"The development of genetics and genomics for analysis of quantitative traits"

描述(由申请人提供)：这项赠款提案的目标是开发工具并向社区提供工具，以确定可在模式丝状真菌粗面脉孢子菌中测量到的任何表型的基因。我们建议开发两个大的作图群体作为社区资源，这将使识别控制自然变化的复杂表型的数量性状基因座(QTL)成为可能。我们的一个种群包括500个野生分离株，它们来自粗毛拟青霉的一个系统发育支系，用于关联作图，这是识别小效应基因座的首选方法。另一个群体是两个不同的粗毛拟青霉菌株之间的高级杂交，以便以高遗传分辨率绘制稀有等位基因的连锁图谱。对于每个群体，我们将使用Solexa平台通过大规模并行签名测序来测量基因型和基因表达。这些资源将使任何研究实验室能够对感兴趣的性状的品系进行评分，并绘制潜在的QTL。作为原则的证明，我们将描述野生和高级杂交菌株在表型方面的特征，这些表型对脉孢子菌研究界具有广泛的兴趣：无性孢子繁殖、有性繁殖、营养生长、菌丝构筑和孢子萌发期间的合作行为。我们将率先使用我们的Solexa实验中的mRNA表达数据来识别这些宏观特征背后的分子参与者，因为基因的表达被证明与不同个体的特征存在协同变化。此外，表达测量将被用来详细描述N.crassa调控网络，因为我们分析了表达水平之间的协变，并从基因上定位了它们的控制调控因子。我们的具体目标是(I)构建高级杂交并鉴定这些菌株和野生分离物之间不同的表型；(Ii)使用Solexa平台对每个作图群体中每个个体的cDNA进行短读测序，生成密集的基因分型数据并测量基因表达；以及(Iii)对mRNA表达和我们的原则验证组织性状进行连锁和关联作图。我们相信，我们所提出的基因类型、表型和基因表达水平之间的映射将把粗毛拟青霉作为研究所有真核物种自然变异的模型推向前列。 与公共卫生相关：我们建议使用粗毛新菌研究个体之间的遗传差异，这些差异控制着生长、生物体形状和对药物的敏感性等特征。粗糙奈瑟氏菌是病原真菌的模型，我们的目标是了解它的生物学的许多方面，这些方面对疾病和治疗很重要。此外，由于人们对个体间遗传差异的原理知之甚少，我们的工作将为其他物种的遗传学提供假说，比如人类。

DESCRIPTION (provided by applicant): The objective of this grant proposal is to develop and make available to the community tools to identify genes responsible for any phenotype that can be measured in the model filamentous fungus, Neurospora crassa. We propose to develop as a community resource two large mapping populations, which will enable the identification of quantitative trait loci (QTLs) controlling naturally varying complex phenotypes. One of our populations comprises 500 wild isolates from a single phylogenetic clade of N. crassa, to be used for association mapping, the method of choice for identification of loci of small effect. The other population is an advanced intercross between two divergent N. crassa strains, to allow linkage mapping of rare alleles at high genetic resolution. For each population, we will measure genotype and gene expression via massively parallel signature sequencing using the Solexa platform. These resources will enable any research lab to score the strains for a trait of interest and map the underlying QTLs. As a proof of principle, we will characterize the wild and advanced intercross strains with respect to phenotypes that have broad interest to the Neurospora research community: asexual spore reproduction, sexual reproduction, vegetative growth, hyphal architecture and cooperative behavior during spore germination. We will pioneer the use of the mRNA expression data from our Solexa experiment to identify the molecular players underlying these macroscopic traits, as the expression of genes is shown to co-vary with traits across individuals. In addition, the expression measurements will be used to detail the N. crassa regulatory network, as we analyze covariation between expression levels and genetically map their controlling regulators. Our specific aims are (i) to construct the advanced intercross and characterize phenotypes that vary among these strains and the wild isolates; (ii) to perform short-read sequencing on cDNAs using the Solexa platform from each individual in each mapping population, to generate dense genotyping data and measure gene expression; and (iii) to conduct linkage and association mapping of mRNA expression and our proof-of-principle organismal traits. We believe that the mapping between genotypes, phenotypes, and gene expression levels that we propose would propel N. crassa to the forefront as a model for the study of natural variation in all eukaryotic species. Relevance to Public Health: Using N. crassa, we propose to study genetic differences between individuals that control traits like growth, organism shape, and sensitivity to drugs. N. crassa is a model for pathogenic fungi, and we aim to understand many aspects of its biology that are important for disease and treatment. Also, since so little is known about the 'principles of -genetic differences between individuals, our work will provide hypotheses about the genetics of other species, like humans.