Picture from Dave Burt, Roslin Institute

POULTRY GENOME NEWSLETTER-1999

ISSUE NO. 1, JANUARY, 1999

HAPPY HOLIDAYS

HAPPY NEW YEAR TO ALL READERS OF THIS NEWSLETTER! We hope the Holiday Season has been enyoyable and has provided some respite, as we rush headlong towards the end of the millenium and the infamous Y2K problem.

Many of us will soon converge on San Diego for this year's NC-168 meeting, held jointly with the NAGRP and PAG-VII. NC-168 will begin at 6:30 p.m. on Saturday, Jan. 16 in the Sunset Room at the Town & Country Hotel. and Station Reports will begin at 7:00 p.m. (please bring plenty of copies of your report to pass out). Marlene Emara is Coordinator for Objective 1, Jim Pettite for Objective 2, and Hans Cheng for Objective 3. Station Reports will resume at 9:00 a.m. on Jan. 17 to be followed by Bob Ivarie (of Avigenics) as a guest speaker, along with Visitors' Presentations and the Business Meetings for both NC-168 and the poultry subcommittee of NAGRP (Ron Okimoto and Hans Cheng are the respective chairs). Hopefully, everything can be completed by about 6:00 p.m. on Sunday. PAG-VII will continue from Jan. 17 to 21. More information and abstracts from past meetings can be found at the new PAG Website: http://www.intl-pag.org. A special guest this year will be Emeritus Coordinator Lyman Crittenden, who has been persuaded to leave the winter snows of Madison, WI and join us in San Diego. Several new industry representatives have also been invited, so we are hopeful of getting their input on future directions in poultry genomics.

CONGRATULATIONS

Congratulations go to Mehmet Karaca of the Department of Animal and Food Sciences, University of Delaware, who will receive the Neal A. Jorgensen Genome Student Travel Award for poultry at the NAGRP/PAG VII meetings. Jorgensen Award winners will be announced for all the relevant species during the meetings. Mehmet's poster presentation will be titled "Preliminary Analysis of Microsatellite Loci in Commercial Broiler Chickens".

HOLIDAY TURKEY

The University of Minnesota and Iowa State University are beginning a program under the leadership of Craig Beattie to create a "high resolution comprehensive map for the turkey genome and use it to map loci involved in susceptibility to Pasturella sp." Additional partners in this effort are being sought, with plans to submit for funding to the NRI this February (see below). A brief workshop presenting initial results and discussing further plans will occur at PAG-VII. This research will build upon the earlier work of Ed Smith and others on the turkey genome, and it will be a welcome addition to the overall poultry genome mapping effort. Interested parties are encouraged to attend the workshop.

CHANGES IN ACCESSING THE POULTRY DATABASE

Those of you who follow angenmap, the Animal Genome Mapping email listserver, will have already heard that Iowa State is now home to the U.S. nodes for both the swine and poultry genome mapping databases, just as the Roslin Institute remains home to the European versions. This allows you to choose whichever site works fastest and easiest for you. When using the U.S. site, go to http://www.genome.iastate.edu/. If you then click on the poultry icon, you will get a local ISU version of our East Lansing homepage (http://poultry.mph.msu.edu). Clicking the "Database" image on the left will get you into the Iowa State node of the same database that's in Roslin (choose either CHICKGBASE or CHICK MAP). (If you still wish to access to the Roslin site for whatever reason, connect to it through the East Lansing homepage or go directly to http://www.ri.bbsrc.ac.uk/chickmap/chickgbase/chickgbase.html). Thanks to Max Rothschild and Zhiliang H u for their assistance in putting up the Iowa State nodes.

As mentioned last time, the program announcement of the 1999 USDA National Research Inititiative-Competitive Grants Program (NRI) is posted at http://www.reeusda.gov/nri. The deadline for the Animal Genome and Genetic Mechanisms Program is Feb. 15, 1999. Questions can be directed to the NRI at nricgp@reeusda.gov or (202) 401-5022. Poultry geneticists are strongly encouraged to submit (or resubmit) proposals to the Animal Genome Program or to other NRI Programs this year. Joan Burnside of the U. of Delaware has graciously agreed to succeed yours truly as Animal Genome Program Director for next year. My congratulations and condolences go to Joan.

On a related note, as most of you already know, there is good news and bad news for agricultural genomics in this year's Agriculture Appropriations Bill that emerged from Congress in early October. The good news is that funding for the NRI was increased substantially, from $97.2 million to $119.3 million. The four different Programs in Animal Systems received an impressive 21% increase from $24 million to $29 million (so Joan will be able to be much more generous than I was). The bad news is that the Conference Committee specifically prohibited any funds going to either the Initiative for Future Ag. and Food Systems (which included the Agricultural Genome Initiative) and the Fund for Rural America. However, the authorization language for the Initiative remains in effect, so another attempt will be made to get it funded next year.

