Pig Genome Update No. 10

January 1, 1995

  1. New Developments In The Database
  2. A Searchable Version Of ANGENMAP
  3. Browser Recommendations
  4. Your Input And Help Are Requested
  5. The Recent National Swine Improvement Federation Meetings
  6. Effort To Highlight Information From Other Species
  7. Due Dates and Contact Information Of USDA Grants For NRI Program
  8. Meeting Dates For 1994-95


New developments in the database continue. In this newsletter we would like to highlight 1) Direct links to GDB for pig loci with human homologs, 2) The availability of gel images for select loci, and 3) new map controls. On the map displays if a locus has a human homolog it is highlighted in magenta (depends on your machine). Clicking on that locus takes the user to the detail page which includes a direct link to GDB, which if selected makes the connection and retrieves the relevant information for the human locus. At that point the full resources of GDB [citations, links to OMIM (disease phenotypes), GSDB (sequence information), etc.] are available or the user can return to PiGBASE and follow another line of inquiry. The inclusion of selected images relevant to the mapping of a particular locus demonstrates the power of the database to act as both an electronic journal and a repository of experimental results. If a locus has an image or images attached (try TSHB for example) this is indicated by the presence of a hypertext link on the locus detail display. Lastly, the user has been given more control over the display of the linkage and cytological maps. Not only can the whole display be magnified by choosing the magnify button at the bottom of the screen, only those loci localized to an individual band can be highlighted by clicking on a band in the cytological display or a region of the linkage map can be magnified by successively clicking on the portion of the chromosome in which the user is interested. If multiple maps are displayed those loci occurring on multiple maps can be highlighted by selecting the common button. On the cytogenetic map if multiple localizations exist for a single locus they can all be displayed by clicking on the bar indicating the preferred localization.

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A searchable version of ANGENMAP is now available (http://rio3.ac.uk/angenmap.html or follow the links from the U.S. Pig Mapping home page). A Wide Area Information Server (WAIS) version allows searches on any term which appears in the documents - keywords, names, addresses etc. For each query a list of documents is returned which match the query. Clicking on any item in the list will bring up that ANGENMAP entry with the search terms highlighted. Once the relevant document(s) are found they can be printed or stored as a file by your WWW browser. Boolean searches are also possible allowing search terms to be combined in a number of ways. New discussion group traffic is added weekly.

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Browser recommendations. The WWW browsers are rapidly evolving and are implementing different portions of the HTML standard. In order to use the map displays fully, we are currently recommending netscape 0.94 (0.93 on the Macintosh). Information on current versions and a list of available ftp sites are available from Netscape Communications: http://mcom.com. (update provided by Alan Hillyard).

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Your input and help are requested. We are now ready to make the next round of microsatellites from those that have been published over the past few months. Choosing them is an important function and while the committee of Drs. Lunney, Kirkpatrick, Troyer, Tuggle and Rothschild make most of the choices your input is important. We are choosing markers that fill in the spaces and the ends of the chromosomes. The maps are in the PIGBASE MANAGERs. By using the WWW address of http://www.genome.iastate.edu you can see those. If you have ideas please send them along. Remember we are choosing markers to benefit all labs. This year our goal will be to produce another 125 markers to reach a total of 300 microsatellite markers for gene mapping and QTL research.

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The recent National Swine Improvement Federation Meetings was attended by 80 people. Several speakers, including myself, discussed QTL research and the use of markers now and in the future.

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In an effort to highlight information from the other species we will add information as space permits. The genetic map of the chicken continues to expand rapidly. There are two internationally recognized reference mapping populations, the East Lansing panel and the Compton (England) panel. Over 340 markers have been mapped on the East Lansing population, and at least 200 more have been mapped on the Compton panel. The East Lansing DNA panel is available to interested scientists on request. Two goals are of particular importance this year. First, an effort being led in the U.S. by Hans Cheng of the USDA-ARS Avian Disease and Oncology Laboratory (East Lansing), is to continue to expand the number of polymorphic microsatellite loci mapped. Once the preferred set of microsatellite loci can be decided upon, primer kits will be available from the Poultry Genome Coordinator free of charge. Second is to coalesce the two reference panel maps, in consultation with Nat Bumstead, who developed the Compton panel. On the bioinformatics side, a shell has been developed for Chickbase which is available on the World Wide Web. Most of the existing data and references have been entered into Chickbase by Dave Burt of the Roslin Institute (Edinburgh), but considerably more remains to be done. Database development has also been assisted by Alan Hillyard of Jackson Labs, acting as a consultant, and by Scott Eisensmith who has recently been hired to work on the U.S. node for Chickbase. As a result, Chickbase will eventually be on line from East Lansing. Long range goals include the development of tools and resources for physical genome mapping and the application of the map to several resource (or QTL) populations. Other poultry species maps are also being examined, with turkey as the first step. (Information supplied by Poultry Genome Coordinator Jerry Dodgson)

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USDA grants are due this winter for the NRI program. Due dates and contact phone numbers are as follows:
January 9, 1995 for program 44.0 Sustaining Animal Health
     and Well-Being (202-410-6303)
January 17, 1995 for program 41.0 Enhancing Animal
     Reproductive Efficiency (202-401-6234)
February 21, 1995 for program 42.0 Improving Animal
     Growth and Development (202-205-0250)
February 21, 1995 for program 43.0 Identifying Animal
     Genetic Mechanisms and Gene Mapping (202-401-4399)

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Meeting dates for 1994-95 include the following:

Gordon Conference on Quantitative Genetics and Biotechnology,
	Ventura, CA, Feb. 12-17, 1995
AAAS annual meeting, Atlanta, GA, Feb. 16-21, 1995
Genome Mapping and Sequencing, Cold Spring Harbor Laboratory, 
	May 10-14, 1995
Biotechnology's role in the Genetic Improvement of Farm
	Animals, Beltsville, MD, May 14-17, 1995
4th Int. Veterinary Immunology Symposium, Davis, CA, July 16-21, 1995
9th North American Colloquium on Domestic Animal Cytogenetics and Gene 
	Mapping, College Station,TX, July 18-21, 1995
American Society of Animal Science Meeting, Orlando FL, July 25-28, 1995
Swine in Biomedical Research: 1995 Animal Models, College Park, MD 
	Oct. 22-25, 1995
NC-210 and NRSP-8, College Park, MD Oct. 26-27, 1995

If you have a meeting to announce please send details! Thanks.

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Contributions to Pig Genome Update 11 are always welcome. Please send by the 20th of February.

May the New Year bring good health, prosperity and happiness to you and your families.

                    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

Paid for by funds from the NRSP-8
USDA/CSREES sponsored
Pig Genome Coordination Program
Mailing list: angenmap@db.genome.iastate.edu

© US Pig Genome Coordination Program