SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5,321 candidate adaptive genes associated with known immunological, metabolic, and growth functions in ovids and other ungulates. We selectively targeted 8,161 exons in protein-coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (O. canadensis) exon capture data and directly from the domestic sheep genome (O. aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2,350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP-chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (LOSITAN and BayeScan), we detected 28 SNP loci potential...鉴定自然选择基因组特征背后的基因，是理解生物对本地环境适应性的关键所在。我们采用靶向重测序技术，在羊类及其他有蹄类动物中，针对5321个与已知免疫、代谢及生长功能相关的候选适应性基因，完成单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记的鉴定。我们针对性捕获了所选候选基因的蛋白质编码区，以及其邻近的5′端与3′端非翻译区域内的8161个外显子。本次靶向测序的序列来源包括大角羊（Ovis canadensis）的外显子捕获数据，以及家羊基因组（Ovis aries v.3；oviAri3）的直接序列数据。用于多尔羊（Ovis dalli dalli）外显子捕获的大角羊序列，可比对至oviAri3基因组上的2350个基因，每个基因平均对应2个外显子。我们开发了一款基于微流控实时定量聚合酶链反应（qPCR）的SNP芯片，对遍布其活动分布区的476只多尔羊进行基因分型，并以此检测自然选择的作用模式。我们采用LOSITAN与BayeScan等多种验证性分析方法，共检测到28个具有潜在选择信号的SNP位点……