High-throughput Mapping Tools for Maize Genomics

玉米基因组学高通量作图工具

• 批准号: 9975868
• 负责人: Patrick Schnable
• 金额: $ 294.77万
• 依托单位: Iowa State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-09-01 至 2003-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9975868&HistoricalAwards=false
• 关键词: throughput; Mapping; Tools; Maize; Genomics

A greater understanding of the organization and function of the maize genome is essential if US agriculture is to be successful in meeting the growing needs for maize as food, feed and a source of industrial raw materials as the US moves towards a "plant-based" economy. A team of molecular, quantitative and evolutionary geneticists and bioinformaticists has been assembled to build upon existing NSF investments in plant genomics to develop the novel high-throughput genetic mapping technologies and resources needed to meet this challenge. IDPs (InDel Polymorphisms) are a new class of co-dominant, allele-specific, genetic markers suitable for high-throughput analyses. The project team will identify, develop and genetically map 500 IDP markers specific to two widely used inbred lines (B73 and Mo17). To identify efficient IDP isolation strategies, the rates of IDP identification will be compared from four sources: 1) GenBank genic sequences; 2) Mu transposon flanking sequences; 3) 3' UTRs from ESTs; and 4) previously mapped RFLP markers. In addition, computational and wet lab approaches for the high-throughput acquisition and mapping of IDPs will be developed and optimized. The Mapping Array is a novel chip-based technology designed to genetically map a large number of non-redundant, sequence-defined cDNAs. During Phase I, an existing nylon-based protocol will be adapted to DNA "chips"; hybridization conditions optimized; various sources of "target" sequences (e.g., 3' UTRs, exons, full-length cDNAs and RFLP markers) tested; experimental design parameters determined; and mapping software developed. Upon successful completion of Phase I, 10,000 ESTs will be genetically mapped (Phase II). The sequences of EST 3' UTRs are of great value in distinguishing members of gene families, as potential sources of IDPs and for producing the gene-specific probes needed for the Mapping Array. The project team will sequence the 3' ends of 20,000 of the ESTs being isolated by the NSF-supported maize genome project headquartered at Stanford University. In addition, the insert size associated with each of these 20,000 clones will be ascertained. Because the proposed research will occur at the interface between molecular and computational genetics, it will provide important cross-disciplinary training opportunities for graduate students and post-doctoral scientists.

随着美国向“植物性”经济迈进，美国农业要想成功满足对玉米作为食品、饲料和工业原材料来源不断增长的需求，就必须更好地了解玉米基因组的组织和功能。 一个由分子、定量和进化遗传学家和生物信息学家组成的团队已经组建起来，以 NSF 在植物基因组学方面现有投资为基础，开发应对这一挑战所需的新型高通量遗传图谱技术和资源。 IDP（InDel 多态性）是一类新型共显性、等位基因特异性遗传标记，适用于高通量分析。 该项目团队将识别、开发和遗传定位两个广泛使用的自交系（B73 和 Mo17）特有的 500 个 IDP 标记。 为了确定有效的 IDP 分离策略，将从四个来源比较 IDP 识别率：1）GenBank 基因序列； 2) Mu转座子侧翼序列； 3) 来自 EST 的 3' UTR； 4) 先前定位的 RFLP 标记。 此外，还将开发和优化用于高通量采集和绘制 IDP 的计算和湿实验室方法。 Mapping Array 是一种基于芯片的新型技术，旨在对大量非冗余、序列定义的 cDNA 进行基因定位。 在第一阶段，现有的基于尼龙的方案将适用于 DNA“芯片”；优化杂交条件；测试各种来源的“目标”序列（例如，3' UTR、外显子、全长 cDNA 和 RFLP 标记）；确定实验设计参数；并开发了地图软件。 第一阶段成功完成后，将对 10,000 个 EST 进行基因图谱绘制（第二阶段）。 EST 3' UTR 的序列对于区分基因家族成员、作为 IDP 的潜在来源以及生产作图阵列所需的基因特异性探针具有重要价值。 该项目团队将对 20,000 个 EST 的 3' 末端进行测序，这些 EST 是由总部位于斯坦福大学的 NSF 支持的玉米基因组项目分离出来的。 此外，还将确定与这 20,000 个克隆中每个克隆相关的插入片段大小。 由于拟议的研究将发生在分子遗传学和计算遗传学之间的界面，因此它将为研究生和博士后科学家提供重要的跨学科培训机会。