As reported last issue, a proposal to sequence the chicken genome was submitted to NIH's National Human Genome Research Institute (NHGRI) for the Feb. 10, 2002 deadline. The proposal, composed by John McPherson (Washington U. Genome Center), Robb Krumlauf (Stowers Institute), Olivier Pourquié (soon to join the Stowers Institute) and myself is posted under "Information" at http://poultry.mph.msu.edu. Thanks go to the many poultry biologists who sent emails of support for our proposal! NHGRI subsequently rated the chicken genome sequence as a "high priority", along with those of the chimpanzee, honeybee, sea urchin, Tetrahymena thermophila, and a collection of fungal genomes. (See www.genome.gov/page.cfm?pageID=10002154.) This ranking doesn't automatically provide funding for the project, but it does place the chicken among those genomes that the NHGRI Genome Centers will be encouraged to sequence. At last report, NIH was negotiating with USDA in hopes of getting joint funding for the chicken and honeybee sequences. USDA has expressed interest, but hopes to get at least the bovine genome sequence and possibly other genomes included in the package. NHGRI expressed interest in the bovine sequence but put this proposal on hold until additional mammalian (non-primate) proposals were received and analyzed. Joseph Jen, USDA Undersecretary for Research, Education and Economics, is leading USDA's effort as coordinator of the newly established Domestic Animal Genome Interagency Work Group. In the meantime, the Washington U. Genome Center continues to prepare the groundwork for the chicken sequence (see "The BAC Page" below). (The effect, if any, of the recently announced departure of Center Director, Bob Waterston, from Wash. U. to U. Wash. on their efforts to obtain the chicken genome sequence is uncertain, at present.)

As reported last issue, several investigators have been exploring the development of chicken microarray ("chicken chip") technology. Some of the U.S. efforts were described at PAMG-X by Joan Burnside and Larry Cogburn (U. of Delaware). In addition, Paul Neiman (Fred Hutchinson Cancer Research Center, FHCRC) has developed a glass slide-based, 4000-spot microarray focused on immune system-related and/or DT40 cell-expressed cDNAs. The opportunities for chicken microarrays have been enhanced by the chicken expressed sequence tags (ESTs) generated by the European Union consortium (especially, U. of Manchester Inst. of Science and Technology, U. of Nottingham, U. of Dundee, and the Roslin Institute) collaboration with Incyte Genomics (www.chick.umist.ac.uk). As mentioned in our last issue, Paul, Joan, and others have begun to plan the development of a second generation, more general, 10K spot glass slide microarray. Favorable prices for printing such arrays have been offered by the FHCRC facility. Subsequent to the last newsletter, Dave Burt (Roslin Institute) proposed that European and U.S. efforts (and resources) be combined in hopes of generating larger and/or more widely available chicken arrays. This will require some fairly detailed clustering of the available EST databases and selection of those sequences optimal (and of greatest interest) for spotting on arrays. This will be one topic of discussion at the upcoming Chicken Gene Mapping Workshop at ISAG (see below), and plans are underway for Dave, Paul and Joan to meet to discuss this (probably before the TIGR meeting at the start of October). Stay tuned for further details. Additional indications of interest can be emailed to Paul Neiman (pneiman@fred.fhcrc.org).

Poultry Science Association Annual Meeting, August 11-14, 2002, University of Delaware, Newark, DE. See www.poultryscience.org for more information.

International Society of Animal Genetics, Göttingen, Germany, August 11-15, 2002. See http://www.gwdg.de/~bbrenig/ISAG2002.html for further information. Chicken Gene Mapping Workshop will be held on August 11, led by Alain Vignal (vignal@toulouse.inra.fr).

2^nd Symposium on Candidate Genes for Animal Health, August 16-18, Montpellier, France. Information at http://cgah.cirad.fr

7^th World Congress of Genetics Applied to Livestock Production, August 19-23, 2002, Montpellier, France. See http://www.wcgalp.org.

11^th European Poultry Conference, September 6-10, 2002, Bremen, Germany. See www.epc2002.de for further information.

2^nd UK Farm Animal Functional Genomics Workshop (ARK-Genomics Workshop), September 12, 2002, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ. Email info@arkgenomics.org for details and a registration form.

TIGR's 14^th International Genome Sequencing and Analysis Conference, October 2-5, 2002, Boston, MA. See www.tigr.org/conf/gsac/ .

International Workshop on Experimental Models from the Bursa of Fabricius, October 4-6, 2002, Fred Hutchinson Cancer Research Center, Seattle, WA. See www.fhcrc.org/events/scientific/bursa for more information.

