Genetic map of the Xenopus tropicalis genome

热带爪蟾基因组的遗传图谱

• 批准号: 7017058
• 负责人: DAN E WELLS
• 金额: $ 43.29万
• 依托单位: UNIVERSITY OF HOUSTON
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-03-15 至 2008-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7017058
• 关键词: Xenopus; bioinformatics; fluorescent in situ hybridization; genetic mapping; genetic markers; genetic models; genetic polymorphism; genome; information dissemination; linkage mapping; model design /development; molecular biology information system; nucleic acid purification

DESCRIPTION (provided by applicant): The proposed work will generate key resources for genetic and molecular studies of the amphibian Xenopus tropicalis. Xenopus tropicalis is an emerging model system for the genetic analysis of vertebrate development, combining the many advantages of its versatile sister species, X. laevis, with the promise of genetics. The chief goal of this project is to generate a genetic map of 5000 Simple Sequence Length Polymorphisms (SSLPs) for use as a community resource. First, a bioinformatics-based strategy will be used to identify Simple Sequence Repeats (SSRs) from sequences generated by the X. tropicalis Genome Project. A data-mining algorithm will select unique sequences containing SSRs; these sequences will be tested for polymorphisms in the length of the repeat against DNAs from Nigerian (N) and Ivory Coast (IC) individuals, the two major strains of X. tropicalis currently in use. The data mining approach should prove significantly faster and more cost-effective than conventional methods of identifying SSLPs, and it will permit the relatively rapid identification of a large number of markers. Second, a map cross of N x IC will be performed to generate a panel of DNAs from over 550 F2 individuals, representing over 1100 informative meioses and providing a theoretical limit of resolution of less than 0.1 cM. Third, the SSLPs will be tested against the F2 DNA panel in three steps. All of the markers will initially be tested against a subset of 192 samples, and a preliminary linkage analysis will be performed using MAPMAKER. This initial test should resolve over half of the markers; markers that are not resolved in the first round will be tested against a second subset. After a second round of linkage analysis, the remaining unresolved markers would be tested against the third subset. This iterative strategy should decrease the amount of time required to prepare a preliminary map and reduce the number of required mapping reactions. Fluorescence In Situ Hybridization (FISH) will perform physical confirmation of marker order for 5 percent of markers. Finally, the genetic map, the SSLP database, and information regarding mapping will be made publicly available on a website. These tools will be essential for the mapping and positional cloning of genes identified by mutation and will support rapid advancement in X. tropicalis genetics and genomics. As such, they will play a critical role in the emergence of X. tropicalis as a model system for the genetic analysis of vertebrate development.

描述（由申请人提供）： 所提出的工作将为两栖动物热带植物的遗传和分子研究生成关键资源。 Tropicalis是一种新兴模型系统，用于脊椎动物发育的遗传分析，结合了其多功能姊妹物种X. laevis的许多优势和遗传学的承诺。该项目的主要目的是生成5000个简单序列长度多态性（SSLP）的遗传图作为社区资源。首先，将使用基于生物信息学的策略来识别X. Tropicalis基因组项目产生的序列中的简单序列重复序列（SSR）。数据挖掘算法将选择包含SSR的唯一序列；这些序列将在重复的长度上测试对来自尼日利亚（N）和象牙海岸（IC）个体的DNA的多态性，这是当前正在使用的X. Tropicalis的两个主要菌株。与识别SSLP的常规方法相比，数据挖掘方法应更快，更具成本效益，并且它将允许对大量标记的相对较快地识别。其次，将执行N X IC的地图交叉，以生成来自550多个F2个体的DNA小组，代表1100多个信息性的Meiose，并提供了小于0.1 cm的理论限制。第三，SSLP将通过三个步骤对F2 DNA面板进行测试。最初，所有标记都将根据192个样本的子集进行测试，并将使用MapMaker进行初步链接分析。最初的测试应解析超过一半的标记。在第一轮未解决的标记将针对第二个子集进行测试。经过第二轮连接分析后，将针对第三个子集测试其余未解决的标记。这种迭代策略应减少准备初步地图所需的时间并减少所需的映射反应的数量。荧光原位杂交（FISH）将对5％的标记物进行物理确认。最后，将在网站上公开提供遗传图，SSLP数据库以及有关映射的信息。这些工具对于通过突变鉴定的基因的映射和位置克隆至关重要，并将支持X. Tropicalis遗传学和基因组学的快速发展。因此，它们将在X. topicalis作为脊椎动物发育遗传分析的模型系统中发挥关键作用。

项目成果

Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis.

• DOI: 10.4137/bbi.s561
• 发表时间: 2008-02-26
• 期刊: Bioinformatics and biology insights
• 影响因子: 5.8
• 作者: Xu Z;Gutierrez L;Hitchens M;Scherer S;Sater AK;Wells DE
• 通讯作者: Wells DE

A genetic map of Xenopus tropicalis.

• DOI: 10.1016/j.ydbio.2011.03.022
• 发表时间: 2011-06-01
• 期刊: Developmental biology
• 影响因子: 2.7
• 作者: Wells DE;Gutierrez L;Xu Z;Krylov V;Macha J;Blankenburg KP;Hitchens M;Bellot LJ;Spivey M;Stemple DL;Kowis A;Ye Y;Pasternak S;Owen J;Tran T;Slavikova R;Tumova L;Tlapakova T;Seifertova E;Scherer SE;Sater AK
• 通讯作者: Sater AK