Mapping the genetic basis of natural variation in Arabidopsis thaliana using a heterogenous stock

大多数具有经济和进化利益的特征都是复杂的。复杂性状通常是许多影响较小的基因相互作用的产物，并且容易受到环境效应的影响。因此，用传统的遗传方法来鉴定具有较大影响的单个基因是不合适的。目前，定位和鉴定这些基因的最佳方法是通过数量性状位点（QTL）分析。该分析使用遗传标记和性状之间的统计关联来识别包含影响所研究性状的遗传因子（QTL）的染色体片段。大多数QTL定位研究使用的设计包括两个近交亲本系之间的杂交，这些亲本系因所研究的性状而不同。虽然这种方法是成功的，但它通常只允许识别两个系不同的少数QTL。此外，与这些QTL相关的置信区间往往很大，在克隆之前需要进一步的研究来确定QTL。更重要的是，QTL是在一个简单的背景下被鉴定出来的，这可能与通常在植物中基因表达的复杂遗传背景无关。该提案的目标是在复杂的遗传背景（如真实的植物种群）中精确地确定生活史特征（如发芽率、生长、开花时间和果实产量）的遗传因素。为了实现这一目标，我们建议从拟南芥的异种砧木（RIHS）中开发一套重组自交系。这些系将由19个亲本系杂交而来。由于这些品系将比现有资源具有更高的遗传和表型多样性，因此它们可以用于检测更多性状的更多遗传因素。此外，RIHS可以更精确地定位这些因子（即更小的置信区间），便于从QTL结果中克隆实际基因。拟南芥作为植物遗传学研究的主要模式系统，是开发这些新定位系的理想植物。广泛的基因组工具将有助于克隆QTL。此外，由于拟南芥与许多重要作物（油菜种子、卷心菜、西兰花和其他芥菜）属于同一科，在该模式物种中鉴定的基因将允许鉴定可用于提高作物质量和生产力的同源基因。在这里生产的RIHS种子及其基因型和表型数据将向公众开放，从而提高科学界研究植物复杂性状遗传基础的能力。

Most traits of economical and evolutionary interest are complex. Complex traits are usually the product of the interaction of many genes of small effect, and tend to be affected by environmental effects. Thus, traditional genetic approaches used to identify single genes of large effect are not appropriate. Currently, the best approach to map and identify these genes is through quantitative trait locus (QTL) analysis. This analysis uses statistical associations between genetic markers and traits to identify chromosomal segments that contain genetic factors (QTL) affecting the trait being studied. Most QTL mapping studies use designs that involve a cross between two inbred parental lines that differ for the trait being studied. While this approach has been successful, it usually allows the identification of only a few QTL for which the two lines differ. In addition, the confidence intervals associated with these QTL tend to be large, requiring further studies to identify the QTL before it can be cloned. More importantly, QTL are identified in a simple background which may not be relevant to the usual complex genetic background in which gene expression occurs in plants. The goal of this proposal is to identify the genetic factors that underlie life-history traits (such as germination rate, growth, flowering time, and fruit production) with precision, in a complex genetic background (as in real plant populations). To achieve this goal, we propose to develop a set of Recombinant Inbred Lines from a Heterogeneous Stock (RIHS) in the plant Arabidopsis thaliana. These lines will be derived from a cross between 19 parental lines. Because these lines will have higher genetic and phenotypic diversity than current resources, they can be used to detect a larger number of genetic factors for a larger number of traits. In addition, RIHS allow the localization of these factors with more precision (i.e. smaller confidence intervals), facilitating the cloning of the actual gene from the QTL results. A. thaliana, the primary model system for the study of plant genetics, is an ideal plant in which to develop these new mapping lines. Extensive genomic tools will facilitate cloning QTL. In addition, because A. thaliana is in the same family as a number of important crops (rape seed, cabbage, broccoli and other mustards), genes identified in this model species will allow the identification of homologous genes that can be used to improve crop quality and productivity. Seeds from the RIHS being produced here, together with data on their genotypes and phenotypes will be made publicly available, improving the ability of the scientific community to study the genetic basis of complex traits in plants.