Genetic map of the Xenopus tropicalis genome

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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.