SGER: Conserved Noncoding Sequences (CNS) in Grasses

许多牧草，包括一些重要的经济作物，被认为是“孤立系统”，因为它们没有序列数据库，无法进行有效的遗传指纹、作图和基因片段识别。现代育种依赖于这样的分子工具。支持这一项目作为探索性研究小额赠款(SGER)的理由是，这是一个短期的概念验证项目，将开发出满足这些需求的迫切需要的工具。该项目将开始开发一个保守的非编码(CNS)序列数据库，以覆盖草类。在基因的非蛋白质编码部分，CNS序列是大的、精确的系统发育的“足迹”。它们可以通过对来自全基因组和表达序列标签(EST)集合的序列进行成对比较而获得。CNS序列是很好的聚合酶链式反应(PCR)引物位点。由于CNS序列高度保守，例如通过比较玉米和水稻而设计的PCR引物，也适用于其他1万种牧草。该项目将确定利用现有的序列资源寻找CNS序列和设计引物对的可行性。如果成功，长期目标将是开发约4000对引物序列，在所有禾本科植物中扩增已知的、已绘制的基因的特定多态片段。这些序列将是了解禾本科植物基因组结构以及作图的有价值的工具。更广泛的影响将通过一个项目网站提供结果，该网站将包括查看工具，使用户能够排序和选择感兴趣的序列。该项目的成果将产生广泛的影响，促进对牧草的研究，并使玉米和水稻等特点良好的系统的工具能够被用于欠发达但在农学上重要的亲属，如谷子。

Many grasses, including some economically important crops, are considered "orphan systems" because they do not have sequence databases that permit efficient genetic fingerprinting, mapping and gene fragment identification. Modern breeding depends on molecular tools such as these. The justification for support of this project as a Small Grant for Exploratory Research (SGER) is that this is a short-term, proof-of-concept project that will develop an urgently needed tool to meet these needs.This project will begin to develop a database of Conserved Non-Coding (CNS) sequences to cover the grasses. The CNS sequences are large, exact phylogenetic "footprints" in the non-protein coding parts of genes. They can be obtained by pair-wise comparison of sequences from whole genome and Expressed Sequence Tag (EST) collections. CNS sequences make excellent Polymerase Chain Reaction (PCR) primer sites. Since the CNS sequences are highly conserved, a PCR primer designed by comparing, for example, maize and rice, will work in the other 10,000 grasses as well. This project will determine the feasibility of finding CNS sequences and designing primer pairs using the available sequence resources. If it is successful, the long-term goal will be to develop about 4000 primer sequence pairs that amplify specific polymorphic fragments of known, mapped genes, across all grasses. These sequences will be valuable tools for understanding genome architecture across the grasses, as well as for mapping. Broader impactsThe results will be made available through a project web site that will include viewing tools to enable the user to sort and select sequences of interest. The outcomes of the project will have a broad impact, facilitating research on grasses, and allowing tools from well characterized systems such as maize and rice to be leveraged for less well developed, but agronomically important relatives such millet.