High-throughput Mapping Tools for Maize Genomics

随着美国向“植物型”经济的转变，如果美国农业要成功地满足对玉米作为食品、饲料和工业原材料来源的日益增长的需求，就必须更好地了解玉米基因组的组织和功能。 已组建了一个由分子、定量和进化遗传学家和生物信息学家组成的团队，以NSF在植物基因组学方面的现有投资为基础，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。 IDPs（InDel Polymorphisms）是一类新的共显性、等位基因特异性遗传标记，适合于高通量分析。 该项目小组将确定、开发和遗传作图500个IDP标记，这些标记特异于两个广泛使用的近交系（B73和Mo 17）。 为了鉴定有效的IDP分离策略，将比较来自四个来源的IDP鉴定率：1）GenBank基因序列; 2）Mu转座子侧翼序列; 3）来自EST的3'UTR;和4）先前作图的RFLP标记。 此外，将开发和优化用于国内流离失所者高通量采集和绘图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进行遗传图谱。 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;各种来源的“靶”序列（例如，3'UTR、外显子、全长cDNA和RFLP标记）;确定实验设计参数;并开发作图软件。 在第一阶段成功完成后，将绘制10，000个EST的基因图谱（第二阶段）。 EST 3'UTR序列在区分基因家族成员、作为IDPs的潜在来源以及用于制备Mapping Array所需的基因特异性探针方面具有重要价值。 该项目小组将对总部设在斯坦福大学的国家科学基金会支持的玉米基因组计划分离的20,000个EST的3'端进行测序。 此外，将确定与这20，000个克隆中的每一个相关的插入物大小。 由于拟议的研究将发生在分子和计算遗传学之间的接口，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。

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.