GENOME WIDE ASSOCIATION MAPPING IN ARABIDOPSIS THALIANA

拟南芥全基因组关联图谱

基本信息

批准号：
7907155
负责人：
JUSTIN O BOREVITZ
金额：
$ 33.24万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-18 至 2011-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7907155
关键词：
Accounting Affect Algorithms Alleles Alternative Splicing Arabidopsis Atlases Base Pairing Beds Bioconductor Biological Models Candidate Disease Gene Cataloging Catalogs Color Communities Complex Cues DNA Resequencing Data Data Set Detection Development Disease Association Environment Evolution Flowers Foundations Future Gene Expression Generations Genes Genetic Genetic Complementation Test Genetic Crosses Genetic Polymorphism Genetic Recombination Genetic Variation Genome Genotype Graph Growth Haplotypes Humidity Hybridization Array Individual Inherited Joints Knock-out Light Linkage Disequilibrium Linkage Disequilibrium Mapping Maps Measures Methods Mining Modeling Molecular Molecular Genetics Molecular Profiling Mouse-ear Cress Mutation Natural Selections Noise Nucleotides Oligonucleotides Pattern Phenotype Plant Model Polymorphism Analysis Population Population Genetics Principal Investigator Quantitative Trait Loci Residual state Resolution Resources Sampling Scanning Seasons Seedling Siblings Site Spain Staging Stratification Structure Sum Surveys Sweden System Temperature Testing Time Transgenic Organisms Trees Variant base day length density falls follow-up functional genomics gene discovery genetic resource genome wide association study genome-wide genome-wide linkage insertion/deletion mutation interest light intensity markov model novel open source programs research study response simulation statistics success trait water treatment

项目摘要

Our proposalwill 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 usedto 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 genomeassociation 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 powerof Arabidopsis genetics. Importantly this proposal will develop newtechnological 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 methodswill 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.

我们的提议将研究复杂性状的遗传和分子基础及其与使用模型植物拟南芥的环境。我们将实施多用途的高密度寡素 - 核苷酸瓷砖阵列，用于整个基因组重新配置。该样本将包括一个很大程度上的核心一组384个野生A. thaliana基因组。这将用于开发非常高的分辨率单型映射，揭示基因组宽的变异模式，并建议在自然选择下进行位点。在生态上开花时间和幼苗伸长光响应的相关定量性状将在跨越两个季节性和两个地理环境，跨越了塔利亚纳的天然范围。这个和未来社区表型数据将用于开发和测试精细规模定量特质基因座的方法（QTL）在高密度单倍型图上资本化的关联扫描。整个基因组相结合将使用合并模型进行检测和精细映射开发映射。我们将确定利用拟南芥遗传学的全部幂的两个新型QTL的功能分子变化。重要的是，该提案将发展新技术，以便使用平铺阵列产生高密度单倍型图作为整个基因组关联研究的基础。这些方法一次建立，然后可以扩展到其他模型系统。精细规模联系的发展不平衡的映射方法是广泛适用的。对复杂疾病关联的映射引起了极大的兴趣，但关于不同的辩论迄今为止，接近和几乎没有成功。拟南芥提出的研究将表明成功这项艰巨的任务的路径可以迅速确认，以识别新颖的QTL。