Genetic map of the Xenopus tropicalis genome

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。热带爪蟾是一种新兴的脊椎动物发育遗传分析模式系统，它结合了其多功能姊妹种非洲爪蟾的许多优点。laevis，with the promise承诺of genetics遗传.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，基于生物信息学的策略将用于从X产生的序列中识别简单序列重复（SSR）。热带植物基因组计划。数据挖掘算法将选择包含SSR的独特序列;这些序列将针对来自尼日利亚（N）和象牙海岸（IC）个体（X的两个主要菌株）的DNA重复长度的多态性进行测试。目前正在使用中的Tropical数据挖掘的方法应证明显着更快，更符合成本效益比传统的方法确定SSLP，它将允许相对快速地确定大量的标记。其次，将进行N × IC的图杂交，以从超过550个F2个体产生一组DNA，代表超过1100个信息性减数分裂，并提供小于0.1 cM的分辨率的理论极限。第三，将分三步针对F2 DNA样本组检测SSLP。所有的标记最初将测试对一个子集的192个样本，并进行初步的连锁分析将使用MAPMAKER。该初始测试应解决一半以上的标志物;第一轮未解决的标志物将针对第二个子集进行测试。在第二轮连锁分析之后，将针对第三子集测试剩余的未解决的标记。这种迭代策略应该减少准备初步图谱所需的时间，并减少所需的图谱反应的数量。荧光原位杂交（FISH）将对5%的标记物进行标记顺序的物理确认。最后，遗传图谱、SSLP数据库和有关绘图的信息将在一个网站上公布。这些工具对于通过突变鉴定的基因的定位和定位克隆至关重要，并将支持X的快速发展。热带植物遗传学和基因组学。因此，它们将在X的出现中发挥关键作用。作为脊椎动物发育遗传分析的模型系统。

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.