GENOME

NEWSLETTER

Issue No. 3

October, 1995

FINAL NOTICE FOR THE COMBINED NC-168, NAGRP (NRSP-8) MEETING IN COLLEGE PARK, MARYLAND:

The meeting will be held October 25-27 at the U. of Maryland Continuing Education Center (phone: 301-985-7303; FAX: 301-985-7445) . Poultry gets a head start, as NC-168 will begin the afternoon of Wednesday, Oct. 25 (1:00 p.m.). A large crowd (35-40 or more) is expected. The Swine (and NC-210) and Cattle (NC-209 meets separately this year) Species Subcommittees will join us beginning the morning of Thursday, Oct. 26. On Friday, the whole Animal Genome Technical Committee will meet together, and we'll hear from two keynote lecturers (Leslie Lyons and Lothar Hennighausen), along with representatives of the Washington funding scene. Expect the festivities to end about 3:00 p.m. on Friday. Those of you who are participants in NC-168, have received a mailing on the meeting from our Chairperson, Ed Smith. If you're not a member, but still want to get the meeting information, email Ed at edsmith@acd.tusk.edu. Gail Juvik of the National Agriculture Library will demonstrate the latest developments in the animal genome databases at NAL. These are described, in part, later in this Newsletter.

HEY! PRIMERS! GET YOUR FREE PRIMERS!:

We are now ready to send both of our new free primer kits. The first of these is the Population Tester Kit. This contains 9 primer pairs which define microsatellites with high polymorphic information content (numerous alleles widely distributed in several populations). For those with access to ABI sequencers, they are also fluorescent and can be multiplexed. This kit is available to those who wish to test just a few loci to characterize a strain or genetically fingerprint chickens. Email me (22314jbd@msu.edu) or Hans Cheng (hcheng@msu.edu) if you are interested. The relevant sequences are listed along with collateral information on our WWW homepage at http://poultry.mph.msu.edu.

A larger microsatellite kit containing 120 primer pairs that define markers covering most of the chicken genome, called the Comprehensive Mapping Kit 1, is also available. These are also fluorescently labeled sets that can be used with either automated or manual mapping techniques. The Comprehensive Mapping Kit 1 will be provided free to any public scientists who are involved in major mapping efforts. Again, contact Jerry Dodgson (22314jbd@msu.edu) or Hans Cheng (hcheng@msu.edu). The Homepage also has a larger table which includes information on all published microsatellite loci to date (and a few unpublished ones from Hans Cheng). We welcome information from everyone on useful microsatellite (or other) primers for posting on the WWW and for inclusion in free primer packages for distribution (send the info to 22314jbd@msu.edu ). To be widely useful, primer sets to be synthesized should be demonstrated to be polymorphic on one or both of the international reference populations and/or in important resource populations. As more data becomes available, we plan to synthesize further primer kits containing additional informative loci.

SOON TO COME, CONSENSUS POULTRY MAP:

As advertised previously, Lyman Crittenden has been hard at work (despite his hypothetical "retirement") with Nat Bumstead in generating a consensus genetic map that combines data from both the East Lansing and Compton reference populations. This allows one to fuse some linkage groups that are separate in one or the other population and to derive broader linkage relationships. Nat is reviewing and adding to the consensus map at the moment. As soon as possible, we will attempt to add it to the homepage (http://poultry.mph.msu.edu/) and we hope to publish it in Animal Genetics, much like the recent consensus bovine map (Eggen and Fries, Animal Genetics 26:215-236, August, 1995).

NEW LOOK FOR POULTRY HOMEPAGE ON WWW:

We have reorganized the U.S. Poultry Gene Mapping homepage on the World Wide Web (WWW) to make it easier to reach the growing volume of information and links therein. Remember, our Web address is http://poultry.mph.msu.edu/. If you forget or lose our URL, you can probably find the Michigan State University homepage fairly easily and, again, just click on our listing, or enter from the Pig Genome Homepage (at http://www.public.iastate.edu/~pigmap ). FYI there is also The ChickMap Homepage at the Roslin Institute developed by Andy Law and Dave Burt at Roslin. Their URL is http://www.ri.bbsrc.ac.uk/chickmap/ChickMapHomePage.html but the Roslin Homepage and the U.S. Homepages are linked such that anytime you are in one, you can just click on the appropriate heading for the other to be transferred there via the Web.. To access WWW, you will need browser software. Browsers are under continuous development and refinement, so you should upgrade your version as time goes by. Widely used browsers are Mosaic and Netscape (see your local computer expert to obtain these, if necessary.) Browsers vary widely in speed and presentation, so we can't always be sure you'll see exactly what we see, but we'll do the best we can. In particular, to see Tables, such as those of microsatellite loci, your browser must have the appropriate capabilities. If you have problems, contact Scott Eisensmith at eisensmi@poultry.mph.msu.edu. Also, our homepage is under continuous refinement, so don't forget to reload items every once in awhile (or your browser will keep giving you the old version out of its cache). OUR HOMEPAGE IS REALLY YOUR HOMEPAGE. PLEASE MAKE SUGGESTIONS. THERE IS A HANDY ELECTRONIC SIGN-UP AND COMMENT SHEET AT THE BOTTOM WHICH MAKES IN VERY EASY FOR YOU TO TELL US WHAT YOU WANT. Note: Please check your address information on the Homepage and use this feature to provide us any needed corrections.

