Pig Genome Update No. 6

May 1, 1994

  1. PiGMaP
  3. Production of Microsattlite Primer
  4. Project Ideas on Gene Mapping
  5. Individual Chromosome Sorting
  6. Chinese Pig Agreement

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.    [go to top]

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.    [go to top]

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.    [go to top]

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.    [go to top]

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).    [go to top]

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.    [go to top]

Contributions to Pig Genome Update 7 are always welcome. Please send by the 15th of June.
                    Max Rothschild
                    U.S. Pig Genome Coordinator
                    2255 Kildee Hall, Department of Animal Science
                    Iowa State University
                    Ames, Iowa 50011
                    Phone: 515-294-6202, Fax: 515-294-2401

cc: Dick Frahm, CSREES and Roger Gerrits, ARS
Paid for by funds from the NRSP-8
USDA/CSREES sponsored
Pig Genome Coordination Program
Mailing list: angenmap@db.genome.iastate.edu

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