Plant, Animal and Microbial Genome XI, joint with NC-168 and NAGRP annual meetings, Jan. 11-15, 2003, Town & Country Convention Center, San Diego, CA. More information above and/or see www.intl-pag.org/.

Microsatellite primer kits: Information on microsatellite primer pairs can be found at http://poultry.mph.msu.edu/resources/microkits.htm. A new version of a framework primer kit (with 147 well-spaced microsatellite marker primer pairs) called the "Comprehensive Mapping Kit #7" is now available (thanks in part to a generous donation from Hy-Line International). Due to our limited budget (and the cost of the Marshfield microsatellite patent), we now can supply only our Population Tester Kit (9 highly polymorphic microsatellite markers for strain identification, gene flow studies or testing in other birds [not usually recommended]) or the new Comprehensive Mapping Kit #7. If interested, contact: (dodgson@.msu.edu) or (hcheng@.msu.edu), describing your desired application.

Gene primers: (Reminder) Two sets of PCR primer pairs (300 primer pairs corresponding to 300 chicken genes) complementary to chicken mRNAs are still available. In each case, a likely primer pair for PCR was derived based on DNA sequence data (mostly cDNA sequences, so they should be used for RT-PCR). See "Chicken Gene Primers #1 and #2" under "Resources" (scroll down) at http://poultry.mph.msu.edu.

The chicken BAC library constructed at Texas A&M by Hongbin Zhang and colleagues, using (a female of) the UCD001 Jungle Fowl line as its DNA source, now consists of over 115,000 BACs (~39,400 each in three sublibraries with BamHI, EcoRI and HindIII partial digest inserts). Filter sets with 36,864 BACs from each of the three sub-libraries are available. If interested, email me at dodgson@msu.edu. A requirement for receiving a free filter set is that the user agree to provide the name of the probe used and clone locations at a later date, so all users can benefit from coordination resources. Alternatively, filter sets can be obtained directly from GENEfinder Genomic Resources (http://hbz.tamu.edu) at the cost of preparing them. In either case, once your clone of interest is identified, individual clones can be obtained for a fee from GENEfinder. Contact Felipe Santos, at contact@bac-center.tamu.edu, to purchase BACs.

The chicken BAC contig map web interface developed by Zhang and his group at Texas A&M is now on-line. Fingerprint data from over 60,000 BACS (20,000+ from each of the three sublibraries) are included in the database. The web site can be found at http://hbz.tamu.edu - click on Physical Mapping - then on Chicken Map (on the left) - scroll down to "Chicken Clone -> FPC Hitting Tool" and click. Enter the ID number of any BAC and search for overlapping BACs, based on the fingerprint data.

Pieter de Jong (Children's Hospital of Oakland Research Institute) has completed a new chicken BAC library with extra large inserts (CHORI-261), using the same UCD001 source DNA as described above. Pieter has also generating a turkey BAC library (CHORI-260) using DNA from an inbred Nicholas Turkey Breeding Farms bird. Thanks to Dave Harry from Nicholas for providing the DNA. If interested in either library and/or filter arrays, see www.chori.org/bacpac/ and access the "Detailed List of Libraries" and/or "Screening Resources".

For those wishing to use PCR rather than filter hybridization to screen for your gene(s) of interest, Research Genetics has prepared PCR-ready, superplate, column, and row DNA pools of 30,000 BamHI BACs (the same collection offered on our first BAC filter sets). Thus, this portion of the BAC library can be screened by a 3-dimensional strategy that requires 240 PCR reactions. Unfortunately, Research Genetics defaulted on our plans to make panels of these pools available for purchase directly from them. Thus, we will supply limited numbers of screening arrays of aliquots of these pools on request to NRSP-8 member scientists. Alternatively, we hope to set up routine screening of the pools here at ADOL, and it may be possible to include your gene/probe of interest if you send us your PCR primers. If interested, please contact Hans Cheng (hcheng@.msu.edu). A more detailed description of the pools is on our website at (http://poultry.mph.msu.edu/resources/resources.htm).

Martien Groenen and Richard Crooijmans have also constructed a BAC library in collaboration with Texas A&M (Crooijmans et al., Mammalian Genome 11: 360-363, 2000). For more information, see www.zod.wau.nl/vf. If you wish to purchase or use the Groenen-Crooijmans library, either contact www.zod.wau.nl/abg/hs/research/molecular/intro.html, the UK Human Genome Mapping Project Resource Center at http://www.hgmp.mrc.ac.uk, who sell filter sets of this library, or GENEfinder Genomic Resources (http://hbz.tamu.edu).

email: dodgson@msu.edu

email: hcheng@msu.edu