High-Density DNA Microarrays for Global Gene Expression Studies in Plants

用于植物整体基因表达研究的高密度 DNA 微阵列

• 批准号: 9975920
• 负责人: John Quackenbush
• 金额: $ 217.9万
• 依托单位: Institute for Genomic Research
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-09-01 至 2002-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9975920&HistoricalAwards=false
• 关键词: Density; DNA; Microarrays; Global; Gene

As plant biologists approach the 21st century there are tremendous opportunities for understanding the molecular basis of cellular physiology and differentiation, organ development, disease resistance, and stress tolerance, because of advancements in automated DNA sequencing. These fundamental areas of plant research have been inundated with new sequence data that provide clues to the genetic elements central to plant life. The United States along with the international research community has promoted the complete genome sequencing of the model system Arabidopsis thaliana to seed efforts in plant genomic research. The value of this resource can not be overstated because of the significant conservation of gene sequence and protein function throughout evolutionary history. The Institute for Genomic Research (TIGR) has played a major role in the Arabidopsis genome initiative and will publish the complete sequence of Chromosome II, more than 10% of the genome (16-17 megabase pairs out of an estimated 120 megabase pairs), in mid 1999. TIGR has also been funded to annotate the entire Arabidopsis sequence so that data generated by the AGI (Arabidopsis Genome Initiative) international consortium will be curated and maintained in a unified and informative fashion. This award supports the construction of a complete Chromosome II microarray for functional genomic studies of Arabidopsis. The Chromosome II microarray will be used to catalog gene expression at the whole chromosome level and to evaluate and extend the gene prediction algorithms that are now being employed for annotation of the complete genomic sequence. At this stage of the genome program, approximately 30% of the predicted gene products are annotated as "hypothetical proteins." Identification of a corresponding mRNA species for these hypotheticals, using microarray technologies, will immediately add weight to the genome annotation. Moreover, information about chromosomal gene expression patterns will lead to a more refined understanding of genome organization and the activation of gene networks. Validation of our current gene predictions and correction of those hypothesis that are not physiologically relevant will enhance the value of this universal plant resource. The fundamentals of plant biology will be revealed by the Arabidopsis thaliana sequence: a reference genome for plant genomic research in the 21st century. This microarray program will provide a means to map additional physiological data to the Arabdiopsis sequence data and enhance its used for basic and applied plant research beneficial to our agricultural and economic national interests. These observations of the Arabidopsis genome will be directly transferable to genome programs in other plant species, helping all research groups to realize the full potential of a National Plant Genome Research Program.

随着植物生物学家接近21世纪，由于DNA自动测序的进步，人们有巨大的机会了解细胞生理和分化、器官发育、抗病和抗逆性的分子基础。植物研究的这些基本领域已经被新的序列数据淹没，这些数据为植物生命的核心遗传元素提供了线索。美国与国际研究界一道，推动了模式系统拟南芥的完整基因组测序，以期在植物基因组研究中提供种子。这种资源的价值怎么强调都不为过，因为在整个进化史上，基因序列和蛋白质功能都是非常保守的。基因组研究所(TIGR)在拟南芥基因组倡议中发挥了重要作用，并将于1999年年中公布第二号染色体的完整序列，占基因组的10%以上(估计120兆碱基对中有16-17兆碱基对)。还资助了TIGR对整个拟南芥序列进行注释，以便以统一和信息量大的方式管理和维护由AGI(拟南芥基因组倡议)国际联合会产生的数据。该奖项支持构建完整的II号染色体微阵列，用于拟南芥的功能基因组研究。第二染色体微阵列将用于对整个染色体水平的基因表达进行分类，并评估和扩展目前用于注释完整基因组序列的基因预测算法。在基因组计划的这个阶段，大约30%的预测基因产物被注释为“假设蛋白质”。利用微阵列技术识别这些假说的相应信使核糖核酸物种，将立即增加基因组注释的权重。此外，关于染色体基因表达模式的信息将导致对基因组组织和基因网络激活的更精细的理解。验证我们目前的基因预测，并修正那些与生理无关的假设，将提高这一普遍植物资源的价值。拟南芥序列将揭示植物生物学的基本原理：21世纪植物基因组研究的参考基因组。这个微阵列计划将提供一种手段，将更多的生理数据映射到Arabdiopsis序列数据，并加强其用于基础和应用植物研究，有利于我们的农业和经济国家利益。这些对拟南芥基因组的观察将直接转移到其他植物物种的基因组计划中，帮助所有研究小组实现国家植物基因组研究计划的全部潜力。