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Pig Genome Newsletter #006
PIG GENOME UPDATE No. 6
May 1, 1994
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PiGMaP concluded its last official meeting for the third year of its project.
The meeting was held in Edinburgh, Scotland on April 8-10, 1994, and was
followed by a PiGMaP-Industry Day on April 11. Both meetings were very well
attended. About 40 scientists from 21 labs attended and labs represented
included one each from the United States, Japan, and Australia. As with
previous PiGMaP meetings, laboratory reports were given from all the labs and
results continue to be excellent. A primary purpose of this meeting was to
conclude the first three years of the project by prioritizing details on the
international PiGMaP gene linkage map. The map includes approximately 250
markers and covers about 1850 cm (excluding the X chromosome). Of the nearly
250 markers, about 85 are Type I loci and all 18 chromosomes are covered. The
comparative mapping results were extremely interesting. The conserved nature of
the pig genome compared to that of man was quite remarkable. The PiGMaP linkage
map will be submitted shortly for publication. This map will be available prior
to publication since it will be presented at ISAG. In addition, a Nordic
genetic linkage map from the Swedish reference family is in press in Genetics
and should be published soon.
I had a great deal of opportunity to visit with PiGMaP members on a variety of
subjects related to the U.S. gene mapping coordination effort and
collaboration. Two subjects which were especially discussed were the
development of a composite gene map from the PiGMaP, Nordic and Clay Center
maps. A strategy involving several labs was agreed upon to make a composite map
for all chromosomes. On the subject of databases, we reached a very good
agreement on both sharing of information and on further new additions to the
databases (see below). Also at the meeting I presented the ISU mapping results
as part of our collaboration with PiGMaP. In all, it was both an enjoyable and
successful meeting. PiGMaP II, the newly proposed project to follow PiGMaP, is
moving ahead well through approval channels and should be in place soon.
USPIGBASE continues to grow in data and users. An agreement was reached with
Alan Archibald on importing those references and data not in the database and
in future ways to share information. A number of other exciting developments
were also discussed with Alan Hillyard who is on sabbatical at Edinburgh. The
database is continuing to be updated and becoming more user friendly.
The changes in USPIGBASE relate also to the options available to the user. The
latest addition is the [S]yntenic option under the display of the cytogenetic
map. This option provides you with a list of all additional loci on the
chromosome currently being displayed regardless of the mapping method. In this
way the user has access to information about all of the loci associated with a
specific chromosome in one place in the database.
In the next month, USPIGBASE will unveil its WWW home page. The World Wide Web
is a means of providing multimedia documents to the Internet and many of the
browsers have a simple point and click interface using the mouse on your
computer. Not only will this provide a convenient gateway to USPIGBASE, it will
also allow the presentation of graphics and documents germane to pig gene
mapping, e-mail addresses of colleagues, upcoming meeting announcements, and
pointers to other genome related databases. If you have additional ideas for
types of information that would be useful to you and others, please let me
know. Although a number of browsers are available we recommend the Mosaic
software developed at the National Center for Supercomputing Applications which
is available for anonymous ftp (ftp.ncsa.uiuc.edu) and will run on MACs, PCs
using Windows, and UNIX hardware using X windows. If you need further details
or assistance please e-mail Alan Hillyard (alh@jax.org).
In USPIGBASE's continuing effort to provide the latest and most useful
information about the pig genome we are in the process of developing an ACeDB
front end to the database. For those of you able to run X windows, this will
provide a visually appealing display of mapping data. It is a point and click
interface and extremely easy to use and it has the additional advantage of
being used by a number of the genome mapping projects. Our target date for the
first release of USPigDB is early this summer and its availability will be
announced on our WWW home page. If you have questions about these changes,
please give me a call or e-mail me. P Production of microsatellite primers is
continuing. With the excellent help of members of our committee of gene
mappers, another set of about 100 primer pairs for microsatellite markers are
being produced. You will be notified when they are available.
Project ideas for gene mapping which fit the goals of the genome coordination
are always welcome. Funding will depend on the usefulness, cost and budget
availability, and the applicability to all swine genome committee members. I
have reviewed several ideas and plan to fund a number of them. If you have an
idea, please send me complete information and who will be involved.
Individual swine chromosome sorting using bivariate flow cytometry is
progressing well at the ARS in Beltsville, MD. Sorted chromosomes prepared from
normal pig lymphocyte are being used in Dr. Joan Lunneys lab as a source for
establishing a chromosome 6 library. They have also produced chromosome
specific paints for every pig chromosome using DOP-PCR. Researchers are welcome
to contact Dr. Lunney at 301-504-9368 to discuss potential uses of sorted
chromosomes and of biotinylated and fluoresceinated chromosome paints
(information provided by J. Lunney).
Chinese Pig agreement signed: An agreement for exchange of Chinese germplasm
and non-germplasm (tissues, DNA etc.) was signed recently. Those interested in
obtaining pigs or DNA may contact me for further details or the administrators
for the units in charge of the pigs at Iowa State University, University of
Illinois or at Clay Center.
Contributions to Pig Genome Update 7 are always welcome. Please send by the
15th of June.
Max F. Rothschild
Swine Genome Coordinator
225 Kildee Hall
Department of Animal Science
Iowa State University
Ames, Iowa 50011
Phone: 515-294-6202 or 3629
Fax: 515-294-2401
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