With regards to the funding of animal genomics, thanks go to Michael Roberts, presently serving as NRI Director, for his letter to Nature (August 6 issue, 394:517), in response to their earlier editorial and article, which generally supporting enhanced competitive funding of agricultural research, but with a heavy emphasis on plant genomics, as opposed to animal research and other agricultural science (July 16 issue, 394: 207 and 210-211). Hopefully, the NRI-CGP will continue to expand under his enthusiastic and even-handed leadership.

GENEMAP '98

An updated Gene Map of the Human Genome has been released by NCBI at NIH. The new map consists of an ordering of 30,261 gene-based markers within a framework of 1,500 microsatellites. See Deloukas et al., Science 282:744-746 (1998) for a description and go to http://www.ncbi.nlm.nih.gov/genemap98/ to search in GeneMap '98.

CHICKEN GENE PRIMERS AND OTHER RESOURCES

Gene primers: A collection of PCR primer pairs complementary to 200 chicken genes of known sequence has been synthesized. In each case, a likely primer pair for PCR was derived using primer optimization software based on Genbank sequences (most of which are from cDNA clones). A Table is available on our web page which provides the gene name and Genbank ID number for each primer pair, along with the predicted product size, if the primers are used in RT-PCR (http://poultry.mph.msu.edu, click the "Maps and Tables" button, then "Microsatellite Marker Information and Available Primer Kits", and then scroll down near the bottom). The primers have not all been tested and, due to the possibility of introns within the sequenced region, amplification from genomic DNA, rather than from cDNA, may not work or may require special, long PCR conditions. None of these primers are fluorescently labeled. Due to the high cost of synthesis, the number of samples we hav e of each primer pair is limited. Furthermore, it is expected that most labs will have a specific interest in one or a few candidate genes. Therefore, we are not able to provide the whole set of 200 primer pairs on request. However, requests for primer pairs for one or several specific genes will be filled as long as the primers remain. Requests should be forwarded to J. Dodgson (dodgson@pilot.msu.edu) or H. Cheng (hcheng@pilot.msu.edu). Based on the level of interest observed and coordination funds available, additional gene primer kits may be made in the future. (Thanks to Steven Suchyta for help in primer design).

Microsatellite primers: As described previously, 575 fluorescent chicken microsatellite primer pairs are available in four separate kits. Information on all Kits is posted under "Microsatellite Marker Information and Available Primer Kits" in the "Maps and Tables" section of our Homepage (http://poultry.mph.msu.edu). A new kit (kit #5) of 37 more primer pairs based on information provided by Dave Burt of the Roslin Institute and Abel Ponce de Leon of the U. of Minnesota has recently been ordered and will be posted on the Web Site shortly.

Chicken BAC libraries: Construction of a second chicken BAC library by the Texas A&M BAC Center is well underway, and it should be available very soon. This second BAC library uses the UCD 001 Jungle Fowl line as DNA source, the same line used in the East Lansing reference map. As noted previously, Martien Groenen has also constructed a BAC library in collaboration with the Texas A&M Center. For more info on this library, see the Groenen homepage at http://www.zod.wau.nl/vf/chickensite/chicken.html. If you wish to screen the Wageningen BAC library, contact R. Crooijmans at richard.crooijmans@alg.vf.wau.nl. The new library uses a different DNA source and a different restriction enzyme insertion site in the vector, which should make it a useful complement to the Wageningen BAC library.

AFLP primers: As mentioned last time, we've been exploring with Keygene, N.V. (the patent holder on the AFLP technique) the possibility of Coordinators providing AFLP kits that go beyond the limited ones now available which would allow interested animal geneticists to test this technology without breaking their budgets. Unfortunately, Keygene has negotiated a licensing agreement with PE AgGen, and neither company is presently interested in exploring expanded kits for the animal genome mapping community. If there is significant interest expressed at PAG-VII, it may be possible to go ahead with some sort of arrangement among the NAGRP Coordinators. Keygene will do AFLP analysis for you on a contract basis through their Molecular Marker Service. Email keygene@euronet.nl. if interested.

THAT WAS THE YEAR THAT WAS, 1998.

The annual report (don't you just love those things) for 1998 of the NAGRP Poultry Coordinator will soon be posted on our Web Site (http://poultry.mph.msu.edu) under the "About" button. Something to look forward to for those who don't make it to PAG-VII to get their own hard copy version. Coordinator's reports from previous years (1995-1997) are also available.

HOW TO GET THE DT'S

Many labs (including my own) have found the chicken transformed B cell line, DT40, to be of great utility. This line, originally developed in the lab of the late Eric Humphries, was subsequently shown, principally by Jean-Marie Buerstedde's lab, to exhibit an unusually high rate of homologous recombination which facilitates doing knock-out mutagenesis of avian genes in cultured cells. Jean-Marie has now developed a web site dedicated to the DT40 cell line which provides an excellent resource for interested users. The URL is http://www.uke.uni-hamburg.de/Institutes/HPI/div3/dt40.htm.