HEAT SHOCK DIPLOID CROSS, MAPS & DATA
Overview
The Talbot and Postlethwait groups are collaborating to localize zebrafish
genes on an integrated genetic linkage map. 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 F1 females. 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 early August, 743 polymorphisms have been scored in the heat
shock
diploid panel (Kelly, Chu, Ngo-Hazelett, Kimm, Gates, Yan,
Postlethwait,
and Talbot, unpublished). Data for 681 polymorphisms have been
assembled to
produce the first release of the heat shock panel map, and preliminary
assignments for 62 additional markers may be downloaded as Map
Manager
data files. Approximately 550 markers are SSLPs previously mapped by
the
Fishman group; these form a framework that allows 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. These
markers complete the framework of the heat shock panel map, and we
are
now directing our efforts toward mapping genes and ESTs.
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
(Geisler et al., Nature Genetics, in press); these and other shared markers
will
allow a ready comparison of the genetic and physical maps.
Data Release
To allow rapid public access to the heat shock panel map, we are
releasing
data in two forms. (1) Starting with the August release of the heat
shock
panel map, and continuing approximately every 4 months thereafter, we
will
release refined maps supported by data that have been extensively
checked
for discrepancies. We plan to release the next version of the map in
the
first half of October. (2) Between releases of refined maps, genotype
data
are available as downloadable Map Manager files. These files 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.
Refined Maps & Genotype Data
Recent Data Sets (THESE MAP ASSIGNMENTS ARE PRELIMINARY!!)
STANFORD
ZEBRAFISH GENOME PROJECT