SGER: Conserved Noncoding Sequences (CNS) in Grasses

许多草，包括一些经济上重要的作物，被认为是“孤儿系统”，因为它们没有允许有效的遗传指纹，绘图和基因片段鉴定的序列数据库。现代育种依赖于这样的分子工具。作为探索性研究小额赠款（SGER）支持该项目的理由是，这是一个短期的概念验证项目，将开发一个迫切需要的工具，以满足这些需求。该项目将开始开发一个数据库的保守非编码（CNS）序列，以涵盖草。CNS序列是基因的非蛋白质编码部分中的大的、精确的系统发育“足迹”。 它们可以通过来自全基因组和表达序列标签（EST）集合的序列的成对比较来获得。 CNS序列是极好的聚合酶链式反应（PCR）引物位点。 由于CNS序列是高度保守的，通过比较例如玉米和水稻而设计的PCR引物也将在其他10，000种草中起作用。本计画将探讨利用现有序列资源寻找CNS序列及设计引物对的可行性。如果成功，长期目标将是开发约4000个引物序列对，以扩增所有禾本科植物中已知的、定位的基因的特异性多态性片段。 这些序列将是了解禾本科植物基因组结构以及绘制图谱的宝贵工具。更广泛的影响结果将通过一个项目网站提供，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，促进对草的研究，并允许利用来自玉米和水稻等特征良好的系统的工具来开发不太发达，但在农业上重要的亲戚，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.