Data from: Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach

Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. Here we test the candidate gene approach to identifying loci involved in variation in gastrointestinal parasite burden, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources were used to generate a list of candidate genes. In a pilot study these candidates, along with 50 random genes, were then sequenced in pools of Soay sheep with low and high gastrointestinal nematode burden. Further candidates were identified from 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 (FEC), as well as two immune measures. 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.鉴定自然种群中表型变异背后的基因，可为演化过程提供全新的认知。本研究以野生索伊羊（Soay sheep）种群为研究对象，检验候选基因策略在鉴定胃肠道寄生虫负荷变异相关位点中的适用性。研究团队通过全面的文献调研、基因本体（Gene Ontology）数据库以及比较基因组学资源，构建了候选基因列表。在预实验中，我们对这批候选基因及50个随机选取的基因，在高、低胃肠道线虫负荷的索伊羊混合样本中完成了测序。后续又从高、低抗性绵羊品种间分化程度极高的单核苷酸多态性（SNP）位点中筛选得到更多候选基因。随后，我们对960只个体索伊羊的192个候选及对照SNP位点进行基因分型，以探究这些位点能否单独解释以粪便虫卵计数（FEC）衡量的寄生虫负荷变异，以及两项免疫指标的变异。通过在三种性状的动物模型中将遗传关系矩阵（GRMs）作为随机效应，我们估算了候选与对照SNP位点的累积效应。预实验测序与关联分析中鉴定到的显著SNP位点数量并未超出随机预期范畴。此外，在与寄生虫负荷/免疫指标显著关联的位点占比上，候选SNP与对照SNP并无显著差异。候选基因或对照基因的GRMs亦未表现出显著效应。综上，本研究几乎不支持候选基因策略用于鉴定本种群中寄生虫学与免疫学性状变异相关位点的适用性。