A Zebrafish Map for Comparative and Functional Genomics

William S. Talbot, B315 Beckman Center, 279 Campus Drive, Stanford, CA 94305-5329 USA

John H. Postlethwait, Institute of Neuroscience, 1254 University of Oregon, Eugene, OR 97405-1254 USA

The Talbot and Postlethwait groups are collaborating to localize zebrafish genes on an integrated genetic linkage map. Our goal is to construct a map with 3000 genes in a framework of 500 SSLPs from the Fishman group. This map will accelerate the discovery of gene functions by increasing the number of mapped candidate genes for mutations. Furthermore, genes are uniquely suited markers for comparative genomics, and we plan to assemble a map of chromosomal segments conserved between zebrafish and human.

Previous gene maps were constructed with haploid mapping panels, which simplify linkage analysis but allow only 1000-2000 markers to be scored in each individual (because of the limited genomic DNA available in haploid embryos). To overcome this limitation while retaining the benefits of haploid panels, we are employing a homozygous diploid mapping panel produced by heat shock treatment of the embryonic offspring from two C32/SJD F1females. Genomic DNA for 10,000-100,000 markers is available from each of the 47 individuals that comprise the panel. By scoring SSCPs linked to genes and ESTs, we plan to create a dense, gene-based map with a resolution of 2 cM (about 1.2 Mb average physical distance). This resolution will allow investigators to identify genes near mutations of interest; any candidate genes in the interval can then be tested in mutant mapping crosses of higher resolution.

Progress

As of June 2, 1999, we have assigned preliminary map positions to 474 markers scored in the heat shock diploid panel (Kelly, Chu, Ngo-Hazelett, Kimm,Gates, Yan, Postlethwait, and Talbot, unpublished). Approximately 350 of these markers are SSLPs previously mapped by the Fishman group. These markers will form a framework that will allow the heat shock panel map to be integrated with previous maps and mutant mapping crosses. Most of the remaining polymorphisms are SSCPs linked to genes and ESTs. We are planning to score ~150 more SSLPs to complete the framework, after which our efforts will focus on mapping genes for the duration of the project. To facilitate the integration of meiotic and radiation hybrid maps, we have provided primers for more than 600 genes and ESTs to the Tuebingen RH group. Many of these loci have been incorporated into the RH map (Robert Geisler, personal communication); these and other shared markers will allow a straightforward comparison of the genetic and physical maps.

Data Release

(http://cmgm.stanford.edu/~tallab/Frontpage.html)

To allow rapid public access to the heat shock panel map, we plan to release data in two forms.

(1) Starting in July, and continuing every 4-6 months thereafter, we will release refined maps supported by data that have been extensively checked for discrepancies.

(2) Between releases of refined maps, genotype data will be available as downloadable MapManager files (see http://cmgm.stanford.edu/~tallab/Frontpage.html). These files will contain preliminary map assignments and the genotype data that support them. These interim releases will not be extensively checked for errors! It will be the responsibility of users to evaluate the map data and decide for themselves whether a map assignment is reliable for their purposes. The current release (June 2, 1999) contains preliminary assignments for 474 markers. In addition, we have posted published map data and 36 unpublished gene and EST assignments from our haploid mapping panel (Gates, Schier, and Talbot, unpublished).