GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA

拟南芥全基因组关联图谱

• 批准号: 7034823
• 负责人: JUSTIN O BOREVITZ
• 金额: $ 49.05万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-03-01 至 2011-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7034823
• 关键词: angiosperms; biochemical evolution; bioinformatics; computational biology; computer simulation; environmental adaptation; functional /structural genomics; gene environment interaction; genetic models; genetic polymorphism; genotype; geographic difference; linkage mapping; microarray technology; model design /development; natural selections; nucleic acid sequence; oligonucleotides; photobiology; plant genetics; plant population genetics; positional cloning; quantitative trait loci; seasons; species difference

DESCRIPTION (provided by applicant): Our proposal will investigate the genetic and molecular basis of complex traits and their interactions with the environment using the model plant Arabidopsis thaliana. We will implement a multi use, high density oligo- nucleotide tiling array for whole genome resequencing. The sample will include a largely unstructured core set of 384 wild A. thaliana genomes. This will be used to develop a very high resolution haplotype map, reveal genome wide patterns of variation, and suggest sites under natural selection. The ecologically relevant quantitative traits of flowering time and seedling elongation light response will be measured across two seasonal and two geographic environments which span the native range of A. thaliana. This and future community phenotypic data will be used to develop and test methods for fine scale quantitative trait locus (QTL) association scanning capitalizing on the high density haplotype map. Whole genome association mapping will be developed using coalescent models for detection and fine mapping. We will determine the functional molecular changes underlying two novel QTL utilizing the full power of Arabidopsis genetics. Importantly this proposal will develop new technological inroads for using tiling arrays to generate high density haplotype maps as the foundation for whole genome association studies. These methods, once established, can then be extended to other model systems. The development of fine scale linkage disequilibrium mapping methods will be broadly applicable. There is a tremendous interest in complex disease association mapping, but much debate over different approaches and little success to date. The studies proposed here in Arabidopsis will suggest successful paths for this daunting undertaking, as associations can be quickly confirmed to identify novel QTL.

描述（由申请人提供）：我们的提案将使用模式植物拟南芥来研究复杂性状的遗传和分子基础及其与环境的相互作用。我们将实施一种多用途、高密度寡核苷酸平铺阵列，用于全基因组重测序。该样本将包括 384 个野生拟南芥基因组的大部分非结构化核心组。这将用于开发非常高分辨率的单倍型图谱，揭示基因组范围内的变异模式，并建议自然选择下的位点。将在跨越拟南芥原生范围的两个季节和两个地理环境中测量开花时间和幼苗伸长光响应的生态相关数量性状。该群落表型数据和未来的群落表型数据将用于开发和测试利用高密度单倍型图进行精细数量性状基因座（QTL）关联扫描的方法。全基因组关联图谱将使用用于检测和精细图谱的联合模型来开发。我们将利用拟南芥遗传学的全部力量来确定两个新 QTL 背后的功能分子变化。重要的是，该提案将开发新的技术进步，使用平铺阵列生成高密度单倍型图谱，作为全基因组关联研究的基础。这些方法一旦建立，就可以扩展到其他模型系统。精细尺度连锁不平衡作图方法的发展将具有广泛的适用性。人们对复杂疾病关联图谱产生了极大的兴趣，但对不同方法的争论很多，但迄今为止收效甚微。本文在拟南芥中提出的研究将为这项艰巨的任务提供成功的途径，因为可以快速确认关联以识别新的 QTL。