In the new format for the Homepage you will initially get a menu like that shown below:

What's New

About the poultry genome mapping project

Members of International Poultry Gene Mapping Community - Searchable Mail List

Poultry Genetic Maps

Microsatellite Marker Information and Available Primer Kits

CHICKGBASE

Poultry Genome and NAGRP Newsletters

Crittenden Reference Database (Searchable)

Genome Launching Pad (Genome Related Sites)

Inventory of cDNA and Genomic Clone Libraries

See Also: other animal sites and discussion groups

Places to Visit (Other miscellaneous WWW Sites)

Miscellaneous Poultry Information with Art & Sounds

Upcoming Meetings

U.S. PIG GENE MAPPING

ChickMap at the Roslin Institute, Scotland

National Agriculture Library Genome WWW Server

Poultry Newsgroup Registration

All of these items are lists of information or links maintained at MSU except CHICKGBASE (described in detail below in this Newsletter), U.S. PIG GENE MAPPING (the Swine NAGRP HomePage at Iowa State), ChickMap (Roslin Institute Homepage) and the NAL Genome Server (Beltsville) which are connections to other major locations of relevant information. What's New is a rolling list of major changes or developments by the Coordinators. About the poultry genome mapping project is a general description of the NAGRP and Poultry Coordination efforts. "Members" is an address list that can be searched by location, etc. Poultry Genetic Maps provides the latest available genetic linkage and cytogenetic maps (described in earlier editions of the Newsletter). Genome Launching Pad, See Also, and Places to Visit are lists of Web connections (clickable) to gene mapping locations, animal agriculture locations, and WWW or Internet-related locations, respectively. The other items are self-explanatory and several have been previously described. Clicking on any of these items will get you to the desired information or location on the Web.

ChickGBASE:

What is ChickGBASE? ChickGBASE is a collection of chicken gene mapping information in a relational format, similar to GBASE used for the mouse and PiGBASE for swine, etc. The most important components of ChickGBASE are the Locus Manager, Map Manager, and Reference Manager which allow you to examine chicken genetic loci, chicken gene maps, and chicken gene mapping references, respectively. The key component of the database is the ability to quickly move from one collection of information to another in a relational manner, i.e., if you're looking at a genetic map and see a locus that interests you, you can move to the collection of data available about that locus (with a simple mouse click) and then if you see a reference in the locus list information that you wish to learn more about, you click and move to that reference in the reference collection, and so on and so on.

Who is responsible? ChickGBASE in its present form has been developed by Dave Burt, Andy Law and Chris Mungall of the Roslin Institute (Scotland) with assistance of Alan Hillyard of Jackson Labs. Alan's contributions to ChickGBASE were partially supported by the NAGRP Coordination funds. The Roslin Institute team has done and is doing an outstanding job with ChickGBASE and is especially to be commended. Mechanisms by which Roslin and the U.S. can efficiently coordinate further additions to ChickGBASE are being developed with leadership by Andy Law. In addition, Lyman Crittenden, on a recent trip to Scotland for personal reasons, made a detour to visit the group at the Roslin and discuss continued coordination between our two groups.

Where is it and how do I get to it? At this time the most advanced version of ChickGBASE is available at the Roslin Institute. Enter the US Homepage as described above and click on the ChickMap at the Roslin Institute entry or go directly to their URL as described. When you get to Roslin, click on the ChickGBASE Browser to take a look at its capabilities. Wouldn't communications be faster with a U.S.-based connection? Not necessarily, but a US node of ChickGBASE has just been made available at the National Agricultural Library (NAL) at the URL of http://tetra.gig.usda.gov:8400/chickgbase/manager.html. You can also enter from the CHICKGBASE hotlink in our Homepage and the use of ChickGBASE will be demonstrated at the NAGRP meeting. Coordination funds supported a recent visit of Alan Hillyard and Gail Juvik (NAL) to Michigan State to discuss ChickGBASE and U.S. Poultry Homepage developments. As part of this trip, Alan went from East Lansing on to NAL to install this NAL node of ChickGBASE. The present NAL ChickGBASE is a slightly earlier version developed at Roslin which Alan brought back after his last visit there, but it has a couple of deficits for map searches (see below). We hope to correct these soon.

