European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
Genetics. 2014 Mar;196(3):853-65. doi: 10.1534/genetics.113.160291. Epub 2013 Dec 27.
Dissecting the molecular basis of quantitative traits is a significant challenge and is essential for understanding complex diseases. Even in model organisms, precisely determining causative genes and their interactions has remained elusive, due in part to difficulty in narrowing intervals to single genes and in detecting epistasis or linked quantitative trait loci. These difficulties are exacerbated by limitations in experimental design, such as low numbers of analyzed individuals or of polymorphisms between parental genomes. We address these challenges by applying three independent high-throughput approaches for QTL mapping to map the genetic variants underlying 11 phenotypes in two genetically distant Saccharomyces cerevisiae strains, namely (1) individual analysis of >700 meiotic segregants, (2) bulk segregant analysis, and (3) reciprocal hemizygosity scanning, a new genome-wide method that we developed. We reveal differences in the performance of each approach and, by combining them, identify eight polymorphic genes that affect eight different phenotypes: colony shape, flocculation, growth on two nonfermentable carbon sources, and resistance to two drugs, salt, and high temperature. Our results demonstrate the power of individual segregant analysis to dissect QTL and address the underestimated contribution of interactions between variants. We also reveal confounding factors like mutations and aneuploidy in pooled approaches, providing valuable lessons for future designs of complex trait mapping studies.
解析数量性状的分子基础是一项重大挑战，对于理解复杂疾病至关重要。即使在模式生物中，由于难以将区间缩小到单个基因，以及难以检测上位性或连锁的数量性状位点，精确确定致病基因及其相互作用也一直难以实现。这些困难因实验设计的局限性而加剧，例如分析个体数量少或亲本基因组之间的多态性少。我们通过应用三种独立的高通量 QTL 作图方法来解决这些挑战，以绘制两种遗传上不同的酿酒酵母菌株中 11 种表型的遗传变异基础，即 (1) 对 >700 个减数分裂后代进行个体分析，(2) 批量分离分析，以及 (3) 我们开发的新的全基因组方法——互惠半合性扫描。我们揭示了每种方法的性能差异，并通过组合它们，鉴定出影响 8 种不同表型的 8 个多态性基因：菌落形状、絮凝、在两种不可发酵碳源上的生长以及对两种药物、盐和高温的抗性。我们的结果表明，个体分离分析在解析 QTL 方面具有强大的功能，并解决了变异之间相互作用被低估的问题。我们还揭示了 pooled 方法中的混杂因素，如突变和非整倍性，为未来的复杂性状映射研究设计提供了有价值的经验教训。
