Genetic basis of stress tolerance in natural populations of yeast

描述（由申请人提供）：复杂性状是通过群体中数量性状位点分离的综合效应遗传的。这些基因决定因素可能有或大或小的影响，并可能以无数种方式结合在一起。尽管十年来通过全基因组关联研究和其他方法绘制复杂性状的遗传决定因素，但该领域尚未确定从基因型推断表型的最佳方法。我们建议使用酵母遗传学来了解一系列数量性状的潜在遗传结构。酵母系统具有优越的实验工具，跨真核生物的保守生物学，以及越来越多的不同基因组序列的收集。我们将首先关注有强烈影响的基因座，即。“孟德尔”特征。这使得它们很容易通过等位基因交换实验进行基因定位和实验确认。我们的假设是，具有强效应等位基因的基因也会在种群中含有更多数量效应的等位基因。这种想法类似于“罕见变异”假说，即低频强效等位基因导致高疾病风险。我们试图发现这些相同的基因是否在整个人群中也很重要，因为效应较低的等位基因可能更难以识别。我们将在三个具体目标下进行这个项目，每个目标由一位专家调查员负责。在Aim 1中，我们将探索酿酒酵母和悖论酵母天然种群的表型多样性。这些物种具有大量的表型和基因型多样性，可供我们利用。特别是，我们将观察酵母在自然历史中可能经历的环境压力下生长能力的分离。第二个目标是确定那些分离为少数大效应位点的表型的遗传基础。为了绘制致病位点，我们将使用大量分离作图方法与深度测序相结合，然后通过等位基因交换实验来证明因果关系。第三个目的是测试这些相同的基因座是否对大量菌株的表型变异很重要。我们将从数百个遗传多样化的分离株中扩增等位基因，将它们移植到等基因背景中，并通过基于池的定量竞争分析来测定基因功能。等位基因频率将使用深度测序来测量。这些方法的结合将使我们能够识别出胁迫耐受性性状以简单的遗传方式分离的杂交品种，绘制致病基因图谱，并确定这些基因中其他变异在种群中的重要性。我们的研究结果将有助于理解复杂性状的遗传基础。

DESCRIPTION (provided by applicant): Complex traits are inherited via the combined effects of quantitative trait loci segregating in a population. These genetic determinants may have large or small effects, and may combine in a myriad of ways. Despite a decade of work on mapping the genetic determinants of complex traits via genome-wide association studies and other methods, the field has as yet not determined an optimal approach to inferring phenotype from genotype. We propose to use yeast genetics to learn the underlying genetic architecture of a series of quantitative traits. The yeast system has superior experimental tools, conserved biology across eukaryotes, and a growing collection of diverse genome sequences on which to draw. We will first focus on loci of strong effect, i.e. "Mendelian" traits. These lend themselves o easy genetic mapping and experimental confirmation via allele swap experiments. Our hypothesis is that genes with strong effect alleles will also harbor alleles of more quantitative effect across a population. This idea is akin to the "rare variant" hypothesis in which low frequency strong effect alleles contribute to high disease risk. We seek to discover whether these same genes may also be of importance across the population due to lower effect alleles that may be more difficult to identify. We will pursue this project in three specific aims, each le by an expert investigator. In Aim 1, we will explore the phenotypic diversity in natural yeast populations from the species S. cerevisiae and S. paradoxus. These species have a great deal of phenotypic and genotypic diversity that we can utilize. In particular, we will observe segregation of growth ability in the face of environmental stresses that yeasts may have experienced during their natural history. The second aim is to determine the genetic basis of those phenotypes that segregate as a small number of large effect loci. To map the causative loci, we will use a bulk segregant mapping method coupled with deep sequencing, followed by allele swap experiments to prove causation. The third aim is to test whether these same loci are important for phenotypic variation across a large panel of strains. We will amplify alleles from hundreds of genetically diverse isolates, transplant them into an isogenic background, and assay gene function via a pool-based, quantitative, competitive assay. Allele frequency will be measured using deep sequencing. This combination of methods will allow us to identify crosses in which stress tolerance traits segregate in a genetically simple manner, map the causative genes, and determine the importance of additional variants in these genes across a population. Our results will inform the understanding of the genetic basis of complex traits. PUBLIC HEALTH RELEVANCE: Most human diseases have a complex underlying genetic basis; however, a subset segregates as simple Mendelian traits. We will utilize the model eukaryote budding yeast to determine whether the genes whose variants are associated with genetically simple traits also harbor quantitative variation across populations. Our results could influence the study of such traits in humans.