的显著 SNP 被鉴定出来。此外，在与寄生虫负担/免疫措施显著相关的候选基因或对照基因 SNP 比例方面，没有发现显著差异。候选基因或对照基因 GRM 也没有显著影响。因此，候选基因方法在鉴定该群体寄生虫学和免疫学特征变异的基因座方面支持甚少。然而，一些 SNP 解释了多个特征的显著变异，并且在多个特征中单个 SNP 解释的方差比例之间发现了显著相关性。因此，本研究中鉴定的显著 SNP 可能仍值得进一步研究。
