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)： 拟议的工作将为两栖动物热带非洲爪哇的遗传和分子研究产生关键资源。热带非洲爪哇是一种新兴的脊椎动物发育遗传分析模式系统，它结合了其多才多艺的姊妹物种非洲爪哇的许多优势和遗传学的前景。该项目的主要目标是生成5000个简单序列长度多态(SSLP)的遗传图谱，作为社区资源使用。首先，一种基于生物信息学的策略将被用来从热带疟原虫基因组计划产生的序列中识别简单序列重复(SSR)。数据挖掘算法将选择包含SSR的独特序列；这些序列将与尼日利亚(N)和象牙海岸(IC)个体的DNA进行重复长度多态测试，这两个个体是目前使用的两个主要热带疟原虫菌株。事实证明，数据挖掘方法比识别SSLP的传统方法要快得多，成本效益更高，而且它将能够相对快速地识别大量标记。其次，将进行N×IC的图谱交叉，从550多个F2个体中产生一组DNA，代表1100多个信息性减数分裂，并提供低于0.1 cm的理论分辨率极限。第三，SSLP将分三步与F2 DNA面板进行测试。所有标记最初将针对192个样本的子集进行测试，并将使用MapMaker进行初步连锁分析。这一初始测试应能分辨一半以上的标记；第一轮未分辨的标记将对照第二个子集进行测试。在第二轮连锁分析之后，剩余的未分辨标记将对照第三个子集进行测试。这一迭代战略应该会减少编制初步地图所需的时间，并减少所需的地图反应次数。荧光原位杂交(FISH)将对5%的标记进行物理确认。最后，遗传图谱、SSLP数据库和有关图谱的信息将在一个网站上公开提供。这些工具将对绘制和定位克隆由突变确定的基因至关重要，并将支持热带疟原虫遗传学和基因组学的快速发展。因此，它们将在热带X线虫的出现中发挥关键作用，成为脊椎动物发育的遗传分析的模式系统。

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