Utility of pooled sequencing for association mapping in non-model organisms

High density genome-wide sequencing increases the likelihood of discovering genes of major effect and genomic structural variation in organisms. While there is an increasing availability of reference genomes across broad taxa, the greatest limitation to whole-genome sequencing of multiple individuals continues to be the costs associated with sequencing. To alleviate excessive costs, pooling multiple individuals with similar phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high genome coverage, but at the loss of individual genotypes. Although Pool-Seq has been an effective method for association mapping in model organisms, it has not been frequently utilized in natural populations. To extend bioinformatic tools for rapid implementation of Pool-Seq data in non-model organisms, we developed a pipeline called PoolParty and illustrate its effectiveness in genetic association mapping. Alignment expectations based on five pooled Chinook salmon (Oncorhynchus tshawytscha) li...高密度全基因组测序可提升在生物体中发现主效基因（major effect gene）与基因组结构变异（genomic structural variation）的概率。尽管跨多个类群的参考基因组（reference genome）可获得性持续提升，但对多个个体开展全基因组测序的最大限制因素仍源于测序相关成本。为缓解过高的测序成本，将表型（phenotype）相似的多个个体混合并对均质化DNA进行测序（Pool-Seq），可实现较高的基因组覆盖度，但会丢失个体基因型信息。尽管Pool-Seq已成为模式生物关联作图（association mapping）的有效方法，但其在自然种群中的应用却并不频繁。为开发可在非模式生物中快速处理Pool-Seq数据的生物信息学（bioinformatics）工具，我们研发了一款名为PoolParty的分析流程，并验证了其在遗传关联作图中的有效性。基于5尾混合奇努克鲑（Oncorhynchus tshawytscha）肝脏样本的序列比对预期……