How do I get started? Once you are into ChickGBASE, you choose between the Locus Manager, the Map Manager or the Reference Manager, depending on the question you wish to ask. Briefly, in each case you will be provided a query sheet to fill out. For example, the Map Manager will ask you first how many maps you want to look at (up to 3 can be displayed at once, 1 map is the default). You choose which linkage group (or chromosome) you wish to see and whether you want the linkage map or cytogenetic map. (If you start the process at Map Manager at NAL, you need to correctly choose both chromosome number where it is known and sex of meioses for a given linkage group map: choose M (male) for an E (East Lansing) linkage group and F for a C (Compton) group. These problems have been eliminated at the Roslin and the Roslin version will be copied to NAL asap. At NAL it's easiest to start with a locus and then click to the linkage map unless you're sure which chromosome you're after.) When the query sheet is complete, you activate the search by clicking on *map* (if you want a map) or *entry*. Once you are into a map or locus or reference, there is an array of (highlighted) options that can link you to more information (all loci on maps are hotlinked to the Locus List), change the presentation mode of maps, etc. Far too much to explain here, experiment on your own and/or come to the NAGRP meetings or use the *help* options. Suggestions and questions can also be sent to Andy Law of the Roslin Institute at Andy.Law@bbsrc.ac.uk

What's in the future? A totally new, improved version of ChickGBASE is in the works, again developed at the Roslin Institute and again, with some help from Alan Hillyard, supported in part by Coordination funds. This will significantly expand the amount of information that can be catalogued and will have a generic structure designed to work for any species. Other developments include the NAL node described above (note that NAL provides additional links and options (see http://tetra.gig.usda.gov:8400/) as part of their informatics efforts) and further work both at Roslin and here to fill and improve ChickGBASE.

OMIA, Oh My!:

As noted in recent communications on the angenmap discussion group, there now exists a Web version of Frank Nicholas's Mendelian Inheritance in Animals (OMIA). You can link to OMIA from the Pig Gene Mapping Homepage, the NAL Homepage or the Genome Launching Pad on our Homepage, all of which are described above.

MORE MEETING NEWS:

Do you know the way to San Diego?: As noted last time, Coordinators and Technical Committee representatives have given tentative approval to a plan to have future NAGRP meetings (after the October meeting in Maryland) jointly with the plant gene mappers in an expanded and retitled version of their annual Plant Genome meetings held each January in San Diego, CA. Plant Genome III was held this January in San Diego and Plant Genome IV will be held in January of 1996. Further information and discussion of this plan will be provided at the NAGRP Business Meeting in Maryland.

Upcoming meetings:

NC-168 and NRSP-8 (National Animal Genome Research Program), College Park, MD, Oct. 26-27, 1995; contact: JLUNNEY@ggpl.arsusda.gov or see above.

HUGO Comparative Genome Organization Workshop, Fraser Island, Queensland, Australia, December 3-6, 1995; contact: hugo@gdb.org Dave Burt (Dave.Burt@bbsrc.ac.uk) and Jim Bitgood (Bitgood @calshp.cals.wisc.edu) will represent poultry at this meeting. (Meeting supported in part by NAGRP.)

Plant Genome IV, San Diego, CA, January 14-18, 1996; contact: scherago@biotechnet.com

XXV International Conference on Animal Genetics, International Society of Animal Genetics, Vinci Congress Centre, Tours, France, 22-26 July, 1996: contact: Dave Burt (Dave.Burt@bbsrc.ac.uk) or Martien Groenen (Martien.Groenen@alg.vf.wau.nl) for more details or sjlamont@iastate.edu re ISAG membership.

XX World's Poultry Congress and International Poultry Exhibition, New Delhi, India, September 2-8, 1996 (abstracts due Jan. 31, 1996). Contact: Dr. B.S. Sathe, Secretary, World's Poultry Science Assoc. (India Branch), Janaka, 189 Bhandarkar Institute Road, Pune - 411, India. Fax: 91-212-361729.

Allerton II, Genetic Analysis of Economically Important Traits in Livestock, Allerton Park, Illinois, (tentative) November 6-9, 1996; contact: blood@vmd.cso.uiuc.edu

Addresses:

Jerry Dodgson, Coord.
Dept. of Microbiology
Giltner Hall
Michigan State University
East Lansing, MI 48824
email: 22314jbd@msu.edu

Lyman Crittenden, Co-Coord.
same MSU address as above
email: slcritte@facstaff.wisc.edu

Hans Cheng, Co-Coord.
ADOL
USDA-ARS
3606 E. Mt. Hope Ave.
East Lansing, MI 48824
email: hcheng@msu.edu

Scott Eisensmith, Database Analyst
same MSU address as above
email: eisensmi@poultry.mph.msu.edu

Supported by Regional Research Funds, Hatch Act, to the National Research Service Program: NRSP-8.

National Animal Genome Research Program, Richard Frahm, Director, CSREES

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