SGER: Conserved Noncoding Sequences (CNS) in Grasses

许多禾草，包括一些经济上重要的作物，被认为是“孤儿系统”，因为它们没有序列数据库，无法进行有效的基因指纹、图谱和基因片段鉴定。现代育种依赖于诸如此类的分子工具。支持该项目作为探索性研究（SGER）小额赠款的理由是，这是一个短期的概念验证项目，将开发一种迫切需要的工具来满足这些需求。该项目将开始建立一个覆盖禾本科植物的非编码序列数据库。CNS序列在基因的非蛋白质编码部分是大而精确的系统发育“足迹”。它们可以通过对来自全基因组和表达序列标签（EST）收集的序列进行成对比较获得。CNS序列是很好的聚合酶链反应（PCR）引物位点。由于CNS序列是高度保守的，因此通过比较（例如玉米和水稻）设计的PCR引物也将适用于其他10,000种禾草。本项目将确定利用现有序列资源寻找CNS序列和设计引物对的可行性。如果成功，长期目标将是开发出大约4000对引物序列，这些引物序列可以在所有禾草中扩增已知基因的特定多态性片段。这些序列将成为了解禾草基因组结构以及绘制地图的宝贵工具。更广泛的影响研究结果将通过一个项目网站公布，该网站将包括查看工具，使用户能够对感兴趣的序列进行排序和选择。该项目的成果将产生广泛的影响，促进对禾本科植物的研究，并允许利用来自玉米和水稻等特征系统的工具，用于不太发达但在农学上重要的近亲，如小米。

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.