Genetic map of the Xenopus tropicalis genome

热带爪蟾基因组的遗传图谱

• 批准号: 6861071
• 负责人: DAN E WELLS
• 金额: $ 58.67万
• 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 2007-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6861071
• 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爪蟾的遗传和分子研究提供关键资源。热带爪蟾是一种用于脊椎动物发育遗传分析的新兴模型系统，结合了其多才多艺的姊妹物种非洲爪蟾的许多优点以及遗传学的前景。该项目的主要目标是生成 5000 个简单序列长度多态性 (SSLP) 的遗传图谱，用作社区资源。首先，将使用基于生物信息学的策略从热带病菌基因组计划生成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；这些序列将针对尼日利亚 (N) 和象牙海岸 (IC) 个体（目前使用的两种主要热带 X. 菌株）的 DNA 进行重复长度多态性测试。事实证明，数据挖掘方法比识别 SSLP 的传统方法更快、更经济，并且可以相对快速地识别大量标记。其次，将进行 N x IC 的图谱杂交，以生成来自超过 550 个 F2 个体的 DNA 组，代表超过 1100 个信息丰富的减数分裂，并提供小于 0.1 cM 的理论分辨率极限。第三，SSLP 将分三步针对 F2 DNA panel 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。该初始测试应解决一半以上的标记；在第一轮中未解决的标记将针对第二个子集进行测试。在第二轮连锁分析之后，剩余的未解析标记将针对第三子集进行测试。这种迭代策略应该减少准备初步地图所需的时间并减少所需的绘图反应的数量。荧光原位杂交 (FISH) 将对 5% 的标记进行标记顺序的物理确认。最后，遗传图谱、SSLP 数据库和有关图谱的信息将在网站上公开。这些工具对于通过突变鉴定的基因的绘图和定位克隆至关重要，并将支持热带 X. 热带线虫遗传学和基因组学的快速发展。因此，它们将在热带 X. 热带菌作为脊椎动物发育遗传分析模型系统的出现中发挥关键作用。